WorldWideScience

Sample records for systems macromolecular assembly

  1. Stochastic dynamics of macromolecular-assembly networks.

    Science.gov (United States)

    Saiz, Leonor; Vilar, Jose

    2006-03-01

    The formation and regulation of macromolecular complexes provides the backbone of most cellular processes, including gene regulation and signal transduction. The inherent complexity of assembling macromolecular structures makes current computational methods strongly limited for understanding how the physical interactions between cellular components give rise to systemic properties of cells. Here we present a stochastic approach to study the dynamics of networks formed by macromolecular complexes in terms of the molecular interactions of their components [1]. Exploiting key thermodynamic concepts, this approach makes it possible to both estimate reaction rates and incorporate the resulting assembly dynamics into the stochastic kinetics of cellular networks. As prototype systems, we consider the lac operon and phage λ induction switches, which rely on the formation of DNA loops by proteins [2] and on the integration of these protein-DNA complexes into intracellular networks. This cross-scale approach offers an effective starting point to move forward from network diagrams, such as those of protein-protein and DNA-protein interaction networks, to the actual dynamics of cellular processes. [1] L. Saiz and J.M.G. Vilar, submitted (2005). [2] J.M.G. Vilar and L. Saiz, Current Opinion in Genetics & Development, 15, 136-144 (2005).

  2. Determining the architectures of macromolecular assemblies

    NARCIS (Netherlands)

    Alber, Frank; Dokudovskaya, Svetlana; Veenhoff, Liesbeth M.; Zhang, Wenzhu; Kipper, Julia; Devos, Damien; Suprapto, Adisetyantari; Karni-Schmidt, Orit; Williams, Rosemary; Chait, Brian T.; Rout, Michael P.; Sali, Andrej

    2007-01-01

    To understand the workings of a living cell, we need to know the architectures of its macromolecular assemblies. Here we show how proteomic data can be used to determine such structures. The process involves the collection of sufficient and diverse high-quality data, translation of these data into

  3. Polymerization of immunoglobulin domains: A model system for the development of facilitated macromolecular assembly

    Energy Technology Data Exchange (ETDEWEB)

    Stevens, F.J.; Myatt, E.A.

    1991-01-01

    We have recently determined that monoclonal immunoglobulin light chains (Bence Jones proteins) are capable of reversible polymerization at room temperature. This property, as exhibited by immunoglobulin light chains (normally a component of an intact antibody molecule), may have novel implications for the development of molecular nanotechnology.'' The polymerization capability of the immunoglobulin light chain is associated with the so-called variable domain of this molecule. The variable domain is a durable, compact beta-sheet structure of molecular weight approximately 12,000. Most of the primary sequence variation is limited to one portion of the molecule, that portion associated with the contribution of immunoglobulin light chains to the recognition and binding of thousand of different antigens by antibodies. As a consequence of these variations, different light chains polymerize with different degrees of avidity, from negligible to extensive. The polymerization process depends on solution parameters such as Ph. Thus, polymerization might be induced at one pH and suppressed or reversed at another. Combinations of molecules of appropriate specificities could assemble into structures of predetermined three-dimensional forms and properties. These features suggest that Bence Jones proteins represent a powerful model system within which to develop empirical rules relevant to a technology of protein-based construction''. Development of these rules will require the combined efforts of biophysical and crystallographic studies, protein engineering, and molecular modeling. 53 refs., 5 figs.

  4. Polymerization of immunoglobulin domains: A model system for the development of facilitated macromolecular assembly

    Energy Technology Data Exchange (ETDEWEB)

    Stevens, F.J.; Myatt, E.A.

    1991-12-31

    We have recently determined that monoclonal immunoglobulin light chains (Bence Jones proteins) are capable of reversible polymerization at room temperature. This property, as exhibited by immunoglobulin light chains (normally a component of an intact antibody molecule), may have novel implications for the development of ``molecular nanotechnology.`` The polymerization capability of the immunoglobulin light chain is associated with the so-called variable domain of this molecule. The variable domain is a durable, compact beta-sheet structure of molecular weight approximately 12,000. Most of the primary sequence variation is limited to one portion of the molecule, that portion associated with the contribution of immunoglobulin light chains to the recognition and binding of thousand of different antigens by antibodies. As a consequence of these variations, different light chains polymerize with different degrees of avidity, from negligible to extensive. The polymerization process depends on solution parameters such as Ph. Thus, polymerization might be induced at one pH and suppressed or reversed at another. Combinations of molecules of appropriate specificities could assemble into structures of predetermined three-dimensional forms and properties. These features suggest that Bence Jones proteins represent a powerful model system within which to develop empirical rules relevant to a technology of protein-based ``construction``. Development of these rules will require the combined efforts of biophysical and crystallographic studies, protein engineering, and molecular modeling. 53 refs., 5 figs.

  5. Mass distributions of a macromolecular assembly based on ...

    Indian Academy of Sciences (India)

    Macromolecular assemblies containing multiple protein subunits and having masses in the megadalton (MDa) range are involved in most of the functions of a living cell. Because of variation in the number and masses of subunits, macromolecular assemblies do not have a unique mass, but rather a mass distribution.

  6. Associative Pattern Recognition Through Macro-molecular Self-Assembly

    Science.gov (United States)

    Zhong, Weishun; Schwab, David J.; Murugan, Arvind

    2017-05-01

    We show that macro-molecular self-assembly can recognize and classify high-dimensional patterns in the concentrations of N distinct molecular species. Similar to associative neural networks, the recognition here leverages dynamical attractors to recognize and reconstruct partially corrupted patterns. Traditional parameters of pattern recognition theory, such as sparsity, fidelity, and capacity are related to physical parameters, such as nucleation barriers, interaction range, and non-equilibrium assembly forces. Notably, we find that self-assembly bears greater similarity to continuous attractor neural networks, such as place cell networks that store spatial memories, rather than discrete memory networks. This relationship suggests that features and trade-offs seen here are not tied to details of self-assembly or neural network models but are instead intrinsic to associative pattern recognition carried out through short-ranged interactions.

  7. IDPs in macromolecular complexes: the roles of multivalent interactions in diverse assemblies.

    Science.gov (United States)

    Fung, Ho Yee Joyce; Birol, Melissa; Rhoades, Elizabeth

    2018-01-04

    Intrinsically disordered proteins (IDPs) have critical roles in a diverse array of cellular functions. Of relevance here is that they are components of macromolecular complexes, where their conformational flexibility helps mediate interactions with binding partners. IDPs often interact with their binding partners through short sequence motifs, commonly repeated within the disordered regions. As such, multivalent interactions are common for IDPs and their binding partners within macromolecular complexes. Here we discuss the importance of IDP multivalency in three very different macromolecular assemblies: biomolecular condensates, the nuclear pore, and the cytoskeleton. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta.

    Science.gov (United States)

    Wang, Ray Yu-Ruei; Song, Yifan; Barad, Benjamin A; Cheng, Yifan; Fraser, James S; DiMaio, Frank

    2016-09-26

    Cryo-EM has revealed the structures of many challenging yet exciting macromolecular assemblies at near-atomic resolution (3-4.5Å), providing biological phenomena with molecular descriptions. However, at these resolutions, accurately positioning individual atoms remains challenging and error-prone. Manually refining thousands of amino acids - typical in a macromolecular assembly - is tedious and time-consuming. We present an automated method that can improve the atomic details in models that are manually built in near-atomic-resolution cryo-EM maps. Applying the method to three systems recently solved by cryo-EM, we are able to improve model geometry while maintaining the fit-to-density. Backbone placement errors are automatically detected and corrected, and the refinement shows a large radius of convergence. The results demonstrate that the method is amenable to structures with symmetry, of very large size, and containing RNA as well as covalently bound ligands. The method should streamline the cryo-EM structure determination process, providing accurate and unbiased atomic structure interpretation of such maps.

  9. SPring-8 BL44XU, beamline designed for structure analysis of large biological macromolecular assemblies

    Energy Technology Data Exchange (ETDEWEB)

    Higashiura, Akifumi, E-mail: hgsur-a@protein.osaka-u.ac.jp; Yamashita, Eiki [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871 (Japan); Yoshimura, Masato [Taiwan NSRRC, Taiwan Beamline Office at SPring-8, 1-1-1, Kouto, Sayo-cho, Hyogo 679-5198 (Japan); Hasegawa, Kazuya; Furukawa, Yukito; Kumasaka, Takashi [JASRI/SPring-8, 1-1-1, Kouto, Sayo-cho, Hyogo 679-5198 (Japan); Ueno, Go; Yamamoto, Masaki [RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo-cho, Hyogo 679-5198 (Japan); Tsukihara, Tomitake [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871 (Japan); Gradual School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297 (Japan); Nakagawa, Atsushi, E-mail: atsushi@protein.osaka-u.ac.jp [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871 (Japan); CREST, Japan Science and Technology Agency (Japan)

    2016-07-27

    Beamline BL44XU at SPring-8 is operated by the Institute for Protein Research of Osaka University. The beamline is designed for X-ray crystallography of large biological macromolecular assemblies. Here we show its detailed performances, results, and the ongoing upgrade plans.

  10. Phosphorus ionization in silicon doped by self-assembled macromolecular monolayers

    Science.gov (United States)

    Wu, Haigang; Li, Ke; Gao, Xuejiao; Dan, Yaping

    2017-10-01

    Individual dopant atoms can be potentially controlled at large scale by the self-assembly of macromolecular dopant carriers. However, low concentration phosphorus dopants often suffer from a low ionization rate due to defects and impurities introduced by the carrier molecules. In this work, we demonstrated a nitrogen-free macromolecule doping technique and investigated the phosphorus ionization process by low temperature Hall effect measurements. It was found that the phosphorus dopants diffused into the silicon bulk are in nearly full ionization. However, the electrons ionized from the phosphorus dopants are mostly trapped by deep level defects that are likely carbon interstitials.

  11. Macromolecular shape and interactions in layer-by-layer assemblies within cylindrical nanopores

    Directory of Open Access Journals (Sweden)

    Thomas D. Lazzara

    2012-06-01

    Full Text Available Layer-by-layer (LbL deposition of polyelectrolytes and proteins within the cylindrical nanopores of anodic aluminum oxide (AAO membranes was studied by optical waveguide spectroscopy (OWS. AAO has aligned cylindrical, nonintersecting pores with a defined pore diameter d0 and functions as a planar optical waveguide so as to monitor, in situ, the LbL process by OWS. The LbL deposition of globular proteins, i.e., avidin and biotinylated bovine serum albumin was compared with that of linear polyelectrolytes (linear-PEs, both species being of similar molecular weight. LbL deposition within the cylindrical AAO geometry for different pore diameters (d0 = 25–80 nm for the various macromolecular species, showed that the multilayer film growth was inhibited at different maximum numbers of LbL steps (nmax. The value of nmax was greatest for linear-PEs, while proteins had a lower value. The cylindrical pore geometry imposes a physical limit to LbL growth such that nmax is strongly dependent on the overall internal structure of the LbL film. For all macromolecular species, deposition was inhibited in native AAO, having pores of d0 = 25–30 nm. Both, OWS and scanning electron microscopy showed that LbL growth in larger AAO pores (d0 > 25–30 nm became inhibited when approaching a pore diameter of deff,n_max = 25–35 nm, a similar size to that of native AAO pores, with d0 = 25–30 nm. For a reasonable estimation of deff,n_max, the actual volume occupied by a macromolecular assembly must be taken into consideration. The results clearly show that electrostatic LbL allowed for compact macromolecular layers, whereas proteins formed loosely packed multilayers.

  12. Synthesis and Self-Assembly of Amphiphilic Triblock Terpolymers with Complex Macromolecular Architecture

    KAUST Repository

    Polymeropoulos, George

    2015-11-25

    Two star triblock terpolymers (PS-b-P2VP-b-PEO)3 and one dendritic-like terpolymer [PS-b-P2VP-b-(PEO)2]3 of PS (polystyrene), P2VP (poly(2-vinylpyridine)), and PEO (poly(ethylene oxide)), never reported before, were synthesized by combining atom transfer radical and anionic polymerizations. The synthesis involves the transformation of the -Br groups of the previously reported Br-terminated 3-arm star diblock copolymers to one or two -OH groups, followed by anionic polymerization of ethylene oxide to afford the star or dendritic structure, respectively. The well-defined structure of the terpolymers was confirmed by static light scattering, size exclusion chromatography, and NMR spectroscopy. The self-assembly in solution and the morphology in bulk of the terpolymers, studied by dynamic light scattering and transmission electron microscopy, respectively, reveal new insights in the phase separation of these materials with complex macromolecular architecture. © 2015 American Chemical Society.

  13. A Review of Two Multiscale Methods for the Simulation of Macromolecular Assemblies: Multiscale Perturbation and Multiscale Factorization

    Directory of Open Access Journals (Sweden)

    Stephen Pankavich

    2015-02-01

    Full Text Available Many mesoscopic N-atom systems derive their structural and dynamical properties from processes coupled across multiple scales in space and time. That is, they simultaneously deform or display collective behaviors, while experiencing atomic scale vibrations and collisions. Due to the large number of atoms involved and the need to simulate over long time periods of biological interest, traditional computational tools, like molecular dynamics, are often infeasible for such systems. Hence, in the current review article, we present and discuss two recent multiscale methods, stemming from the N-atom formulation and an underlying scale separation, that can be used to study such systems in a friction-dominated regime: multiscale perturbation theory and multiscale factorization. These novel analytic foundations provide a self-consistent approach to yield accurate and feasible long-time simulations with atomic detail for a variety of multiscale phenomena, such as viral structural transitions and macromolecular self-assembly. As such, the accuracy and efficiency of the associated algorithms are demonstrated for a few representative biological systems, including satellite tobacco mosaic virus (STMV and lactoferrin.

  14. The dynamics of signal amplification by macromolecular assemblies for the control of chromosome segregation

    Directory of Open Access Journals (Sweden)

    Semin eLee

    2014-09-01

    Full Text Available The control of chromosome segregation relies on the spindle assembly checkpoint (SAC, a complex regulatory system that ensures the high fidelity of chromosome segregation in higher organisms by delaying the onset of anaphase until each chromosome is properly bi-oriented on the mitotic spindle. Central to this process is the establishment of multiple yet specific protein-protein interactions in a narrow time-space window. Here we discuss the highly dynamic nature of multi-protein complexes that control chromosome segregation in which an intricate network of weak but cooperative interactions modulate signal amplification to ensure a proper SAC response. We also discuss the current structural understanding of the communication between the SAC and the kinetochore; how transient interactions can regulate the assembly and disassembly of the SAC as well as the challenges and opportunities for the definition and the manipulation of the flow of information in SAC signaling.

  15. Single-step antibody-based affinity cryo-electron microscopy for imaging and structural analysis of macromolecular assemblies.

    Science.gov (United States)

    Yu, Guimei; Vago, Frank; Zhang, Dongsheng; Snyder, Jonathan E; Yan, Rui; Zhang, Ci; Benjamin, Christopher; Jiang, Xi; Kuhn, Richard J; Serwer, Philip; Thompson, David H; Jiang, Wen

    2014-07-01

    Single particle cryo-electron microscopy (cryo-EM) is an emerging powerful tool for structural studies of macromolecular assemblies (i.e., protein complexes and viruses). Although single particle cryo-EM requires less concentrated and smaller amounts of samples than X-ray crystallography, it remains challenging to study specimens that are low-abundance, low-yield, or short-lived. The recent development of affinity grid techniques can potentially further extend single particle cryo-EM to these challenging samples by combining sample purification and cryo-EM grid preparation into a single step. Here we report a new design of affinity cryo-EM approach, cryo-SPIEM, that applies a traditional pathogen diagnosis tool Solid Phase Immune Electron Microscopy (SPIEM) to the single particle cryo-EM method. This approach provides an alternative, largely simplified and easier to use affinity grid that directly works with most native macromolecular complexes with established antibodies, and enables cryo-EM studies of native samples directly from cell cultures. In the present work, we extensively tested the feasibility of cryo-SPIEM with multiple samples including those of high or low molecular weight, macromolecules with low or high symmetry, His-tagged or native particles, and high- or low-yield macromolecules. Results for all these samples (non-purified His-tagged bacteriophage T7, His-tagged Escherichiacoli ribosomes, native Sindbis virus, and purified but low-concentration native Tulane virus) demonstrated the capability of cryo-SPIEM approach in specifically trapping and concentrating target particles on TEM grids with minimal view constraints for cryo-EM imaging and determination of 3D structures. Copyright © 2014 Elsevier Inc. All rights reserved.

  16. Structure and property relations of macromolecular self-assemblies at interfaces

    Science.gov (United States)

    Yang, Zhihao

    Hydrophilic polymer chains, poly(ethylene glycol) (PEG), are attached to glass surfaces by silylation of the silanol groups on glass surfaces with the omega-(methoxyl terminated PEG) trimethoxysilanes. These tethered polymer chains resemble the self-assembled monolayers (SAMs) of PEG, which exhibit excellent biocompatibility and provide a model system for studying the interactions of proteins with polymer surfaces. The low molecular weight PEGs tend to extend, forming a brush-like monolayer, whereas the longer polymer chains tend to interpenetrate each other, forming a mushroom-like PEG monolayer at the interface. Interactions between a plasma protein, bovine serum albumin, and the PEG-SAMs are investigated in terms of protein adsorption and diffusion on the surfaces by the technique of fluorescence recovery after photobleaching (FRAP). The diffusion and aggregation behaviors of the protein on the two monolayers are found to be quite different despite the similarities in adsorption and desorption behaviors. The results are analyzed with a hypothesis of the hydrated surface dynamics. A method of covalently bonding phospholipid molecules to silica substrates followed by loading with free phospholipids is demonstrated to form well organized and stable phospholipid self-assembled monolayers. Surfaces of such SAMs structurally mimic the aqueous sides of phospholipid bilayer membranes. The dynamics of phospholipids and an adsorbed protein, lipase, in the SAMs are probed with FRAP, in terms of lateral diffusion of both phospholipids and protein molecules. The esterase activity of lipase on the SAM surfaces is confirmed by the hydrolysis reaction of a substrate, umbelliferone stearate, showing such lipid SAMs posess biomembrane functionality in terms of interfacial activation of the membranous enzymes. Dynamics of polyethylene oxide and polypropylene oxide tri-block copolymers, PEO-PPO-PEO and PPO-PEO-PPO, at the air/water interface upon thermal stimulation is studied by

  17. Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution

    Directory of Open Access Journals (Sweden)

    Xiaojun Xu

    2015-01-01

    Full Text Available While conventional high-resolution techniques in structural biology are challenged by the size and flexibility of many biological assemblies, recent advances in low-resolution techniques such as cryo-electron microscopy (cryo-EM and small angle X-ray scattering (SAXS have opened up new avenues to define the structures of such assemblies. By systematically combining various sources of structural, biochemical and biophysical information, integrative modeling approaches aim to provide a unified structural description of such assemblies, starting from high-resolution structures of the individual components and integrating all available information from low-resolution experimental methods. In this review, we describe integrative modeling approaches, which use complementary data from either cryo-EM or SAXS. Specifically, we focus on the popular molecular dynamics flexible fitting (MDFF method, which has been widely used for flexible fitting into cryo-EM maps. Second, we describe hybrid molecular dynamics, Rosetta Monte-Carlo and minimum ensemble search (MES methods that can be used to incorporate SAXS into pseudoatomic structural models. We present concise descriptions of the two methods and their most popular alternatives, along with select illustrative applications to protein/nucleic acid assemblies involved in DNA replication and repair.

  18. Davisson-Germer Prize in Atomic or Surface Physics Lecture: Line 'Em All Up: Macromolecular Assembly at Liquid Interfaces

    Science.gov (United States)

    Richmond, Geraldine

    2013-03-01

    Advances in our molecular level understanding of the ubiquitous fluid interface comprised of a hydrophobic fluid medium, and an aqueous solution of soluble ions and solutes has been slow until recently. This more recent upsurge in interest and progress comes from advances in both experimental and computational techniques as well as the increasingly important role that this interface is playing in such areas as green chemistry, nanoparticle synthesis, improved oil and mineral recovery and water purification. The presentation will focus on our most recent efforts in understanding (1) the molecular structure of the interface between two immiscible liquids, (2) the penetration of aqueous phase ions into the interfacial region and their effect on its properties, and (3) the structure and dynamics of the adsorption of surfactants, polymers and nanoparticles at this interface. To gain insights into these processes we use a combination of vibrational sum frequency spectroscopy, surface tension measurements using the pendant drop method, and molecular dynamics simulations. The results demonstrate that weak interactions between interfacial oil and water molecules create an interface that exhibits a high degree of molecular structuring and ordering, and with properties quite different than what is observed at the air-water interface. As a consequence of these interfacial oil-water interactions, the interface provides a unique environment for the adsorption and assembly of ions, polymers and nanoparticles that are drawn to its inner-most regions. Examples of our studies that provide new insights into the unique nature of adsorption, adsorption dynamics and macromolecular assembly at this interface will be provided.

  19. Biomimetic polymers responsive to a biological signaling molecule: nitric oxide triggered reversible self-assembly of single macromolecular chains into nanoparticles.

    Science.gov (United States)

    Hu, Jinming; Whittaker, Michael R; Duong, Hien; Li, Yang; Boyer, Cyrille; Davis, Thomas P

    2014-07-21

    Novel nitric oxide (NO) responsive monomers (NAPMA and APUEMA) containing o-phenylenediamine functional groups have been polymerized to form NO-responsive macromolecular chains as truly biomimetic polymers. Upon exposure to NO--a ubiquitous cellular signaling molecule--the NAPMA- and APUEMA-labeled thermoresponsive copolymers exhibited substantial changes in solubility, clearly characterized by tuneable LCST behavior, thereby inducing self-assembly into nanoparticulate structures. Moreover, the NO-triggered self-assembly process in combination with environmentally sensitive fluorescence dyes could be employed to detect and image endogenous NO. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. PHENIX: a comprehensive Python-based system for macromolecular structure solution.

    Science.gov (United States)

    Adams, Paul D; Afonine, Pavel V; Bunkóczi, Gábor; Chen, Vincent B; Davis, Ian W; Echols, Nathaniel; Headd, Jeffrey J; Hung, Li-Wei; Kapral, Gary J; Grosse-Kunstleve, Ralf W; McCoy, Airlie J; Moriarty, Nigel W; Oeffner, Robert; Read, Randy J; Richardson, David C; Richardson, Jane S; Terwilliger, Thomas C; Zwart, Peter H

    2010-02-01

    Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.

  1. Rational Control of Electronic Structure and Lattice Architecture in Electrically Conducting Molecular/Macromolecular Assemblies.

    Science.gov (United States)

    1981-12-23

    partial oxidation (6+) follows from this information and the stoichiometry. As an example, nickel phthalocyanine iodide, (Ni(Pc)]1lI , crystallizes in...tetrathiafulvalene: TMTTF tetramethyttetrathiafulvalette; TTT - tetrathiatetracene; M(OEP) " 2,3,7,8,12,13,17,18- octaethylporphyrin . donor systems known to...Partially Oxidized Nickel and Palladium Bisdiphenylglyoximates," J. Am. Chem. Soc., 101, 2921 (1979), and referen- ces therein. 18. T. J. Marks, D. F. Webster

  2. ISPyB: an information management system for synchrotron macromolecular crystallography.

    Science.gov (United States)

    Delagenière, Solange; Brenchereau, Patrice; Launer, Ludovic; Ashton, Alun W; Leal, Ricardo; Veyrier, Stéphanie; Gabadinho, José; Gordon, Elspeth J; Jones, Samuel D; Levik, Karl Erik; McSweeney, Seán M; Monaco, Stéphanie; Nanao, Max; Spruce, Darren; Svensson, Olof; Walsh, Martin A; Leonard, Gordon A

    2011-11-15

    Individual research groups now analyze thousands of samples per year at synchrotron macromolecular crystallography (MX) resources. The efficient management of experimental data is thus essential if the best possible experiments are to be performed and the best possible data used in downstream processes in structure determination pipelines. Information System for Protein crystallography Beamlines (ISPyB), a Laboratory Information Management System (LIMS) with an underlying data model allowing for the integration of analyses down-stream of the data collection experiment was developed to facilitate such data management. ISPyB is now a multisite, generic LIMS for synchrotron-based MX experiments. Its initial functionality has been enhanced to include improved sample tracking and reporting of experimental protocols, the direct ranking of the diffraction characteristics of individual samples and the archiving of raw data and results from ancillary experiments and post-experiment data processing protocols. This latter feature paves the way for ISPyB to play a central role in future macromolecular structure solution pipelines and validates the application of the approach used in ISPyB to other experimental techniques, such as biological solution Small Angle X-ray Scattering and spectroscopy, which have similar sample tracking and data handling requirements.

  3. Life in a Crowd: Macromolecular Crowding and Confinement Effects on Protein Interactions in Living Systems

    Science.gov (United States)

    Cheung, Margaret

    2007-03-01

    Biological polymers carry out their functions in living systems where the environment is very concentrated or crowded by macromolecules. Physically, the composition of a cell is more than ``a sack of water''; its consistency is closer to Jell-O. Experiments suggests that, because of this macromolecular crowding effect that confines polymeric dynamics, the kinetics and thermodynamics of protein folding and the association rate constants of protein-protein interactions in a cell (in vivo) are very different from that ina diluted test tube (in vitro). In order to quantitatively understand macromolecular crowding and confinement effects on protein dynamics, we used coarse-grained models that physically captured interactions between crowders and a protein. The folding rates of a model protein nonmonotonically increased with the volume fraction of the crowders. At lower volume fractions, depletion-induced attractions from crowders could be mapped according to the spherical confinement model. A result of spherical confinement was the destabilization of denatured states by disallowing extended configurations that were longer than the pore size. However, at higher volume fractions, conformational fluctuations of a protein were susceptible to the shape of the confining condition. Thus, an approximation of the spherical confinement to mimic crowding effects was no longer effective.

  4. Phenix - a comprehensive python-based system for macromolecular structure solution

    Energy Technology Data Exchange (ETDEWEB)

    Terwilliger, Thomas C [Los Alamos National Laboratory; Hung, Li - Wei [Los Alamos National Laboratory; Adams, Paul D [UC BERKELEY; Afonine, Pavel V [UC BERKELEY; Bunkoczi, Gabor [UNIV OF CAMBRIDGE; Chen, Vincent B [DUKE UNIV; Davis, Ian [DUKE UNIV; Echols, Nathaniel [LBNL; Headd, Jeffrey J [DUKE UNIV; Grosse Kunstleve, Ralf W [LBNL; Mccoy, Airlie J [UNIV OF CAMBRIDGE; Moriarty, Nigel W [LBNL; Oeffner, Robert [UNIV OF CAMBRIDGE; Read, Randy J [UNIV OF CAMBRIDGE; Richardson, David C [DUKE UNIV; Richardson, Jane S [DUKE UNIV; Zwarta, Peter H [LBNL

    2009-01-01

    Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages, and the repeated use of interactive three-dimensional graphics. Phenix has been developed to provide a comprehensive system for crystallographic structure solution with an emphasis on automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand, and finally the development of a framework that allows a tight integration between the algorithms.

  5. Sample preparation of biological macromolecular assemblies for the determination of high-resolution structures by cryo-electron microscopy.

    Science.gov (United States)

    Stark, Holger; Chari, Ashwin

    2016-02-01

    Single particle cryo-EM has recently developed into a powerful tool to determine the 3D structure of macromolecular complexes at near-atomic resolution, which allows structural biologists to build atomic models of proteins. All technical aspects of cryo-EM technology have been considerably improved over the last two decades, including electron microscopic hardware, image processing software and the ever growing speed of computers. This leads to a more widespread use of the technique, and it can be anticipated that further automation of electron microscopes and image processing tools will soon fully shift the focus away from the technological aspects, onto biological questions that can be answered. In single particle cryo-EM, no crystals of a macromolecule are required. In contrast to X-ray crystallography, this significantly facilitates structure determination by cryo-EM. Nevertheless, a relatively high level of biochemical control is still essential to obtain high-resolution structures by cryo-EM, and it can be anticipated that the success of the cryo-EM technology goes hand in hand with further developments of sample purification and preparation techniques. This will allow routine high-resolution structure determination of the many macromolecular complexes of the cell that until now represent evasive targets for X-ray crystallographers. Here we discuss the various biochemical tools that are currently available and the existing sample purification and preparation techniques for cryo-EM grid preparation that are needed to obtain high-resolution images for structure determination. © The Author 2015. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  6. Self-assembly of hierarchically ordered structures in DNA nanotube systems

    Science.gov (United States)

    Glaser, Martin; Schnauß, Jörg; Tschirner, Teresa; Schmidt, B. U. Sebastian; Moebius-Winkler, Maximilian; Käs, Josef A.; Smith, David M.

    2016-05-01

    The self-assembly of molecular and macromolecular building blocks into organized patterns is a complex process found in diverse systems over a wide range of size and time scales. The formation of star- or aster-like configurations, for example, is a common characteristic in solutions of polymers or other molecules containing multi-scaled, hierarchical assembly processes. This is a recurring phenomenon in numerous pattern-forming systems ranging from cellular constructs to solutions of ferromagnetic colloids or synthetic plastics. To date, however, it has not been possible to systematically parameterize structural properties of the constituent components in order to study their influence on assembled states. Here, we circumvent this limitation by using DNA nanotubes with programmable mechanical properties as our basic building blocks. A small set of DNA oligonucleotides can be chosen to hybridize into micron-length DNA nanotubes with a well-defined circumference and stiffness. The self-assembly of these nanotubes to hierarchically ordered structures is driven by depletion forces caused by the presence of polyethylene glycol. This trait allowed us to investigate self-assembly effects while maintaining a complete decoupling of density, self-association or bundling strength, and stiffness of the nanotubes. Our findings show diverse ranges of emerging structures including heterogeneous networks, aster-like structures, and densely bundled needle-like structures, which compare to configurations found in many other systems. These show a strong dependence not only on concentration and bundling strength, but also on the underlying mechanical properties of the nanotubes. Similar network architectures to those caused by depletion forces in the low-density regime are obtained when an alternative hybridization-based bundling mechanism is employed to induce self-assembly in an isotropic network of pre-formed DNA nanotubes. This emphasizes the universal effect inevitable

  7. Multiscale macromolecular simulation: role of evolving ensembles.

    Science.gov (United States)

    Singharoy, A; Joshi, H; Ortoleva, P J

    2012-10-22

    Multiscale analysis provides an algorithm for the efficient simulation of macromolecular assemblies. This algorithm involves the coevolution of a quasiequilibrium probability density of atomic configurations and the Langevin dynamics of spatial coarse-grained variables denoted order parameters (OPs) characterizing nanoscale system features. In practice, implementation of the probability density involves the generation of constant OP ensembles of atomic configurations. Such ensembles are used to construct thermal forces and diffusion factors that mediate the stochastic OP dynamics. Generation of all-atom ensembles at every Langevin time step is computationally expensive. Here, multiscale computation for macromolecular systems is made more efficient by a method that self-consistently folds in ensembles of all-atom configurations constructed in an earlier step, history, of the Langevin evolution. This procedure accounts for the temporal evolution of these ensembles, accurately providing thermal forces and diffusions. It is shown that efficiency and accuracy of the OP-based simulations is increased via the integration of this historical information. Accuracy improves with the square root of the number of historical timesteps included in the calculation. As a result, CPU usage can be decreased by a factor of 3-8 without loss of accuracy. The algorithm is implemented into our existing force-field based multiscale simulation platform and demonstrated via the structural dynamics of viral capsomers.

  8. Modelling And Numerical Analysis Of Assembly System

    Directory of Open Access Journals (Sweden)

    Budniak Zbigniew

    2015-09-01

    Full Text Available The present articles covers a concept of the creation and testing of assembly systems with the use of modern CAD and CAE systems on the example of an assembly system designed for joining parts with circular surfaces that are fitted with positive clearance. The numerical investigations were based on the constructed spatial skeleton pattern of the system. The purpose of the simulation tests was to determine the impact of the measurement and angular inaccuracies of all the elements of the assembly system as well as the inaccuracy of the positioning of the robot’s drives on the positioning accuracy of the parts joined taking into consideration the conditions of assembly in automatic assembly.

  9. Modelling And Numerical Analysis Of Assembly System

    OpenAIRE

    Budniak Zbigniew

    2015-01-01

    The present articles covers a concept of the creation and testing of assembly systems with the use of modern CAD and CAE systems on the example of an assembly system designed for joining parts with circular surfaces that are fitted with positive clearance. The numerical investigations were based on the constructed spatial skeleton pattern of the system. The purpose of the simulation tests was to determine the impact of the measurement and angular inaccuracies of all the elements of the assemb...

  10. Determination of macromolecular exchange and PO2 in the microcirculation: a simple system for in vivo fluorescence and phosphorescence videomicroscopy

    Directory of Open Access Journals (Sweden)

    Torres L.N.

    2001-01-01

    Full Text Available We have developed a system with two epi-illumination sources, a DC-regulated lamp for transillumination and mechanical switches for rapid shift of illumination and detection of defined areas (250-750 µm² by fluorescence and phosphorescence videomicroscopy. The system permits investigation of standard microvascular parameters, vascular permeability as well as intra- and extravascular PO2 by phosphorescence quenching of Pd-meso-tetra (4-carboxyphenyl porphine (PORPH. A Pechan prism was used to position a defined region over the photomultiplier and TV camera. In order to validate the system for in vivo use, in vitro tests were performed with probes at concentrations that can be found in microvascular studies. Extensive in vitro evaluations were performed by filling glass capillaries with solutions of various concentrations of FITC-dextran (diluted in blood and in saline mixed with different amounts of PORPH. Fluorescence intensity and phosphorescence decay were determined for each mixture. FITC-dextran solutions without PORPH and PORPH solutions without FITC-dextran were used as references. Phosphorescence decay curves were relatively unaffected by the presence of FITC-dextran at all concentrations tested (0.1 µg/ml to 5 mg/ml. Likewise, fluorescence determinations were performed in the presence of PORPH (0.05 to 0.5 mg/ml. The system was successfully used to study macromolecular extravasation and PO2 in the rat mesentery circulation under controlled conditions and during ischemia-reperfusion.

  11. JBluIce-EPICS: a fast and flexible open-source beamline control system for macromolecular crystallography

    Science.gov (United States)

    Stepanov, S.; Hilgart, M.; Makarov, O.; Pothineni, S. B.; Yoder, D.; Ogata, C.; Sanishvili, R.; Venugopalan, N.; Becker, M.; Clift, M.; Smith, J. L.; Fischetti, R. F.

    2013-03-01

    This paper overviews recent advances in the JBluIce-EPICS open-source control system designed at the macromolecular crystallography beamlines of the National Institute of General Medical Sciences and National Cancer Institute at the Advanced Photon Source (GM/CA@APS). We discuss some technical highlights of this system distinguishing it from the competition, such as reduction of software layers to only two, possibility to operate JBluIce in parallel with other beamline controls, plugin-enabled architecture where the plugins can be written in any programming language, and utilization of the whole power of the Java integrated development environment in the Graphical User Interface. Then, we demonstrate how these highlights help to make JBluIce fast, easily adaptable to new beamline developments, and intuitive for users. In particular, we discuss several recent additions to the system including a bridge between crystal rastering and data collection, automatic detection of raster polygons from optical crystal centering, background data processing, and a pathway to a fully automated pipeline from crystal screening to solving crystal structure.

  12. Analysis of reconfigurable assembly system framing systems in automotive industry

    Directory of Open Access Journals (Sweden)

    Md Zain Mohamad Zamri

    2017-01-01

    Full Text Available Current trend in automotive industry shows increasing demand for multiple models with lean production. Prior to that, automotive manufacturing systems evolved from mass production to flexible automation. Material handling systems and equipment in a single assembly line with multiple models require high investment but with low throughput thus making production cost relatively high. Current assembly process of side structure and undercarriage with downtime occurrence during assembly process affecting production performance (quality, cost and delivery. Manufacturing facilities should allow more flexibility and increase intelligence evolving toward novel reconfigurable assembly systems (RAS. RAS is envisaged capable of increasing factor flexibility and responsiveness by incorporating assembly jig, robot and framing, which could be next generation of world class automotive assembly systems. This project research proposes a new methodology of framework reconfigurable assembly systems principles in automotive framing systems i.e. enhance assembly process between side structure assembly and undercarriage assembly which a new RAS is capable to reconfigure the assembly processes of multiple model on a single assembly line. Simulation software (Witness will be used to simulate and validate current and proposed assembly process. RAS is expected to be a solution for rapid change in structure and for a responsively adjustable production capacity. Quality, cost and delivery are production key parameters that can be achieved by implementing RAS.

  13. System and method for conveying an assembly

    KAUST Repository

    Eitelhuber, Georg

    2015-01-15

    An apparatus, system, and method for conveying an assembly along a track. A rail can include a first planar side, a second planar side, and a third planar side. The first, second, and third planar sides can be arranged to form at least two acute angles. A carriage assembly can include a drive wheel and at least two roller sets. The drive wheel can be configured to contact the first planar side and is configured to translate the carriage assembly along the rail. The at least two roller sets can be configured to contact the two other sides to maintain the carriage in contact with the rail.

  14. A Microfluidics-HPLC/Differential Mobility Spectrometer Macromolecular Detection System for Human and Robotic Missions

    Science.gov (United States)

    Coy, S. L.; Killeen, K.; Han, J.; Eiceman, G. A.; Kanik, I.; Kidd, R. D.

    2011-01-01

    Our goal is to develop a unique, miniaturized, solute analyzer based on microfluidics technology. The analyzer consists of an integrated microfluidics High Performance Liquid Chromatographic chip / Differential Mobility Spectrometer (?HPLCchip/ DMS) detection system

  15. Analysis of reconfigurable assembly system framing systems in automotive industry

    OpenAIRE

    Md Zain Mohamad Zamri; Abdul Rani Ahmad Majdi; Abd Majid Mohd Amin

    2017-01-01

    Current trend in automotive industry shows increasing demand for multiple models with lean production. Prior to that, automotive manufacturing systems evolved from mass production to flexible automation. Material handling systems and equipment in a single assembly line with multiple models require high investment but with low throughput thus making production cost relatively high. Current assembly process of side structure and undercarriage with downtime occurrence during assembly process aff...

  16. [Macromolecular systems and bactericidal films based on chitin derivatives and silver nanoparticles].

    Science.gov (United States)

    Shirokova, L N; Aleksandrova, V A; Egorova, E M; Vikhoreva, G A

    2009-01-01

    A new polymer composite based on carboxymethylchitin and silver nanoparticles was obtained in order to produce biodegradable wound coating films. The number of metal nanoparticles in the composite may be easily regulated as was verified by UV-VIS-spectroscopy data. A comparative evaluation of silver nanoparticle size in the initial system and in the polymer composition was performed by means of photon correlation spectroscopy. Composite films revealed a pronounced concentration-dependent antibacterial activity towards strains Salmonella typhimurium and Staphilococcus aureus.

  17. Essential components of the Ti plasmid trb system, a type IV macromolecular transporter.

    Science.gov (United States)

    Li, P L; Hwang, I; Miyagi, H; True, H; Farrand, S K

    1999-08-01

    The trb operon from pTiC58 is one of three loci that are required for conjugal transfer of this Ti plasmid. The operon, which probably codes for the mating bridge responsible for pair formation and DNA transfer, contains 12 genes, 11 of which are related to genes from other members of the type IV secretion system family. The 12th gene, traI, codes for production of Agrobacterium autoinducer (AAI). Insertion mutations were constructed in each of the 12 genes, contained on a full-length clone of the trb region, using antibiotic resistance cassettes or a newly constructed transposon. This transposon, called mini-Tn5Ptrb, was designed to express genes downstream of the insertion site from a promoter regulated by TraR and AAI. Each mutation could trans complement downstream Tn3HoHo1 insertions in the trb operon of full-sized Ti plasmids. When marker-exchanged into the transfer-constitutive Ti plasmid pTiC58DeltaaccR mutations in trbB, -C, -D, -E, -L, -F, -G, and -H abolished conjugal transfer from strain UIA5, which lacks the 450-kb catabolic plasmid pAtC58. However, these mutants retained residual conjugal transfer activity when tested in strain NT1, which contains this large plasmid. The trbJ mutant failed to transfer at a detectable frequency from either strain, while the trbI mutant transferred at very low but detectable levels from both donors. Only the trbK mutant was unaffected in conjugal transfer from either donor. Transfer of each of the marker-exchange mutants was restored by a clone expressing only the wild-type allele of the corresponding mutant trb gene. An insertion mutation in traI abolished the production of AAI and also conjugal transfer. This defect was restored by culturing the mutant donor in the presence of AAI. We conclude that all of the trb genes except trbI and trbK are essential for conjugal transfer of pTiC58. We also conclude that mutations in any one of the trb genes except traI and trbJ can be complemented by functions coded for by pAtC58.

  18. Outpost Assembly Using the ATHLETE Mobility System

    Science.gov (United States)

    Howe, A. Scott; Wilcox, Brian

    2016-01-01

    A planetary surface outpost will likely consist of elements delivered on multiple manifests, that will need to be assembled from a scattering of landings. Using the All-Terrain Hex-Limbed Extra-Terrestrial Explorer (ATHLETE) limbed robotic mobility system, the outpost site can be prepared in advance through leveling, paving, and in-situ structures. ATHLETE will be able to carry pressurized and non-pressurized payloads overland from the lander descent stage to the outpost location, and perform precision docking and assembly of components. In addition, spent descent stages can be carried to assembly locations to form elevated decks for external work platforms above the planet surface. This paper discusses several concepts that have been studied for possible inclusion in the NASA Evolvable Mars Campaign human exploration mission scenarios.

  19. Macromolecular ion accelerator.

    Science.gov (United States)

    Hsu, Yun-Fei; Lin, Jung-Lee; Lai, Szu-Hsueh; Chu, Ming-Lee; Wang, Yi-Sheng; Chen, Chung-Hsuan

    2012-07-03

    Presented herein are the development of macromolecular ion accelerator (MIA) and the results obtained by MIA. This new instrument utilizes a consecutive series of planar electrodes for the purpose of facilitating stepwise acceleration. Matrix-assisted laser desorption/ionization (MALDI) is employed to generate singly charged macromolecular ions. A regular Z-gap microchannel plate (MCP) detector is mounted at the end of the accelerator to record the ion signals. In this work, we demonstrated the detection of ions with the mass-to-charge (m/z) ratio reaching 30,000,000. Moreover, we showed that singly charged biomolecular ions can be accelerated with the voltage approaching 1 MV, offering the evidence that macromolecular ions can possess much higher kinetic energy than ever before.

  20. Mudular Product Families and Assembly Systems

    DEFF Research Database (Denmark)

    Thyssen, Jesper

      The main objective of this thesis is to investigate the phenomenon of product modularization as an apparently both powerful and complex means. The focal research objective is to obtain an improved insight and understanding of the relationship between variables associated with configuration...... of modular product families and the interacting assembly system.   The thesis reviews extant theory and provides various classifications and discussions guided by the overall theme of product modularity and assembly systems. The empirical system analysis, based upon a longitudinal single case study...... of theoretical and managerial implications are identified. From a management point of view, the most important finding is that modularization needs to be configured for two competitive situations, i.e. the volume flexible configuration focusing on generational product variety and the mix flexible configuration...

  1. Modular Product Families and Assembly Systems

    DEFF Research Database (Denmark)

    Thyssen, Jesper

    2005-01-01

    of the rela-tionship between variables associated with configuration of modular product families and the interacting assembly system. One core result is the development of a system model based on the longitudinal case study incorporating both structural and performance elements. Based on the system model...... a number of theoretical and managerial implications are identified. From a management point of view, the most im-portant finding is that modularization needs to be configured for the two competitive situations, i.e. 1) the volume flexible configuration focusing on generational product variety and 2...... one important contribution to the understanding and utilization of product modularization....

  2. Feasibility of Using a Bone-Targeted, Macromolecular Delivery System Coupled with Prostaglandin E1 to Promote Bone Formation in Aged, Estrogen-Deficient Rats

    Science.gov (United States)

    Miller, S. C.; Pan, H.; Wang, D.; Bowman, B. M.; Kopečková, P.; Kopeček, J.

    2009-01-01

    Purpose Macromolecular delivery systems have therapeutic uses because of their ability to deliver and release drugs to specific tissues. The uptake and localization of HPMA copolymers using Asp8 as the bone-targeting moiety was determined in aged, ovariectomized (ovx) rats. PGE1 was attached via a cathepsin K-sensitive linkage to HPMA copolymer–Asp8 conjugate and was tested to determine if it could promote bone formation. Materials and Methods The uptake of FITC-labeled HPMA copolymer–Asp8 conjugate (P-Asp8-FITC) on bone surfaces was compared with the mineralization marker, tetracycline. Then a targeted PGE1-HPMA copolymer conjugate (P-Asp8-FITC-PGE1) was given as a single injection and its effects on bone formation were measured 4 weeks later. Results P-Asp8-FITC preferentially deposited on resorption surfaces, unlike tetracycline. A single injection of P-Asp8-FITC-PGE1 resulted in greater indices of bone formation in aged, ovx rats. Conclusions HPMA copolymers can be targeted to bone surfaces using Asp8, with preferential uptake on resorption surfaces. Additionally, PGE1 attached to the Asp8-targeted HPMA copolymers and given by a single injection resulted in greater bone formation measured 4 weeks later. This initial in vivo study suggests that macromolecular delivery systems targeted to bone may offer some therapeutic opportunities and advantages for the treatment of skeletal diseases. PMID:18758923

  3. Scanning tunneling microscope assembly, reactor, and system

    Science.gov (United States)

    Tao, Feng; Salmeron, Miquel; Somorjai, Gabor A

    2014-11-18

    An embodiment of a scanning tunneling microscope (STM) reactor includes a pressure vessel, an STM assembly, and three spring coupling objects. The pressure vessel includes a sealable port, an interior, and an exterior. An embodiment of an STM system includes a vacuum chamber, an STM reactor, and three springs. The three springs couple the STM reactor to the vacuum chamber and are operable to suspend the scanning tunneling microscope reactor within the interior of the vacuum chamber during operation of the STM reactor. An embodiment of an STM assembly includes a coarse displacement arrangement, a piezoelectric fine displacement scanning tube coupled to the coarse displacement arrangement, and a receiver. The piezoelectric fine displacement scanning tube is coupled to the coarse displacement arrangement. The receiver is coupled to the piezoelectric scanning tube and is operable to receive a tip holder, and the tip holder is operable to receive a tip.

  4. Lung surface-active fraction as a model system for macromolecular ultrastructural studies with Crotalus atrox venom.

    Science.gov (United States)

    Frosolono, M F; Pawlowski, R; Charms, B L; Corbusier, C; Abrams, M; Jones, J

    1973-01-01

    The dog lung surface-active fraction and phosphatidylcholine constituents were subjected to hydrolysis by Crotalus atrox phospholipase A(2). Relative rates of hydrolysis were: dipalmitoyl glycerophosphorylcholine > phosphatidylcholine isolated from the surface-active fraction > phosphatidylcholine as an integral component of the intact surface-active macromolecular structure. Cholesterol markedly inhibited, whereas tripalmitin increased, the rate of hydrolysis with both pure phosphatidylcholine substrates. The effect of temperature on the velocity indicated the enzyme was most active when the substrates were in the gel state. These kinetic results, in conjunction with surface chemistry studies, can be interpreted to indicate that the phosphatidylcholine in the intact surface-active macromolecular particle is liquid crystalline due to molecular interactions with other constituents. Gas-liquid chromatographic analysis of the 2-lysophosphatidylcholines and fatty acids produced from the enzymatic hydrolysis of the intact surface-active fraction indicated that palmitoyl residues were more accessible to the enzyme, perhaps because they occupied positions near the surface of the particle.

  5. System and method for controlling a combustor assembly

    Science.gov (United States)

    York, William David; Ziminsky, Willy Steve; Johnson, Thomas Edward; Stevenson, Christian Xavier

    2013-03-05

    A system and method for controlling a combustor assembly are disclosed. The system includes a combustor assembly. The combustor assembly includes a combustor and a fuel nozzle assembly. The combustor includes a casing. The fuel nozzle assembly is positioned at least partially within the casing and includes a fuel nozzle. The fuel nozzle assembly further defines a head end. The system further includes a viewing device configured for capturing an image of at least a portion of the head end, and a processor communicatively coupled to the viewing device, the processor configured to compare the image to a standard image for the head end.

  6. PGAAS: a prokaryotic genome assembly assistant system.

    Science.gov (United States)

    Yu, Zhou; Li, Tao; Zhao, Jindong; Luo, Jingchu

    2002-05-01

    In order to accelerate the finishing phase of genome assembly, especially for the whole genome shotgun approach of prokaryotic species, we have developed a software package designated prokaryotic genome assembly assistant system (PGAAS). The approach upon which PGAAS is based is to confirm the order of contigs and fill gaps between contigs through peptide links obtained by searching each contig end with BLASTX against protein databases. We used the contig dataset of the cyanobacterium Synechococcus sp. strain PCC7002 (PCC7002), which was sequenced with six-fold coverage and assembled using the Phrap package. The subject database is the protein database of the cyanobacterium, Synechocystis sp. strain PCC6803 (PCC6803). We found more than 100 non-redundant peptide segments which can link at least 2 contigs. We tested one pair of linked contigs by sequencing and obtained satisfactory result. PGAAS provides a graphic user interface to show the bridge peptides and pier contigs. We integrated Primer3 into our package to design PCR primers at the adjacent ends of the pier contigs. We tested PGAAS on a Linux (Redhat 6.2) PC machine. It is developed with free software (MySQL, PHP and Apache). The whole package is distributed freely and can be downloaded as UNIX compress file: ftp://ftp.cbi.pku.edu.cn/pub/software/unix/pgaas1.0.tar.gz. The package is being continually updated.

  7. RAMPART: a workflow management system for de novo genome assembly

    National Research Council Canada - National Science Library

    Mapleson, Daniel; Drou, Nizar; Swarbreck, David

    2015-01-01

    ... assembly for publication. Herein, we present RAMPART, a configurable workflow management system for de novo genome assembly, which helps the user identify combinations of third-party tools and settings that provide good...

  8. Macromolecular recognition in the Protein Data Bank

    Energy Technology Data Exchange (ETDEWEB)

    Janin, Joël, E-mail: joel.janin@ibbmc.u-psud.fr [Laboratoire d’Enzymologie et de Biochimie Structurales, UPR9063, CNRS, 91198 Gif-sur-Yvette (France); Institut de Biochimie et Biologie Moléculaire et Cellulaire, UMR8619, Bâtiment 430, Université Paris-Sud, 91405 Orsay (France); Rodier, Francis [Laboratoire d’Enzymologie et de Biochimie Structurales, UPR9063, CNRS, 91198 Gif-sur-Yvette (France); Chakrabarti, Pinak [Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Calcutta 700 054 (India); Bahadur, Ranjit P. [Institut de Biochimie et Biologie Moléculaire et Cellulaire, UMR8619, Bâtiment 430, Université Paris-Sud, 91405 Orsay (France); Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Calcutta 700 054 (India); Laboratoire d’Enzymologie et de Biochimie Structurales, UPR9063, CNRS, 91198 Gif-sur-Yvette (France)

    2007-01-01

    X-ray structures in the PDB illustrate both the specific recognition of two polypeptide chains in protein–protein complexes and dimeric proteins and their nonspecific interaction at crystal contacts. Crystal structures deposited in the Protein Data Bank illustrate the diversity of biological macromolecular recognition: transient interactions in protein–protein and protein–DNA complexes and permanent assemblies in homodimeric proteins. The geometric and physical chemical properties of the macromolecular interfaces that may govern the stability and specificity of recognition are explored in complexes and homodimers compared with crystal-packing interactions. It is found that crystal-packing interfaces are usually much smaller; they bury fewer atoms and are less tightly packed than in specific assemblies. Standard-size interfaces burying 1200–2000 Å{sup 2} of protein surface occur in protease–inhibitor and antigen–antibody complexes that assemble with little or no conformation changes. Short-lived electron-transfer complexes have small interfaces; the larger size of the interfaces observed in complexes involved in signal transduction and homodimers correlates with the presence of conformation changes, often implicated in biological function. Results of the CAPRI (critical assessment of predicted interactions) blind prediction experiment show that docking algorithms efficiently and accurately predict the mode of assembly of proteins that do not change conformation when they associate. They perform less well in the presence of large conformation changes and the experiment stimulates the development of novel procedures that can handle such changes.

  9. Improvability theory for assembly systems: Two component—one assembly machine case

    Directory of Open Access Journals (Sweden)

    C.-T Kuo

    1996-01-01

    Full Text Available Improvability theory for a simple assembly system consisting of two components and one assembly machine is developed. Both constrained and unconstrained formulations are addressed. In the constrained case, it is shown that the assembly is unimprovable with respect to workforce if each component machine is blocked as frequently as the assembly machine is starved for parts produced by this particular assembly machine. The system is unimprovable with respect to work-in-process if, roughly speaking, all buffers have equal average steady state occupancy. In the unconstrained improvability case, it is shown that the bottleneck machine can be identified by analyzing the probabilities of the so-called manufacturing blockages and starvations. A generalization to n component—one assembly machine system is also included.

  10. Implementation of a robotic flexible assembly system

    Science.gov (United States)

    Benton, Ronald C.

    1987-01-01

    As part of the Intelligent Task Automation program, a team developed enabling technologies for programmable, sensory controlled manipulation in unstructured environments. These technologies include 2-D/3-D vision sensing and understanding, force sensing and high speed force control, 2.5-D vision alignment and control, and multiple processor architectures. The subsequent design of a flexible, programmable, sensor controlled robotic assembly system for small electromechanical devices is described using these technologies and ongoing implementation and integration efforts. Using vision, the system picks parts dumped randomly in a tray. Using vision and force control, it performs high speed part mating, in-process monitoring/verification of expected results and autonomous recovery from some errors. It is programmed off line with semiautomatic action planning.

  11. Systemic analysis of the caulking assembly process

    Directory of Open Access Journals (Sweden)

    Rodean Claudiu

    2017-01-01

    Full Text Available The present paper highlights the importance of a caulking process which is nowadays less studied in comparison with the growing of its usage in the automotive industry. Due to the fact that the caulking operation is used in domains with high importance such as shock absorbers and brake systems there comes the demand of this paper to detail the parameters which characterize the process, viewed as input data and output data, and the requirements asked for the final product. The paper presents the actual measurement methods used for analysis the performance of the caulking assembly. All this parameters leads to an analysis algorithm of performance established for the caulking process which it is used later in the paper for an experimental research. The study is a basis from which it will be able to go to further researches in order to optimize the following processing.

  12. Complex macromolecular chimeras.

    Science.gov (United States)

    Karatzas, Anastasis; Iatrou, Hermis; Hadjichristidis, Nikos; Inoue, Kyouichi; Sugiyama, Kenji; Hirao, Akira

    2008-07-01

    By combining two living polymerizations, anionic and ring opening (ROP), the following novel multiblock multicomponent linear and miktoarm star (micro-star) polymer/polypeptide hybrids (macromolecular chimeras) were synthesized: Linear, PBLL-b-PBLG-b-PS-b-PBLG-b-PBLL; 3micro-stars, (PS)2(PBLG or PBLL), (PS)(PI)(PBLG or PBLL); 4micro-stars, (PS)2[P(alpha-MeS)](PBLG or PBLL), (PS)2(PBLG or PBLL)2 [PS, polystyrene; PI, polyisoprene; P(alpha-MeS), poly(alpha-methylstyrene); PBLG, poly(gamma-benzyl-L-glutamate); and PBLL, poly(-tert-butyloxycarbonyl-L-lysine)]. The procedure involves (a) the synthesis of end- or in-chain amino-functionalized polymers, by anionic polymerization high vacuum techniques and appropriate linking chemistry and (b) the use of the amino groups for the ROP of alpha-amino acid carboxyanhydrides (NCAs). Molecular characterization revealed the high molecular weight and compositional homogeneity of the macromolecular chimeras prepared. The success of the synthesis was based mainly on the high vacuum techniques used for the ROP of NCAs, ensuring the avoidance of unwanted polymerization mechanisms and termination reactions.

  13. Optical Assembly and Characterization System for Nano-Photonics Research

    Science.gov (United States)

    2016-03-01

    Unlimited Final Report: Optical Assembly and Characterization System for Nano -Photonics Research The views, opinions and/or findings contained in this...reviewed journals: Final Report: Optical Assembly and Characterization System for Nano -Photonics Research Report Title With this equipment funding support...Assembly and Characterization System for Nano -Photonics Research PI: Prof. Weidong Zhou, University of Texas at Arlington (UTA) 500 S. Cooper St

  14. Homogenization Theory for the Prediction of Obstructed Solute Diffusivity in Macromolecular Solutions.

    Science.gov (United States)

    Donovan, Preston; Chehreghanianzabi, Yasaman; Rathinam, Muruhan; Zustiak, Silviya Petrova

    2016-01-01

    The study of diffusion in macromolecular solutions is important in many biomedical applications such as separations, drug delivery, and cell encapsulation, and key for many biological processes such as protein assembly and interstitial transport. Not surprisingly, multiple models for the a-priori prediction of diffusion in macromolecular environments have been proposed. However, most models include parameters that are not readily measurable, are specific to the polymer-solute-solvent system, or are fitted and do not have a physical meaning. Here, for the first time, we develop a homogenization theory framework for the prediction of effective solute diffusivity in macromolecular environments based on physical parameters that are easily measurable and not specific to the macromolecule-solute-solvent system. Homogenization theory is useful for situations where knowledge of fine-scale parameters is used to predict bulk system behavior. As a first approximation, we focus on a model where the solute is subjected to obstructed diffusion via stationary spherical obstacles. We find that the homogenization theory results agree well with computationally more expensive Monte Carlo simulations. Moreover, the homogenization theory agrees with effective diffusivities of a solute in dilute and semi-dilute polymer solutions measured using fluorescence correlation spectroscopy. Lastly, we provide a mathematical formula for the effective diffusivity in terms of a non-dimensional and easily measurable geometric system parameter.

  15. Development of a virtual manufacturing assembly simulation system

    Directory of Open Access Journals (Sweden)

    Abdulrahman M Al-Ahmari

    2016-03-01

    Full Text Available Assembly operations are a key component of modern manufacturing systems. Designing, planning, and conducting assembly operations represent an important part of the cost of a product. Virtual reality provides an efficient and cost-effective solution to manufacturing design, planning, and prototyping. Still there are certain issues (such as data translation, integration of various hardware and software systems, and real-time collision detection faced while applying this advanced technology to the assembly domain. For example, existing works focus on using virtual reality systems and environments mainly to design new products and to plan for assembly. Little focus has been given to develop virtual reality environments that contribute to train operators on assembly operations and to bridge the gap between design and implementation/execution of assembly. Therefore, the research work presented in this article focuses on developing a fully functional virtual manufacturing assembly simulation system that solves the issues related to virtual reality environments. The proposed system uses a virtual environment to create an interactive workbench that can be used for evaluating assembly decisions and training assembly operations. It is a comprehensive system that provides visual, auditory, tactile, as well as force feedback. The system works successfully even with large components.

  16. Macromolecular organization of chicken type X collagen in vitro

    OpenAIRE

    1991-01-01

    The macromolecular structure of type X collagen in the matrices of primary cultures of chick hypertrophic chondrocytes was initially investigated using immunoelectron microscopy. Type X collagen was observed to assemble into a matlike structure with-in the matrix elaborated by hypertrophic chondrocytes. The process of self assembly was investigated at the molecular level using purified chick type X collagen and rotary-shadowing EM. It was shown that under neutral conditions at 34 degrees C, i...

  17. Self-assembled Nanomaterials for Hybrid Electronic and Photonic Systems

    Science.gov (United States)

    2015-05-15

    Self-assembled Nanomaterials for Hybrid Electronic and Photonic Systems This grant studied DNA nanostructures and their applications in a variety of...Number of Papers published in non peer-reviewed journals: Final Report: Self-assembled Nanomaterials for Hybrid Electronic and Photonic Systems Report

  18. Optimization of Flexible Assembly Systems for Electrical Motors

    OpenAIRE

    Bruqi, Mirlind; Likaj, Ramë; Kaqani, Jorgaq

    2012-01-01

    Part 2: Design, Manufacturing and Production Management; International audience; The modern assembly systems are fully integrated production systems. They consist of interconnected components of hardware and software. Large flexible assembly systems are being composed of high number of components and managing requires an enormous volume of data. For that reason the controlling and optimization of such systems is too complex. Nowadays that can achieved, using just computers and software tools....

  19. Condenser assembly system for an appliance

    Energy Technology Data Exchange (ETDEWEB)

    Litch, Andrew David

    2017-10-17

    An appliance includes a compact condenser assembly formed with at least two separately and independently produced wire on tube condensers. Each of the at least two wire on tube condensers has a condenser inlet and a condenser outlet. The at least two wire on tube condensers are at least substantially locked and positioned in a matingly engaged configuration forming a compact condenser assembly. The at least two wire on tube condensers are configured to be operationally connected in at least one of a parallel configuration, a series configuration, a selectable configuration, and a bypass configuration.

  20. SSME component assembly and life management expert system

    Science.gov (United States)

    Ali, M.; Dietz, W. E.; Ferber, H. J.

    1989-01-01

    The space shuttle utilizes several rocket engine systems, all of which must function with a high degree of reliability for successful mission completion. The space shuttle main engine (SSME) is by far the most complex of the rocket engine systems and is designed to be reusable. The reusability of spacecraft systems introduces many problems related to testing, reliability, and logistics. Components must be assembled from parts inventories in a manner which will most effectively utilize the available parts. Assembly must be scheduled to efficiently utilize available assembly benches while still maintaining flight schedules. Assembled components must be assigned to as many contiguous flights as possible, to minimize component changes. Each component must undergo a rigorous testing program prior to flight. In addition, testing and assembly of flight engines and components must be done in conjunction with the assembly and testing of developmental engines and components. The development, testing, manufacture, and flight assignments of the engine fleet involves the satisfaction of many logistical and operational requirements, subject to many constraints. The purpose of the SSME Component Assembly and Life Management Expert System (CALMES) is to assist the engine assembly and scheduling process, and to insure that these activities utilize available resources as efficiently as possible.

  1. Managing an Assemble-to-Order System with Returns

    OpenAIRE

    Gregory A. DeCroix; Jing-Sheng Song; Paul H. Zipkin

    2009-01-01

    We consider a multiproduct assemble-to-order (ATO) system, in which inventory is kept only at the component level and the finished products are assembled in response to customer demands. In addition to stochastic demand for finished products, the system experiences stochastic returns of subsets of components, which can then be used to satisfy subsequent demands. The system is managed over an infinite horizon using a component-level base-stock policy. We identify several ways in which returns ...

  2. Macromolecular nanotheranostics for multimodal anticancer therapy

    Science.gov (United States)

    Huis in't Veld, Ruben; Storm, Gert; Hennink, Wim E.; Kiessling, Fabian; Lammers, Twan

    2011-10-01

    Macromolecular carrier materials based on N-(2-hydroxypropyl)methacrylamide (HPMA) are prototypic and well-characterized drug delivery systems that have been extensively evaluated in the past two decades, both at the preclinical and at the clinical level. Using several different imaging agents and techniques, HPMA copolymers have been shown to circulate for prolonged periods of time, and to accumulate in tumors both effectively and selectively by means of the Enhanced Permeability and Retention (EPR) effect. Because of this, HPMA-based macromolecular nanotheranostics, i.e. formulations containing both drug and imaging agents within a single formulation, have been shown to be highly effective in inducing tumor growth inhibition in animal models. In patients, however, as essentially all other tumor-targeted nanomedicines, they are generally only able to improve the therapeutic index of the attached active agent by lowering its toxicity, and they fail to improve the efficacy of the intervention. Bearing this in mind, we have recently reasoned that because of their biocompatibility and their beneficial biodistribution, nanomedicine formulations might be highly suitable systems for combination therapies. In the present manuscript, we briefly summarize several exemplary efforts undertaken in this regard in our labs in the past couple of years, and we show that long-circulating and passively tumor-targeted macromolecular nanotheranostics can be used to improve the efficacy of radiochemotherapy and of chemotherapy combinations.

  3. Improvability of assembly systems I: Problem formulation and performance evaluation

    Directory of Open Access Journals (Sweden)

    S.-Y. Chiang

    2000-01-01

    Full Text Available This work develops improvability theory for assembly systems. It consists of two parts. Part I includes the problem formulation and the analysis technique. Part II presents the so-called improvability indicators and a case study.

  4. Energy transfer in macromolecular arrays

    Science.gov (United States)

    Andrews, David L.; Jenkins, Robert D.

    2003-11-01

    Macromolecular systems comprised of many light-sensitive centres (the photosynthetic unit, dendrimers, and other highly symmetric multichromophore arrays) are important structures offering challenges to theoreticians and synthetic chemists alike. Here we outline novel photophysical interactions predicted and observed in such arrays. Using the tools of molecular quantum electrodynamics (QED) we present quantum amplitudes for a variety of higher-order resonance energy transfer (RET) schemes associated with well-known nonlinear optical effects such as two- and three-photon absorption. The initial analysis is extended to account for situations where the participant donor species are identical and exist in a highly symmetric environment, leading to the possible formation of excitons. It emerges from the QED theory that such excitons are closely associated with the higher-order RET processes. General results are interpreted by analyzing particular molecular architectures which offer interesting features such as rate enhancement or limitation and exciton pathway quenching. Applications in the areas of photosynthesis, molecular logic gates and low-intensity fluorescence energy transfer are predicted.

  5. Root-Contact/Pressure-Plate Assembly For Hydroponic System

    Science.gov (United States)

    Morris, Carlton E.; Loretan, Philip A.; Bonsi, Conrad K.; Hill, Walter A.

    1994-01-01

    Hydroponic system includes growth channels equipped with rootcontact/pressure-plate assemblies. Pump and associated plumbing circulate nutrient liquid from reservoir, along bottom of growth channels, and back to reservoir. Root-contact/pressure-plate assembly in each growth channel stimulates growth of roots by applying mild contact pressure. Flat plate and plate connectors, together constitute pressure plate, free to move upward to accommodate growth of roots. System used for growing sweetpotatoes and possibly other tuber and root crops.

  6. Optimisation of assembly scheduling in VCIM systems using genetic algorithm

    Science.gov (United States)

    Dao, Son Duy; Abhary, Kazem; Marian, Romeo

    2017-01-01

    Assembly plays an important role in any production system as it constitutes a significant portion of the lead time and cost of a product. Virtual computer-integrated manufacturing (VCIM) system is a modern production system being conceptually developed to extend the application of traditional computer-integrated manufacturing (CIM) system to global level. Assembly scheduling in VCIM systems is quite different from one in traditional production systems because of the difference in the working principles of the two systems. In this article, the assembly scheduling problem in VCIM systems is modeled and then an integrated approach based on genetic algorithm (GA) is proposed to search for a global optimised solution to the problem. Because of dynamic nature of the scheduling problem, a novel GA with unique chromosome representation and modified genetic operations is developed herein. Robustness of the proposed approach is verified by a numerical example.

  7. Functional self-assembled lipidic systems derived from renewable resources.

    Science.gov (United States)

    Silverman, Julian R; Samateh, Malick; John, George

    2016-01-01

    Self-assembled lipidic amphiphile systems can create a variety of multi-functional soft materials with value-added properties. When employing natural reagents and following biocatalytic syntheses, self-assembling monomers may be inherently designed for degradation, making them potential alternatives to conventional and persistent polymers. By using non-covalent forces, self-assembled amphiphiles can form nanotubes, fibers, and other stimuli responsive architectures prime for further applied research and incorporation into commercial products. By viewing these lipid derivatives under a lens of green principles, there is the hope that in developing a structure-function relationship and functional smart materials that research may remain safe, economic, and efficient.

  8. RAMPART: a workflow management system for de novo genome assembly.

    Science.gov (United States)

    Mapleson, Daniel; Drou, Nizar; Swarbreck, David

    2015-06-01

    The de novo assembly of genomes from whole- genome shotgun sequence data is a computationally intensive, multi-stage task and it is not known a priori which methods and parameter settings will produce optimal results. In current de novo assembly projects, a popular strategy involves trying many approaches, using different tools and settings, and then comparing and contrasting the results in order to select a final assembly for publication. Herein, we present RAMPART, a configurable workflow management system for de novo genome assembly, which helps the user identify combinations of third-party tools and settings that provide good results for their particular genome and sequenced reads. RAMPART is designed to exploit High performance computing environments, such as clusters and shared memory systems, where available. RAMPART is available under the GPLv3 license at: https://github.com/TGAC/RAMPART. © The Author 2015. Published by Oxford University Press.

  9. Coordination in the Decentralized Assembly System with Dual Supply Modes

    Directory of Open Access Journals (Sweden)

    Xu Guan

    2013-01-01

    Full Text Available This paper investigates a decentralized assembly system that consists of one assembler and two independent suppliers; wherein one supplier is perfectly reliable for the production, while the other generates yield uncertainty. Facing the random market demand, the assembler has to order the components from one supplier in advance and meanwhile requires the other supplier to deliver the components under VMI mode. We construct a Nash game between the supplier and the assembler so as to derive their equilibrium procurement/production strategies. The results show that the channel’s performance is highly undermined by the decentralization between players and also the combination of two supply modes. Compared to the centralized system, we propose an advance payment contract to perfectly coordinate the supply chain performance. The numerical examples indicate some management implications on the supply mode comparison and sensitivity analysis.

  10. Control system for the 2nd generation Berkeley automounters (BAM2) at GM/CA-CAT macromolecular crystallography beamlines

    Energy Technology Data Exchange (ETDEWEB)

    Makarov, O., E-mail: makarov@anl.gov [GM/CA-CAT, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439 (United States); Hilgart, M.; Ogata, C.; Pothineni, S. [GM/CA-CAT, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439 (United States); Cork, C. [Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States)

    2011-09-01

    GM/CA-CAT at Sector 23 of the Advanced Photon Source (APS) is an NIH funded facility for crystallographic structure determination of biological macromolecules by X-ray diffraction. A second-generation Berkeley automounter is being integrated into the beamline control system at the 23BM experimental station. This new device replaces the previous all-pneumatic gripper motions with a combination of pneumatics and XYZ motorized linear stages. The latter adds a higher degree of flexibility to the robot including auto-alignment capability, accommodation of a larger capacity sample Dewar of arbitrary shape, and support for advanced operations such as crystal washing, while preserving the overall simplicity and efficiency of the Berkeley automounter design.

  11. Spatial Configuration of Macromolecular Chains

    Indian Academy of Sciences (India)

    highlight in this lecture give promise of far-reaching advances in our understanding of macromolecular ... in articles of commerce. The chemical bonds in macromolecules differ in no discernible respect from those in ... The number and variety of configurations (or conformations in the language of organic chemistry) that.

  12. Recent advances in macromolecular prodrugs

    DEFF Research Database (Denmark)

    Riber, Camilla Frich; Zelikin, Alexander N.

    2017-01-01

    Macromolecular prodrugs (MP) are high molar mass conjugates, typically carrying several copies of a drug or a drug combination, designed to optimize delivery of the drug, that is — its pharmacokinetics. From its advent several decades ago, design of MP has undergone significant development and es...

  13. Precision Assembly of Systems on Surfaces (PASS)

    Science.gov (United States)

    2015-02-06

    selected extended π-electronic structures based upon porphyrins . The modularity of this system with regard to the metal ions incorporated provides... porphyrin complexes. These materials have extended π-electron systems that make them ideal candidates to bind through non- covalent mechanisms to the...surfaces of carbon nanotubes. To promote strong interactions we initially focused on a porphyrin system containing fused pyrene systems that had been

  14. Simulation as a support tool in assembly systems planning

    Directory of Open Access Journals (Sweden)

    Václav Štefan

    2017-01-01

    Full Text Available This paper deals with assumption that simulation is the only reliable method for manufacturing and assembly systems profiling. Simulation is essential software tool that improve design and planning of complex automated manufacturing and assembly systems. Systems with high level of complexity need to be tested even before they are constructed in real manufacturing plant. Elimination of errors in production before the first test production is initiated means huge savings in expenses and time. In this article are mentioned theoretical base of topic and example as a case study. For case study was used software Tecnomatix plant simulation from company SIEMENS.

  15. Oxidative macromolecular alterations in the rat central nervous system in response to experimentally co-induced chlorpyrifos and cold stress: a comparative assessment in aging rats.

    Science.gov (United States)

    Basha, P Mahaboob; Poojary, Annappa

    2012-02-01

    Reactive oxygen species are generated as a result of a number of physiological and pathological processes which can promote multiple forms of oxidative damage including protein oxidation, and thereby influence the function of a diverse array of cellular processes. In our previous study we have reported that co-exposure to chlorpyrifos and cold stress in aging rats markedly influence the toxic outcome as a result of oxidative stress. In the present study, key neurochemical/enzymes were measured in order to evaluate the macromolecular alterations in response to experimentally co-induced chlorpyrifos and cold stress (15 and 20°C) either concurrently or individually in vivo for 48 h in discrete regions of brain and spinal cord of different age group rats. CPF and cold stress exposure either individually or in combination substantially increased the activity/levels of protein carbonyls, AST, ALT and decreased protein thiols, DNA, RNA and total proteins in discrete regions of CNS. Overall, the effects of co-exposure were appreciably different from either of the exposures. However, synergistic-action of CPF and cold stress at 15°C showed higher dyshomeostasis in comparison with CPF and cold stress alone and together at 20°C indicating the extent of oxidative macromolecular damage in discrete regions of brain and spinal cord. Furthermore, the present study demonstrates that macromolecular oxidative damage is highly pronounced in neonates and juveniles than the young adults.

  16. Optical systems fabricated by printing-based assembly

    Energy Technology Data Exchange (ETDEWEB)

    Rogers, John; Nuzzo, Ralph; Meitl, Matthew; Menard, Etienne; Baca, Alfred; Motala, Michael; Ahn, Jong-Hyun; Park, Sang-Il; Yu, Chang-Jae; Ko, Heung Cho; Stoykovich, Mark; Yoon, Jongseung

    2017-03-21

    Provided are optical devices and systems fabricated, at least in part, via printing-based assembly and integration of device components. In specific embodiments the present invention provides light emitting systems, light collecting systems, light sensing systems and photovoltaic systems comprising printable semiconductor elements, including large area, high performance macroelectronic devices. Optical systems of the present invention comprise semiconductor elements assembled, organized and/or integrated with other device components via printing techniques that exhibit performance characteristics and functionality comparable to single crystalline semiconductor based devices fabricated using conventional high temperature processing methods. Optical systems of the present invention have device geometries and configurations, such as form factors, component densities, and component positions, accessed by printing that provide a range of useful device functionalities. Optical systems of the present invention include devices and device arrays exhibiting a range of useful physical and mechanical properties including flexibility, shapeability, conformability and stretchablity.

  17. Macromolecular systems for vaccine delivery

    Czech Academy of Sciences Publication Activity Database

    Mužíková, Gabriela; Laga, Richard

    2016-01-01

    Roč. 65, Suppl. 2 (2016), S203-S216 ISSN 0862-8408 R&D Projects: GA MŠk(CZ) LQ1604 Institutional support: RVO:61389013 Keywords : vaccine delivery * cellular and humoral immunity * polymer immunostimulants Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.461, year: 2016 http://www.biomed.cas.cz/physiolres/pdf/65%20Suppl%202/65_S203.pdf

  18. Hyper bio assembler for 3D cellular systems

    CERN Document Server

    Arai, Fumihito; Yamato, Masayuki

    2015-01-01

    Hyper Bio Assembler for Cellular Systems is the first book to present a new methodology for measuring and separating target cells at high speed and constructing 3D cellular systems in vitro. This book represents a valuable resource for biologists, biophysicists and robotic engineers, as well as researchers interested in this new frontier area, offering a better understanding of the measurement, separation, assembly, analysis and synthesis of complex biological tissue, and of the medical applications of these technologies. This book is the outcome of the new academic fields of the Ministry of Education, Culture, Sports, Science and Technology’s Grant-in-Aid for Scientific Research in Japan.

  19. Electrode assemblies, plasma apparatuses and systems including electrode assemblies, and methods for generating plasma

    Science.gov (United States)

    Kong, Peter C; Grandy, Jon D; Detering, Brent A; Zuck, Larry D

    2013-09-17

    Electrode assemblies for plasma reactors include a structure or device for constraining an arc endpoint to a selected area or region on an electrode. In some embodiments, the structure or device may comprise one or more insulating members covering a portion of an electrode. In additional embodiments, the structure or device may provide a magnetic field configured to control a location of an arc endpoint on the electrode. Plasma generating modules, apparatus, and systems include such electrode assemblies. Methods for generating a plasma include covering at least a portion of a surface of an electrode with an electrically insulating member to constrain a location of an arc endpoint on the electrode. Additional methods for generating a plasma include generating a magnetic field to constrain a location of an arc endpoint on an electrode.

  20. Single-Step Affinity Purification (ssAP) and Mass Spectrometry of Macromolecular Complexes in the Yeast S. cerevisiae.

    Science.gov (United States)

    Trahan, Christian; Aguilar, Lisbeth-Carolina; Oeffinger, Marlene

    2016-01-01

    Cellular functions are mostly defined by the dynamic interactions of proteins within macromolecular networks. Deciphering the composition of macromolecular complexes and their dynamic rearrangements is the key to getting a comprehensive picture of cellular behavior and to understanding biological systems. In the last decade, affinity purification coupled to mass spectrometry has emerged as a powerful tool to comprehensively study interaction networks and their assemblies. However, the study of these interactomes has been hampered by severe methodological limitations. In particular, the affinity purification of intact complexes from cell lysates suffers from protein and RNA degradation, loss of transient interactors, and poor overall yields. In this chapter, we describe a rapid single-step affinity purification method for the efficient isolation of dynamic macromolecular complexes. The technique employs cell lysis by cryo-milling, which ensures nondegraded starting material in the submicron range, and magnetic beads, which allow for dense antibody-conjugation and thus rapid complex isolation, while avoiding loss of transient interactions. The method is epitope tag-independent, and overcomes many of the previous limitations to produce large interactomes with almost no contamination. The protocol described here has been optimized for the yeast S. cerevisiae.

  1. Implications of macromolecular crowding and reducing conditions for in vitro ribosome construction

    Science.gov (United States)

    Fritz, Brian R.; Jamil, Osman K.; Jewett, Michael C.

    2015-01-01

    In vitro construction of Escherichia coli ribosomes could elucidate a deeper understanding of these complex molecular machines and make possible the production of synthetic variants with new functions. Toward this goal, we recently developed an integrated synthesis, assembly and translation (iSAT) system that allows for co-activation of ribosomal RNA (rRNA) transcription and ribosome assembly, mRNA transcription and protein translation without intact cells. Here, we discovered that macromolecular crowding and reducing agents increase overall iSAT protein synthesis; the combination of 6% w/v Ficoll 400 and 2 mM DTBA yielded approximately a five-fold increase in overall iSAT protein synthesis activity. By utilizing a fluorescent RNA aptamer, fluorescent reporter proteins and ribosome sedimentation analysis, we showed that crowding agents increase iSAT yields by enhancing translation while reducing agents increase rRNA transcription and ribosome assembly. Finally, we showed that iSAT ribosomes possess ∼70% of the protein synthesis activity of in vivo-assembled E. coli ribosomes. This work improves iSAT protein synthesis through the addition of crowding and reducing agents, provides a thorough understanding of the effect of these additives within the iSAT system and demonstrates how iSAT allows for manipulation and analysis of ribosome biogenesis in the context of an in vitro transcription-translation system. PMID:25897121

  2. Interactive Systems for Designing Machine Elements and Assemblies

    OpenAIRE

    Kacalak Wojciech; Majewski Maciej; Stuart Keith Douglas; Budniak Zbigniew

    2015-01-01

    The article describes the development of fundamentals of machine elements and assemblies design processes automation using artificial intelligence, and descriptions of structural elements’ features in a natural language. In the proposed interactive automated design systems, computational artificial intelligence methods allow communication by speech and natural language, resulting in analyses of design engineer’s messages, analyses of constructions, encoding and assessments of constructions, C...

  3. New concepts and applications in the macromolecular chemistry of fullerenes.

    Science.gov (United States)

    Giacalone, Francesco; Martín, Nazario

    2010-10-08

    A new classification on the different types of fullerene-containing polymers is presented according to their different properties and applications they exhibit in a variety of fields. Because of their interest and novelty, water-soluble and biodegradable C(60)-polymers are discussed first, followed by polyfullerene-based membranes where unprecedented supramolecular structures are presented. Next are compounds that involve hybrid materials formed from fullerenes and other components such as silica, DNA, and carbon nanotubes (CNTs) where the most recent advances have been achieved. A most relevant topic is still that of C(60)-based donor-acceptor (D-A) polymers. Since their application in photovoltaics D-A polymers are among the most realistic applications of fullerenes in the so-called molecular electronics. The most relevant aspects in these covalently connected fullerene/polymer hybrids as well as new concepts to improve energy conversion efficiencies are presented.The last topics disccused relate to supramolecular aspects that are in involved in C(60)-polymer systems and in the self-assembly of C(60)-macromolecular structures, which open a new scenario for organizing, by means of non-covalent interactions, new supramolecular structures at the nano- and micrometric scale, in which the combination of the hydrofobicity of fullerenes with the versatility of the noncovalent chemistry afford new and spectacular superstructures.

  4. Modelling the self-assembly of virus capsids

    Science.gov (United States)

    Johnston, Iain G.; Louis, Ard A.; Doye, Jonathan P. K.

    2010-03-01

    We use computer simulations to study a model, first proposed by Wales (2005 Phil. Trans. R. Soc. A 363 357), for the reversible and monodisperse self-assembly of simple icosahedral virus capsid structures. The success and efficiency of assembly as a function of thermodynamic and geometric factors can be qualitatively related to the potential energy landscape structure of the assembling system. Even though the model is strongly coarse-grained, it exhibits a number of features also observed in experiments, such as sigmoidal assembly dynamics, hysteresis in capsid formation and numerous kinetic traps. We also investigate the effect of macromolecular crowding on the assembly dynamics. Crowding agents generally reduce capsid yields at optimal conditions for non-crowded assembly, but may increase yields for parameter regimes away from the optimum. Finally, we generalize the model to a larger triangulation number T = 3, and observe assembly dynamics more complex than that seen for the original T = 1 model.

  5. A modular cloning system for standardized assembly of multigene constructs.

    Directory of Open Access Journals (Sweden)

    Ernst Weber

    Full Text Available The field of synthetic biology promises to revolutionize biotechnology through the design of organisms with novel phenotypes useful for medicine, agriculture and industry. However, a limiting factor is the ability of current methods to assemble complex DNA molecules encoding multiple genetic elements in various predefined arrangements. We present here a hierarchical modular cloning system that allows the creation at will and with high efficiency of any eukaryotic multigene construct, starting from libraries of defined and validated basic modules containing regulatory and coding sequences. This system is based on the ability of type IIS restriction enzymes to assemble multiple DNA fragments in a defined linear order. We constructed a 33 kb DNA molecule containing 11 transcription units made from 44 individual basic modules in only three successive cloning steps. This modular cloning (MoClo system can be readily automated and will be extremely useful for applications such as gene stacking and metabolic engineering.

  6. Storage, transportation and disposal system for used nuclear fuel assemblies

    Science.gov (United States)

    Scaglione, John M.; Wagner, John C.

    2017-01-10

    An integrated storage, transportation and disposal system for used fuel assemblies is provided. The system includes a plurality of sealed canisters and a cask sized to receive the sealed canisters in side by side relationship. The plurality of sealed canisters include an internal basket structure to receive a plurality of used fuel assemblies. The internal basket structure includes a plurality of radiation-absorbing panels and a plurality of hemispherical ribs generally perpendicular to the canister sidewall. The sealed canisters are received within the cask for storage and transportation and are removed from the cask for disposal at a designated repository. The system of the present invention allows the handling of sealed canisters separately or collectively, while allowing storage and transportation of high burnup fuel and damaged fuel to the designated repository.

  7. A force-feedback control system for micro-assembly

    Science.gov (United States)

    Lu, Zhe; Chen, Peter C. Y.; Ganapathy, Anand; Zhao, Guoyong; Nam, Joohoo; Yang, Guilin; Burdet, Etienne; Teo, Cheeleong; Meng, Qingnian; Lin, Wei

    2006-09-01

    In this paper, we report the development of an explicit force-feedback control system for micro-assembly, focusing on the key issues of force transmission and control. The force-feedback system is incorporated with a compound flexure stage, which is driven by a voice-coil actuator and designed to provide frictionless translation motion along one axis. A force sensor measures the interaction force between the micromanipulator and its environment, while an explicit force controller controls the interaction force to follow a desired force trajectory. The effectiveness of this prototype force-control system has been demonstrated in an experimental application, where parts (with dimensions in microns) were picked up and assembled under explicit force-feedback control.

  8. Paradigm shift from self-assembly to commanded assembly of functional materials: recent examples in porphyrin/fullerene supramolecular systems

    Science.gov (United States)

    Li, Mao; Ishihara, Shinsuke; Ji, Qingmin; Akada, Misaho; Hill, Jonathan P.; Ariga, Katsuhiko

    2012-10-01

    Current nanotechnology based on top-down nanofabrication may encounter a variety of drawbacks in the near future so that development of alternative methods, including the so-called bottom-up approach, has attracted considerable attention. However, the bottom-up strategy, which often relies on spontaneous self-assembly, might be inefficient in the development of the requisite functional materials and systems. Therefore, assembly processes controlled by external stimuli might be a plausible strategy for the development of bottom-up nanotechnology. In this review, we demonstrate a paradigm shift from self-assembly to commanded assembly by describing several examples of assemblies of typical functional molecules, i.e. porphyrins and fullerenes. In the first section, we describe recent progress in the design and study of self-assembled and co-assembled supramolecular architectures of porphyrins and fullerenes. Then, we show examples of assembly induced by external stimuli. We emphasize the paradigm shift from self-assembly to commanded assembly by describing the recently developed electrochemical-coupling layer-by-layer (ECC-LbL) methodology.

  9. Paradigm shift from self-assembly to commanded assembly of functional materials: recent examples in porphyrin/fullerene supramolecular systems

    Directory of Open Access Journals (Sweden)

    Mao Li, Shinsuke Ishihara, Qingmin Ji, Misaho Akada, Jonathan P Hill and Katsuhiko Ariga

    2012-01-01

    Full Text Available Current nanotechnology based on top-down nanofabrication may encounter a variety of drawbacks in the near future so that development of alternative methods, including the so-called bottom-up approach, has attracted considerable attention. However, the bottom-up strategy, which often relies on spontaneous self-assembly, might be inefficient in the development of the requisite functional materials and systems. Therefore, assembly processes controlled by external stimuli might be a plausible strategy for the development of bottom-up nanotechnology. In this review, we demonstrate a paradigm shift from self-assembly to commanded assembly by describing several examples of assemblies of typical functional molecules, i.e. porphyrins and fullerenes. In the first section, we describe recent progress in the design and study of self-assembled and co-assembled supramolecular architectures of porphyrins and fullerenes. Then, we show examples of assembly induced by external stimuli. We emphasize the paradigm shift from self-assembly to commanded assembly by describing the recently developed electrochemical-coupling layer-by-layer (ECC-LbL methodology.

  10. Simulations of curved assemblies in soft matter and biological systems

    Science.gov (United States)

    Qiao, Cong

    regularly packed regions with local hexagonal order and vacancies. A similar lattice structure has been observed in experiments in which mutually attractive colloidal particles pack on the surface of a spherical droplet (G. Meng, J. Paulose, D. R. Nelson, and V. N. Manoharan, ''Elastic instability of a crystal growing on a curved surface'', Science 343, 634-637 (2014).), suggesting that the two systems experience a similar form of geometric frustration. We therefore study the adsorption and packing of spherical particles on a spherical template, as a function of the strength and range of interparticle attractions, as well as the radius of the spherical template. We observe that the adsorbed particles form two different classes of packing arrangements, one with icosahedrally ordered topological defects, and the other with highly disordered defects and vacancies. The latter regime is consistent with experiments on colloidal packing on spherical droplets and the immature HIV lattice. Our results suggest that the transition between these regimes is controlled by the range of the interparticle attractions. In the last chapter, we study a model for the assembly and budding of a capsid on a membrane, such as occurs during the exit of the immature HIV virus from a cell. We use a coarse-grained subunit model to represent the capsid proteins, and a fluid membrane model to represent the cell membrane. We find that the size and structure of the assembled capsid depends sensitively on the timescale of budding.

  11. A parameter estimation technique for stochastic self-assembly systems and its application to human papillomavirus self-assembly

    Science.gov (United States)

    Senthil Kumar, M.; Schwartz, Russell

    2010-12-01

    Virus capsid assembly has been a key model system for studies of complex self-assembly but it does pose some significant challenges for modeling studies. One important limitation is the difficulty of determining accurate rate parameters. The large size and rapid assembly of typical viruses make it infeasible to directly measure coat protein binding rates or deduce them from the relatively indirect experimental measures available. In this work, we develop a computational strategy to deduce coat-coat binding rate parameters for viral capsid assembly systems by fitting stochastic simulation trajectories to experimental measures of assembly progress. Our method combines quadratic response surface and quasi-gradient descent approximations to deal with the high computational cost of simulations, stochastic noise in simulation trajectories and limitations of the available experimental data. The approach is demonstrated on a light scattering trajectory for a human papillomavirus (HPV) in vitro assembly system, showing that the method can provide rate parameters that produce accurate curve fits and are in good concordance with prior analysis of the data. These fits provide an insight into potential assembly mechanisms of the in vitro system and give a basis for exploring how these mechanisms might vary between in vitro and in vivo assembly conditions.

  12. Strategies and perspectives of assembling multi-enzyme systems.

    Science.gov (United States)

    Wang, Shi-Zhen; Zhang, Yong-Hui; Ren, Hong; Wang, Ya-Li; Jiang, Wei; Fang, Bai-Shan

    2017-12-01

    Multi-enzyme complexes have the potential to achieve high catalytic efficiency for sequence reactions due to their advantages in eliminating product inhibition, facilitating intermediate transfer and in situ regenerating cofactors. Constructing functional multi-enzyme systems to mimic natural multi-enzyme complexes is of great interest for multi-enzymatic biosynthesis and cell-free synthetic biotransformation, but with many challenges. Currently, various assembly strategies have been developed based on the interaction of biomacromolecules such as DNA, peptide and scaffolding protein. On the other hand, chemical-induced assembly is based on the affinity of enzymes with small molecules including inhibitors, cofactors and metal ions has the advantage of simplicity, site-to-site oriented structure control and economy. This review summarizes advances and progresses employing these strategies. Furthermore, challenges and perspectives in designing multi-enzyme systems are highlighted.

  13. AutoAssemblyD: a graphical user interface system for several genome assemblers.

    Science.gov (United States)

    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.

  14. Data Mining of Macromolecular Structures.

    Science.gov (United States)

    van Beusekom, Bart; Perrakis, Anastassis; Joosten, Robbie P

    2016-01-01

    The use of macromolecular structures is widespread for a variety of applications, from teaching protein structure principles all the way to ligand optimization in drug development. Applying data mining techniques on these experimentally determined structures requires a highly uniform, standardized structural data source. The Protein Data Bank (PDB) has evolved over the years toward becoming the standard resource for macromolecular structures. However, the process selecting the data most suitable for specific applications is still very much based on personal preferences and understanding of the experimental techniques used to obtain these models. In this chapter, we will first explain the challenges with data standardization, annotation, and uniformity in the PDB entries determined by X-ray crystallography. We then discuss the specific effect that crystallographic data quality and model optimization methods have on structural models and how validation tools can be used to make informed choices. We also discuss specific advantages of using the PDB_REDO databank as a resource for structural data. Finally, we will provide guidelines on how to select the most suitable protein structure models for detailed analysis and how to select a set of structure models suitable for data mining.

  15. Localized reconstruction of subunits from electron cryomicroscopy images of macromolecular complexes.

    Science.gov (United States)

    Ilca, Serban L; Kotecha, Abhay; Sun, Xiaoyu; Poranen, Minna M; Stuart, David I; Huiskonen, Juha T

    2015-11-04

    Electron cryomicroscopy can yield near-atomic resolution structures of highly ordered macromolecular complexes. Often however some subunits bind in a flexible manner, have different symmetry from the rest of the complex, or are present in sub-stoichiometric amounts, limiting the attainable resolution. Here we report a general method for the localized three-dimensional reconstruction of such subunits. After determining the particle orientations, local areas corresponding to the subunits can be extracted and treated as single particles. We demonstrate the method using three examples including a flexible assembly and complexes harbouring subunits with either partial occupancy or mismatched symmetry. Most notably, the method allows accurate fitting of the monomeric RNA-dependent RNA polymerase bound at the threefold axis of symmetry inside a viral capsid, revealing for the first time its exact orientation and interactions with the capsid proteins. Localized reconstruction is expected to provide novel biological insights in a range of challenging biological systems.

  16. Rapid assembly of customized TALENs into multiple delivery systems.

    Directory of Open Access Journals (Sweden)

    Zhengxing Zhang

    Full Text Available Transcriptional activator-like effector nucleases (TALENs have become a powerful tool for genome editing. Here we present an efficient TALEN assembly approach in which TALENs are assembled by direct Golden Gate ligation into Gateway(® Entry vectors from a repeat variable di-residue (RVD plasmid array. We constructed TALEN pairs targeted to mouse Ddx3 subfamily genes, and demonstrated that our modified TALEN assembly approach efficiently generates accurate TALEN moieties that effectively introduce mutations into target genes. We generated "user friendly" TALEN Entry vectors containing TALEN expression cassettes with fluorescent reporter genes that can be efficiently transferred via Gateway (LR recombination into different delivery systems. We demonstrated that the TALEN Entry vectors can be easily transferred to an adenoviral delivery system to expand application to cells that are difficult to transfect. Since TALENs work in pairs, we also generated a TALEN Entry vector set that combines a TALEN pair into one PiggyBac transposon-based destination vector. The approach described here can also be modified for construction of TALE transcriptional activators, repressors or other functional domains.

  17. Versatility of cyclodextrins in self-assembly systems of amphiphiles.

    Science.gov (United States)

    Jiang, Lingxiang; Yan, Yun; Huang, Jianbin

    2011-11-14

    Recently, cyclodextrins (CDs) were found to play important yet complicated (or even apparently opposite sometimes) roles in self-assembly systems of amphiphiles or surfactants. Herein, we try to review and clarify the versatility of CDs in surfactant assembly systems by 1) classifying the roles played by CDs into two groups (modulator and building unit) and four subgroups (destructive and constructive modulators, amphiphilic and unamphiphilic building units), 2) comparing these subgroups, and 3) analyzing mechanisms. As a modulator, although CDs by themselves do not participate into the final surfactant aggregates, they can greatly affect the aggregates in two ways. In most cases CDs will destroy the aggregates by depleting surfactant molecules from the aggregates (destructive), or in certain cases CDs can promote the aggregates to grow by selectively removing the less-aggregatable surfactant molecules from the aggregates (constructive). As an amphiphilic building unit, CDs can be chemically (by chemical bonds) or physically (by host-guest interaction) attached to a hydrophobic moiety, and the resultant compounds act as classic amphiphiles. As an unamphiphilic building unit, CD/surfactant complexes or even CDs on their own can assemble into aggregates in an unconventional, unamphiphilic manner driven by CD-CD H-bonds. Moreover, special emphasis is put on two recently appeared aspects: the constructive modulator and unamphiphilic building unit. Copyright © 2011 Elsevier B.V. All rights reserved.

  18. Magnetic Measurement Systems for the LHC Dipole Assembly Companies

    CERN Document Server

    Billan, J; Giloteaux, D; Raimondo, A; Remondino, Vittorio; Reymond, H; Rijllart, A

    2004-01-01

    The LHC superconducting lattice dipole magnets are presently under construction in three European industries. Due to the stringent magnet performance required for the LHC, these magnets have to be built with high accuracy during all the steps of their assembly. In order to detect defects in the earliest industrial production phases and to ensure the quality of the magnetic field as specified by the CERN contracts, dedicated measurement benches have been built and installed in each assembly company to validate the magnetic field quality at two important production stages: the collared coils and the final cold mass. This paper describes the initial requirements and the implementation of the magnetic measurement systems. Details on the technical solutions, the present status and measurement results are presented.

  19. Structural analysis of nanoparticulate carriers for encapsulation of macromolecular drugs

    Czech Academy of Sciences Publication Activity Database

    Angelov, Borislav; Garamus, V.M.; Drechsler, M.; Angelova, A.

    2017-01-01

    Roč. 235, Jun (2017), s. 83-89 ISSN 0167-7322 R&D Projects: GA MŠk EF15_003/0000447; GA MŠk EF15_008/0000162 Grant - others:OP VVV - ELIBIO(XE) CZ.02.1.01/0.0/0.0/15_003/0000447; ELI Beamlines(XE) CZ.02.1.01/0.0/0.0/15_008/0000162 Institutional support: RVO:68378271 Keywords : self-assembled nanocarriers * liquid crystalline phase transitions * cationic lipids * macromolecular drugs Subject RIV: BO - Biophysics Impact factor: 3.648, year: 2016

  20. Block copolymer systems: from single chain to self-assembled nanostructures.

    Science.gov (United States)

    Giacomelli, Cristiano; Schmidt, Vanessa; Aissou, Karim; Borsali, Redouane

    2010-10-19

    Recent advances in the field of macromolecular engineering applied to the fabrication of nanostructured materials using block copolymer chains as elementary building blocks are described in this feature article. By highlighting some of our work in the area and accounting for the contribution of other groups, we discuss the relationship between the physical-chemical properties of copolymer chains and the characteristics of nano-objects originating from their self-assembly in solution and in bulk, with emphasis on convenient strategies that allow for the control of composition, functionality, and topology at different levels of sophistication. In the case of micellar nanoparticles in solution, in particular, we present approaches leading to morphology selection via macromolecular architectural design, the functionalization of external solvent-philic shells with biomolecules (polysaccharides and proteins), and the maximization of micelle loading capacity by the suitable choice of solvent-phobic polymer segments. The fabrication of nanomaterials mediated by thin block copolymer films is also discussed. In this case, we emphasize the development of novel polymer chain manipulation strategies that ultimately allow for the preparation of precisely positioned nanodomains with a reduced number of defects via block-selective chemical reactivity. The challenges facing the soft matter community, the urgent demand to convert huge public and private investments into consumer products, and future possible directions in the field are also considered herein.

  1. Force measuring valve assemblies, systems including such valve assemblies and related methods

    Science.gov (United States)

    DeWall, Kevin George [Pocatello, ID; Garcia, Humberto Enrique [Idaho Falls, ID; McKellar, Michael George [Idaho Falls, ID

    2012-04-17

    Methods of evaluating a fluid condition may include stroking a valve member and measuring a force acting on the valve member during the stroke. Methods of evaluating a fluid condition may include measuring a force acting on a valve member in the presence of fluid flow over a period of time and evaluating at least one of the frequency of changes in the measured force over the period of time and the magnitude of the changes in the measured force over the period of time to identify the presence of an anomaly in a fluid flow and, optionally, its estimated location. Methods of evaluating a valve condition may include directing a fluid flow through a valve while stroking a valve member, measuring a force acting on the valve member during the stroke, and comparing the measured force to a reference force. Valve assemblies and related systems are also disclosed.

  2. Managing lifelike behavior in a dynamic self-assembled system

    Science.gov (United States)

    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.

  3. Tritium Systems Test Assembly: design for major device fabrication review

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, J.L.; Sherman, R.H.

    1977-06-01

    This document has been prepared for the Major Device Fabrication Review for the Tritium Systems Test Assembly (TSTA). The TSTA is dedicated to the development, demonstration, and interfacing of technologies related to the deuterium-tritium fuel cycle for fusion reactor systems. The principal objectives for TSTA are: (a) demonstrate the fuel cycle for fusion reactor systems; (b) develop test and qualify equipment for tritium service in the fusion program; (c) develop and test environmental and personnel protective systems; (d) evaluate long-term reliability of components; (e) demonstrate long-term safe handling of tritium with no major releases or incidents; and (f) investigate and evaluate the response of the fuel cycle and environmental packages to normal, off-normal, and emergency situations. This document presents the current status of a conceptual design and cost estimate for TSTA. The total cost to design, construct, and operate TSTA through FY-1981 is estimated to be approximately $12.2 M.

  4. Building a cognitive map by assembling multiple path integration systems.

    Science.gov (United States)

    Wang, Ranxiao Frances

    2016-06-01

    Path integration and cognitive mapping are two of the most important mechanisms for navigation. Path integration is a primitive navigation system which computes a homing vector based on an animal's self-motion estimation, while cognitive map is an advanced spatial representation containing richer spatial information about the environment that is persistent and can be used to guide flexible navigation to multiple locations. Most theories of navigation conceptualize them as two distinctive, independent mechanisms, although the path integration system may provide useful information for the integration of cognitive maps. This paper demonstrates a fundamentally different scenario, where a cognitive map is constructed in three simple steps by assembling multiple path integrators and extending their basic features. The fact that a collection of path integration systems can be turned into a cognitive map suggests the possibility that cognitive maps may have evolved directly from the path integration system.

  5. EVALUATION OF A MULTIFUNCTIONAL VALVE ASSEMBLY IN A DIRECT EXPANSION REFRIGERATION SYSTEM REPORT

    Science.gov (United States)

    The report describes the performance, including energy consumption, of a refrigeration system incorporating a multifunctional valve (MXV assembly). The MXV assembly (consisting of additional liquid line, an XTC valve, and a larger thermostatic expansion valve) was installed on al...

  6. Interactive Systems for Designing Machine Elements and Assemblies

    Directory of Open Access Journals (Sweden)

    Kacalak Wojciech

    2015-09-01

    Full Text Available The article describes the development of fundamentals of machine elements and assemblies design processes automation using artificial intelligence, and descriptions of structural elements’ features in a natural language. In the proposed interactive automated design systems, computational artificial intelligence methods allow communication by speech and natural language, resulting in analyses of design engineer’s messages, analyses of constructions, encoding and assessments of constructions, CAD system controlling and visualizations. The system is equipped with several adaptive intelligent layers for human biometric identification, recognition of speech and handwriting, recognition of words, analyses and recognition of messages, enabling interpretation of messages, and assessments of human reactions. The article proposes a concept of intelligent processing for analysis of descriptions of machine elements’ structural features in a natural language. It also presents the developed methodology for similarity analysis between structural features of designed machine elements and corresponding antipatterns allowing normalization of parameters of the analysed structural solutions.

  7. The Gas Handling System Assembly for the NIFFTE TPC

    Science.gov (United States)

    Duke, Dana

    2010-11-01

    The Neutron Induced Fission Fragment Tracking Experiment (NIFFTE) uses a Time Projection Chamber (TPC) to obtain more accurate measurements of the fission cross sections of radioactive isotopes such as Pu-239, U-235, U-238, etc. Past cross-section measurements have used various detection methods such as the parallel plate ionization chamber, but by using a TPC, accuracy levels can be improved to sub 1% error. Analysis of TPC data will improve the current understanding of fission dynamics and the fission process. The NIFFTE TPC is located at the 90L beam line at LANSCE-WNR where targets are bombarded with fast neutrons to induce fission. The resulting fission fragments are tracked using gas ionization within the TPC. Gas handling system function and assembly is examined and justified. Major components of the system include solenoid valves, pressure transducers, and mass flow controllers. This gas handling system has the capability of remotely controlling the flow of multiple gas sources into the TPC.

  8. Self-Assembling Multifunctional Peptide Dimers for Gene Delivery Systems

    Directory of Open Access Journals (Sweden)

    Kitae Ryu

    2015-01-01

    Full Text Available Self-assembling multifunctional peptide was designed for gene delivery systems. The multifunctional peptide (MP consists of cellular penetrating peptide moiety (R8, matrix metalloproteinase-2 (MMP-2 specific sequence (GPLGV, pH-responsive moiety (H5, and hydrophobic moiety (palmitic acid (CR8GPLGVH5-Pal. MP was oxidized to form multifunctional peptide dimer (MPD by DMSO oxidation of thiols in terminal cysteine residues. MPD could condense pDNA successfully at a weight ratio of 5. MPD itself could self-assemble into submicron micelle particles via hydrophobic interaction, of which critical micelle concentration is about 0.01 mM. MPD showed concentration-dependent but low cytotoxicity in comparison with PEI25k. MPD polyplexes showed low transfection efficiency in HEK293 cells expressing low level of MMP-2 but high transfection efficiency in A549 and C2C12 cells expressing high level of MMP-2, meaning the enhanced transfection efficiency probably due to MMP-induced structural change of polyplexes. Bafilomycin A1-treated transfection results suggest that the transfection of MPD is mediated via endosomal escape by endosome buffering ability. These results show the potential of MPD for MMP-2 targeted gene delivery systems due to its multifunctionality.

  9. Assembly of Ultra-Dense Nanowire-Based Computing Systems

    National Research Council Canada - National Science Library

    Lieber, Charles M

    2006-01-01

    ..., with highly reliable defect- and fault-tolerant architecture. We have fabricated and assembled molecular-scale logic elements based on overlapping semiconducting nanowire arrays using novel wafer-scale assembly techniques...

  10. Alterations in Peptidoglycan Cross-Linking Suppress the Secretin Assembly Defect Caused by Mutation of GspA in the Type II Secretion System.

    Science.gov (United States)

    Vanderlinde, Elizabeth M; Strozen, Timothy G; Hernández, Sara B; Cava, Felipe; Howard, S Peter

    2017-04-15

    In Gram-negative bacteria, the peptidoglycan (PG) cell wall is a significant structural barrier for outer membrane protein assembly. In Aeromonas hydrophila, outer membrane multimerization of the type II secretion system (T2SS) secretin ExeD requires the function of the inner membrane assembly factor complex ExeAB. The putative mechanism of the complex involves the reorganization of PG and localization of ExeD, whereby ExeA functions by interacting with PG to form a site for secretin assembly and ExeB forms an interaction with ExeD. This mechanism led us to hypothesize that increasing the pore size of PG would circumvent the requirement for ExeA in the assembly of the ExeD secretin. Growth of A. hydrophila in 270 mM Gly reduced PG cross-links by approximately 30% and led to the suppression of secretin assembly defects in exeA strains and in those expressing ExeA mutants by enabling localization of the secretin in the outer membrane. We also established a heterologous ExeD assembly system in Escherichia coli and showed that ExeAB and ExeC are the only A. hydrophila proteins required for the assembly of the ExeD secretin in E. coli and that ExeAB-independent assembly of ExeD can occur upon overexpression of the d,d-carboxypeptidase PBP 5. These results support an assembly model in which, upon binding to PG, ExeA induces multimerization and pore formation in the sacculus, which enables ExeD monomers to interact with ExeB and assemble into a secretin that both is inserted in the outer membrane and crosses the PG layer to interact with the inner membrane platform of the T2SS.IMPORTANCE The PG layer imposes a strict structural impediment for the assembly of macromolecular structures that span the cell envelope and serve as virulence factors in Gram-negative species. This work revealed that by decreasing PG cross-linking by growth in Gly, the absolute requirement for the PG-binding activity of ExeA in the assembly of the ExeD secretin was alleviated in A. hydrophila In a

  11. 75 FR 4265 - Airworthiness Directives; Lifesavings Systems Corp., D-Lok Hook Assembly

    Science.gov (United States)

    2010-01-27

    ... Corp., D-Lok Hook Assembly AGENCY: Federal Aviation Administration (FAA), Department of Transportation... (AD) for the Lifesavings Systems Corp., D-Lok Hook assembly installed on certain rescue hoist assemblies. This AD results from a mandatory continuing airworthiness information (MCAI) AD issued by the...

  12. Improvability of assembly systems I: Problem formulation and performance evaluation

    Directory of Open Access Journals (Sweden)

    Chiang S.-Y.

    2000-01-01

    Full Text Available This work develops improvability theory for assembly systems. It consists of two parts.Part I includes the problem formulation and the analysis technique. Part II presents the so-called improvability indicators and a case study. Improvability theory addresses the questions of improving performance in production systems with unreliable machines. We consider both constrained and unconstrained improvability. In the constrained case, the problem consists of determining if there exists a re-distribution of resources (inventory and workforce, which leads to an increase in the system's production rate. In the unconstrained case, the problem consists of identifying a machine and a buffer, which impede the system performance in the strongest manner. The investigation of the improvability properties requires an expression for the system performance measures as functions of the machine and buffer parameters. This paper presents a method for evaluating these functions and illustrates their practical utility using a case study at an automotive components plant. Part II uses the method developed here to establish conditions of improvability and to describe additional results of the case study.

  13. Space Assembly of Large Structural System Architectures (SALSSA)

    Science.gov (United States)

    Dorsey, John T.; Watson, Judith J.

    2016-01-01

    Developing a robust capability for Space Assembly of Large Spacecraft Structural System Architectures (SALSSA) has the potential to drastically increase the capabilities and performance of future space missions and spacecraft while significantly reducing their cost. Currently, NASA architecture studies and space science decadal surveys identify new missions that would benefit from SALSSA capabilities, and the technologies that support SALSSA are interspersed throughout the fourteen NASA Technology Roadmaps. However, a major impediment to the strategic development of cross-cutting SALSSA technologies is the lack of an integrated and comprehensive compilation of the necessary information. This paper summarizes the results of a small study that used an integrated approach to formulate a SALSSA roadmap and associated plan for developing key SALSSA technologies.

  14. The development of a physics and constraint-based haptic virtual assembly system

    OpenAIRE

    GONZALEZ-BADILLO, Germanico; MEDELLIN-CASTILLO, Hugo; Lim, Theodore; Ritchie, James; GARBAYA, Samir

    2014-01-01

    Purpose – This paper aims to report the development and key features of a novel virtual reality system for assembly planning and evaluation called Haptic Assembly and Manufacturing System (HAMS). The system is intended to be used as a tool for training, design analysis and path planning. Design/methodology/approach – The proposed systemuses the physics-basedmodelling (PBM) to performassemblies in virtual nvironments.Moreover, dynamic assembly constrains have been considered to reduce the deg...

  15. Protective Coatings for Space System Components Fabricated Using Ionic Self Assembled Monolayer Processes

    National Research Council Canada - National Science Library

    Miler, Mike

    1997-01-01

    Self-assembled multilayer thin film fabrication methods offer unique opportunities to incorporate multiple functionalities into coatings for space system materials and structures as well as consumer products...

  16. Ultrasonic transducer chip assembly, ultrasound probe, ultrasonic imaging system and ultrasound assembly and probe manufacturing methods

    NARCIS (Netherlands)

    Weekamp, J.W.; Henneken, V.A.; Groenland, A.W.; Louwerse, M.C.

    2015-01-01

    Disclosed is an ultrasonic transducer assembly comprising an ultrasonic transducer chip (100) having a main surface comprising a plurality of ultrasound transducer elements (112) and a plurality of first contacts (120) for connecting to said ultrasound transducer elements; a contact chip (400)

  17. A modular assembly method of a feed and thruster system for Cubesats

    NARCIS (Netherlands)

    Louwerse, M.C.; Jansen, Henricus V.; Elwenspoek, Michael Curt

    2010-01-01

    A modular assembly method for devices based on micro system technology is presented. The assembly method forms the foundation for a miniaturized feed and thruster system as part of a micro propulsion unit working as a simple blow-down system of a rocket engine. The micro rocket is designed to be

  18. A System for the Automatic Assembly of Test Questions Using a No-SQL Database

    Science.gov (United States)

    Shin, Sanggyu; Hashimoto, Hiroshi

    2014-01-01

    We describe a system that automatically assembles test questions from a set of examples. Our system can create test questions appropriate for each user's level at low cost. In particular, when a user review their lesson, our system provides new test questions which are assembled based on their previous test results and past mistakes, rather than a…

  19. Programming biological operating systems: genome design, assembly and activation.

    Science.gov (United States)

    Gibson, Daniel G

    2014-05-01

    The DNA technologies developed over the past 20 years for reading and writing the genetic code converged when the first synthetic cell was created 4 years ago. An outcome of this work has been an extraordinary set of tools for synthesizing, assembling, engineering and transplanting whole bacterial genomes. Technical progress, options and applications for bacterial genome design, assembly and activation are discussed.

  20. Macromolecular Crystal Growth by Means of Microfluidics

    Science.gov (United States)

    vanderWoerd, Mark; Ferree, Darren; Spearing, Scott; Monaco, Lisa; Molho, Josh; Spaid, Michael; Brasseur, Mike; Curreri, Peter A. (Technical Monitor)

    2002-01-01

    We have performed a feasibility study in which we show that chip-based, microfluidic (LabChip(TM)) technology is suitable for protein crystal growth. This technology allows for accurate and reliable dispensing and mixing of very small volumes while minimizing bubble formation in the crystallization mixture. The amount of (protein) solution remaining after completion of an experiment is minimal, which makes this technique efficient and attractive for use with proteins, which are difficult or expensive to obtain. The nature of LabChip(TM) technology renders it highly amenable to automation. Protein crystals obtained in our initial feasibility studies were of excellent quality as determined by X-ray diffraction. Subsequent to the feasibility study, we designed and produced the first LabChip(TM) device specifically for protein crystallization in batch mode. It can reliably dispense and mix from a range of solution constituents into two independent growth wells. We are currently testing this design to prove its efficacy for protein crystallization optimization experiments. In the near future we will expand our design to incorporate up to 10 growth wells per LabChip(TM) device. Upon completion, additional crystallization techniques such as vapor diffusion and liquid-liquid diffusion will be accommodated. Macromolecular crystallization using microfluidic technology is envisioned as a fully automated system, which will use the 'tele-science' concept of remote operation and will be developed into a research facility for the International Space Station as well as on the ground.

  1. Macromolecular gradients on material surfaces: Formation and applications

    Science.gov (United States)

    Genzer, Jan

    2004-03-01

    In our presentation we will outline several novel multivariant methodologies that facilitate the formation of macromolecular assemblies grafted on flat solid substrates. We will introduce a method for generating polymer assemblies with a gradually increasing position-dependent polymer grafting density. We will document that such a set up can be utilized to probe the "mushroom"-to-"bush" conformational transition in both neutral polymer brushes as well as weak surface-anchored polyelectrolytes. We will also describe a technique leading to the generation of polymer assemblies with a gradually changing molecular weight of the grafted polymers. A simple extension of the latter approach will facilitate the generation of surface grafted block copolymers with gradually varying compositions. We will document that by combining the individual gradients, i.e. the grafting density and molecular weight, one can produce complex substrates in which two material properties change independently in two orthogonal directions. Finally, we will demonstrate that multivariant polymer brush assemblies represent universal soft material scaffolds that can be utilized in adjusting the spatial distribution of non-polymeric objects, such as nanoparticles and proteins.

  2. Rail-Guided Multi-Robot System for 3D Cellular Hydrogel Assembly with Coordinated Nanomanipulation

    Directory of Open Access Journals (Sweden)

    Huaping Wang

    2014-08-01

    Full Text Available The 3D assembly of micro-/nano-building blocks with multi-nanomanipulator coordinated manipulation is one of the central elements of nanomanipulation. A novel rail-guided nanomanipulation system was proposed for the assembly of a cellular vascular-like hydrogel microchannel. The system was equipped with three nanomanipulators and was restricted on the rail in order to realize the arbitrary change of the end-effectors during the assembly. It was set up with hybrid motors to achieve both a large operating space and a 30 nm positional resolution. The 2D components such as the assembly units were fabricated through the encapsulation of cells in the hydrogel. The coordinated manipulation strategies among the multi-nanomanipulators were designed with vision feedback and were demonstrated through the bottom-up assembly of the vascular-like microtube. As a result, the multi-layered microchannel was assembled through the cooperation of the nanomanipulation system.

  3. Characterization of Fissile Assemblies Using Low-Efficiency Detection Systems

    Science.gov (United States)

    Chapline, George F.; Verbeke, Jerome M.

    2017-07-01

    We have investigated the possibility that the amount, chemical form, multiplication, and shape of the fissile material in an assembly can be passively assayed using scintillator detection systems by only measuring the fast neutron pulse height distribution and distribution of time intervals At between fast neutrons. We have previously demonstrated that the alpha ratio can be obtained from the observed pulse height distribution for fast neutrons. In this paper, we report that when the distribution of time intervals is plotted as a function of logΔt, the position of the correlated neutron peak is nearly independent of detector efficiency and determines the internal relaxation rate for fast neutrons. If this information is combined with knowledge of the alpha ratio, then the position of the minimum between the correlated and uncorrelated peaks can be used to rapidly estimate the mass, multiplication, and shape of fissile material. This method does not require a priori knowledge of either the efficiency for neutron detection or the alpha ratio. Although our method neglects three-neutron correlations, we have used previously obtained experimental data for metallic and oxide forms of Pu to demonstrate that our method yields good estimates for multiplications as large as 2, and that the only constraint on detector efficiency/observation time is that a peak in the interval time distribution due to correlated neutrons is visible.

  4. Single-particle cryo-electron microscopy of macromolecular complexes.

    Science.gov (United States)

    Skiniotis, Georgios; Southworth, Daniel R

    2016-02-01

    Recent technological breakthroughs in image acquisition have enabled single-particle cryo-electron microscopy (cryo-EM) to achieve near-atomic resolution structural information for biological complexes. The improvements in image quality coupled with powerful computational methods for sorting distinct particle populations now also allow the determination of compositional and conformational ensembles, thereby providing key insights into macromolecular function. However, the inherent instability and dynamic nature of biological assemblies remain a tremendous challenge that often requires tailored approaches for successful implementation of the methodology. Here, we briefly describe the fundamentals of single-particle cryo-EM with an emphasis on covering the breadth of techniques and approaches, including low- and high-resolution methods, aiming to illustrate specific steps that are crucial for obtaining structural information by this method. © The Author 2015. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  5. Cryo electron microscopy to determine the structure of macromolecular complexes.

    Science.gov (United States)

    Carroni, Marta; Saibil, Helen R

    2016-02-15

    Cryo-electron microscopy (cryo-EM) is a structural molecular and cellular biology technique that has experienced major advances in recent years. Technological developments in image recording as well as in processing software make it possible to obtain three-dimensional reconstructions of macromolecular assemblies at near-atomic resolution that were formerly obtained only by X-ray crystallography or NMR spectroscopy. In parallel, cryo-electron tomography has also benefitted from these technological advances, so that visualization of irregular complexes, organelles or whole cells with their molecular machines in situ has reached subnanometre resolution. Cryo-EM can therefore address a broad range of biological questions. The aim of this review is to provide a brief overview of the principles and current state of the cryo-EM field. Copyright © 2016. Published by Elsevier Inc.

  6. Mass distributions of a macromolecular assembly based on ...

    Indian Academy of Sciences (India)

    Unknown

    quaternary structures are virtually identical at a resolution of ~ 2 nm (Cejka ... low resolution crystallographic structure of Lumbricus Er ...... 1433 217–228. Vinogradov S N and Kolodziej P 1988 The molecular mass of the extracellular hemoglobin of Lumbricus terrestris deter- mined by electron microscopy; Comp. Biochem.

  7. Ceruloplasmin: Macromolecular Assemblies with Iron-Containing Acute Phase Proteins

    Science.gov (United States)

    Samygina, Valeriya R.; Sokolov, Alexey V.; Bourenkov, Gleb; Petoukhov, Maxim V.; Pulina, Maria O.; Zakharova, Elena T.; Vasilyev, Vadim B.; Bartunik, Hans; Svergun, Dmitri I.

    2013-01-01

    Copper-containing ferroxidase ceruloplasmin (Cp) forms binary and ternary complexes with cationic proteins lactoferrin (Lf) and myeloperoxidase (Mpo) during inflammation. We present an X-ray crystal structure of a 2Cp-Mpo complex at 4.7 Å resolution. This structure allows one to identify major protein–protein interaction areas and provides an explanation for a competitive inhibition of Mpo by Cp and for the activation of p-phenylenediamine oxidation by Mpo. Small angle X-ray scattering was employed to construct low-resolution models of the Cp-Lf complex and, for the first time, of the ternary 2Cp-2Lf-Mpo complex in solution. The SAXS-based model of Cp-Lf supports the predicted 1∶1 stoichiometry of the complex and demonstrates that both lobes of Lf contact domains 1 and 6 of Cp. The 2Cp-2Lf-Mpo SAXS model reveals the absence of interaction between Mpo and Lf in the ternary complex, so Cp can serve as a mediator of protein interactions in complex architecture. Mpo protects antioxidant properties of Cp by isolating its sensitive loop from proteases. The latter is important for incorporation of Fe3+ into Lf, which activates ferroxidase activity of Cp and precludes oxidation of Cp substrates. Our models provide the structural basis for possible regulatory role of these complexes in preventing iron-induced oxidative damage. PMID:23843990

  8. Macromolecular diffusion in self-assembling biodegradable thermosensitive hydrogels

    NARCIS (Netherlands)

    Vermonden, T.; Jena, S.S.; Barriet, D.; Censi, R.; Gucht, van der J.; Hennink, W.E.; Siegel, R.A.

    2010-01-01

    Hydrogel formation triggered by a change in temperature is an attractive mechanism for in situ gelling biomaterials for pharmaceutical applications such as the delivery of therapeutic proteins. In this study, hydrogels were prepared from ABA triblock polymers having thermosensitive

  9. Complex macromolecular architectures: synthesis, characterization, and self-assembly

    National Research Council Canada - National Science Library

    Hadjichristidis, Nikos

    2011-01-01

    ...)s and gluco-polymers, star-branched and dendrimer-like hyperbranched polymers, cyclic polymers, dendrigraft polymers, rod-coil and helix-coil block copolymers are introduced chapter by chapter in the book...

  10. Conceptual design of novel IP-conveyor-belt Weissenberg-mode data-collection system with multi-readers for macromolecular crystallography. A comparison between Galaxy and Super Galaxy.

    Science.gov (United States)

    Sakabe, N; Sakabe, K; Sasaki, K

    2004-01-01

    Galaxy is a Weissenberg-type high-speed high-resolution and highly accurate fully automatic data-collection system using two cylindrical IP-cassettes each with a radius of 400 mm and a width of 450 mm. It was originally developed for static three-dimensional analysis using X-ray diffraction and was installed on bending-magnet beamline BL6C at the Photon Factory. It was found, however, that Galaxy was also very useful for time-resolved protein crystallography on a time scale of minutes. This has prompted us to design a new IP-conveyor-belt Weissenberg-mode data-collection system called Super Galaxy for time-resolved crystallography with improved time and crystallographic resolution over that achievable with Galaxy. Super Galaxy was designed with a half-cylinder-shaped cassette with a radius of 420 mm and a width of 690 mm. Using 1.0 A incident X-rays, these dimensions correspond to a maximum resolutions of 0.71 A in the vertical direction and 1.58 A in the horizontal. Upper and lower screens can be used to set the frame size of the recorded image. This function is useful not only to reduce the frame exchange time but also to save disk space on the data server. The use of an IP-conveyor-belt and many IP-readers make Super Galaxy well suited for time-resolved, monochromatic X-ray crystallography at a very intense third-generation SR beamline. Here, Galaxy and a conceptual design for Super Galaxy are described, and their suitability for use as data-collection systems for macromolecular time-resolved monochromatic X-ray crystallography are compared.

  11. Peanut lectin crystallography and macromolecular structural studies ...

    Indian Academy of Sciences (India)

    2007-08-06

    Aug 6, 2007 ... Home; Journals; Journal of Biosciences; Volume 32; Issue 6. Peanut lectin crystallography and macromolecular structural studies in India. M Vijayan. Perspectives Volume 32 Issue 6 September 2007 pp 1059-1066. Fulltext. Click here to view fulltext PDF. Permanent link:

  12. Macromolecular peroxo complexes of Vanadium (V) and ...

    Indian Academy of Sciences (India)

    Macromolecular metal complexes; peroxovanadates; peroxomolybdates; enzyme inhibitors; polymer-supported metal catalysts; bromoperoxidases. ... activity with phosphohydrolase enzyme vis-à-vis free peroxovanadium (pV) or peroxomolybdenum (pMo) complexes, and their activity in biomimetic oxidative bromination ...

  13. Automated data collection for macromolecular crystallography.

    Science.gov (United States)

    Winter, Graeme; McAuley, Katherine E

    2011-09-01

    An overview, together with some practical advice, is presented of the current status of the automation of macromolecular crystallography (MX) data collection, with a focus on MX beamlines at Diamond Light Source, UK. Copyright © 2011 Elsevier Inc. All rights reserved.

  14. Improvability of assembly systems II: Improvability indicators and case study

    Directory of Open Access Journals (Sweden)

    S.-Y. Chiang

    2000-01-01

    Full Text Available Based on the performance analysis technique developed in Part I, this paper presents improvability indicators for assembly lines with unreliable machines. In particular, it shows that assembly lines are unimprovable with respect to workforce re-distribution if each buffer is, on the average, close to being half full. These lines are unimprovable with respect to buffer capacity re-distribution if each machine is starved and blocked with almost equal frequency. In addition, the paper provides indicators for identification of bottleneck machines and bottleneck buffers. Finally, the paper reports on an application of these improvability indicators in a case study at an automotive components plant.

  15. [Model systems based on the lipid-porphyrin assemblies and lipoproteins in biochemical studies].

    Science.gov (United States)

    Pikuz, S S; Sebiakin, Iu L

    1996-01-01

    Reviewed are the modern state and prospects of using lipid-porphyrin assemblies and lipoporphyrins to study fine functional mechanisms of complex biological systems and to solve applied problems in biochemistry and medicine. Data on the interaction of porphyrin derivatives with natural and artificial membranes are summarized. Models for electron transfer and oxygen transport via lipid-porphyrin assemblies are discussed.

  16. Systems and assemblies for transferring high power laser energy through a rotating junction

    Science.gov (United States)

    Norton, Ryan J.; McKay, Ryan P.; Fraze, Jason D.; Rinzler, Charles C.; Grubb, Daryl L.; Faircloth, Brian O.; Zediker, Mark S.

    2016-01-26

    There are provided high power laser devices and systems for transmitting a high power laser beam across a rotating assembly, including optical slip rings and optical rotational coupling assemblies. These devices can transmit the laser beam through the rotation zone in free space or within a fiber.

  17. Quantitative computational models of molecular self-assembly in systems biology.

    Science.gov (United States)

    Thomas, Marcus; Schwartz, Russell

    2017-05-23

    Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally.

  18. Quantitative computational models of molecular self-assembly in systems biology

    Science.gov (United States)

    Thomas, Marcus; Schwartz, Russell

    2017-06-01

    Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally.

  19. Module and System Design in Flexible Automated Assembly

    NARCIS (Netherlands)

    Vos, J.A.W.M.

    2001-01-01

    There is an ongoing trend of increasing variety of products and a decreasing time-to-market of new products. These trends require flexibility in the production and extensive control of the production processes. This is especially true for the assembly: the joining of parts to form a product. These

  20. Industrial-scale spray layer-by-layer assembly for production of biomimetic photonic systems.

    Science.gov (United States)

    Krogman, K C; Cohen, R E; Hammond, P T; Rubner, M F; Wang, B N

    2013-12-01

    Layer-by-layer assembly is a powerful and flexible thin film process that has successfully reproduced biomimetic photonic systems such as structural colour. While most of the seminal work has been carried out using slow and ultimately unscalable immersion assembly, recent developments using spray layer-by-layer assembly provide a platform for addressing challenges to scale-up and manufacturability. A series of manufacturing systems has been developed to increase production throughput by orders of magnitude, making commercialized structural colour possible. Inspired by biomimetic photonic structures we developed and demonstrated a heat management system that relies on constructive reflection of near infrared radiation to bring about dramatic reductions in heat content.

  1. PDBe: improved accessibility of macromolecular structure data from PDB and EMDB.

    Science.gov (United States)

    Velankar, Sameer; van Ginkel, Glen; Alhroub, Younes; Battle, Gary M; Berrisford, John M; Conroy, Matthew J; Dana, Jose M; Gore, Swanand P; Gutmanas, Aleksandras; Haslam, Pauline; Hendrickx, Pieter M S; Lagerstedt, Ingvar; Mir, Saqib; Fernandez Montecelo, Manuel A; Mukhopadhyay, Abhik; Oldfield, Thomas J; Patwardhan, Ardan; Sanz-García, Eduardo; Sen, Sanchayita; Slowley, Robert A; Wainwright, Michael E; Deshpande, Mandar S; Iudin, Andrii; Sahni, Gaurav; Salavert Torres, Jose; Hirshberg, Miriam; Mak, Lora; Nadzirin, Nurul; Armstrong, David R; Clark, Alice R; Smart, Oliver S; Korir, Paul K; Kleywegt, Gerard J

    2016-01-04

    The Protein Data Bank in Europe (http://pdbe.org) accepts and annotates depositions of macromolecular structure data in the PDB and EMDB archives and enriches, integrates and disseminates structural information in a variety of ways. The PDBe website has been redesigned based on an analysis of user requirements, and now offers intuitive access to improved and value-added macromolecular structure information. Unique value-added information includes lists of reviews and research articles that cite or mention PDB entries as well as access to figures and legends from full-text open-access publications that describe PDB entries. A powerful new query system not only shows all the PDB entries that match a given query, but also shows the 'best structures' for a given macromolecule, ligand complex or sequence family using data-quality information from the wwPDB validation reports. A PDBe RESTful API has been developed to provide unified access to macromolecular structure data available in the PDB and EMDB archives as well as value-added annotations, e.g. regarding structure quality and up-to-date cross-reference information from the SIFTS resource. Taken together, these new developments facilitate unified access to macromolecular structure data in an intuitive way for non-expert users and support expert users in analysing macromolecular structure data. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  2. Digital Material Assembly by Passive Means and Modular Isotropic Lattice Extruder System

    Science.gov (United States)

    Carney, Matthew Eli (Inventor); Jenett, Benjamin (Inventor); Gershenfeld, Neil (Inventor)

    2017-01-01

    A set of machines and related systems build structures by the additive assembly of discrete parts. These digital material assemblies constrain the constituent parts to a discrete set of possible positions and orientations. In doing so, the structures exhibit many of the properties inherent in digital communication such as error correction, fault tolerance and allow the assembly of precise structures with comparatively imprecise tools. Assembly of discrete cellular lattices by a Modular Isotropic Lattice Extruder System (MILES) is implemented by pulling strings of lattice elements through a forming die that enforces geometry constraints that lock the elements into a rigid structure that can then be pushed against and extruded out of the die as an assembled, loadbearing structure.

  3. Framework for Defining and Assessing Benefits of a Modular Assembly Design Approach for Exploration Systems

    Science.gov (United States)

    Dorsey, John T.; Collins, Timothy J.; Moe, Rud V.; Doggett,. William R.

    2006-01-01

    A comprehensive modular assembly system model has been proposed that extends the art from modular hardware, to include in-space assembly, servicing and repair and it s critical components of infrastructure, agents and assembly operations. Benefits of modular assembly have been identified and a set of metrics defined that extends the art beyond the traditional measures of performance, with emphasis on criteria that allow life-cycle mission costs to be used as a figure of merit (and include all substantive terms that have an impact on the evaluation). The modular assembly approach was used as a basis for developing a Solar Electric Transfer Vehicle (SETV) concept and three modular assembly scenarios were developed. The modular assembly approach also allows the SETV to be entered into service much earlier than competing conventional configurations and results in a great deal of versatility in accommodating different launch vehicle payload capabilities, allowing for modules to be pre-assembled before launch or assembled on orbit, without changing the space vehicle design.

  4. The Phenix software for automated determination of macromolecular structures.

    Science.gov (United States)

    Adams, Paul D; Afonine, Pavel V; Bunkóczi, Gábor; Chen, Vincent B; Echols, Nathaniel; Headd, Jeffrey J; Hung, Li-Wei; Jain, Swati; Kapral, Gary J; Grosse Kunstleve, Ralf W; McCoy, Airlie J; Moriarty, Nigel W; Oeffner, Robert D; Read, Randy J; Richardson, David C; Richardson, Jane S; Terwilliger, Thomas C; Zwart, Peter H

    2011-09-01

    X-ray crystallography is a critical tool in the study of biological systems. It is able to provide information that has been a prerequisite to understanding the fundamentals of life. It is also a method that is central to the development of new therapeutics for human disease. Significant time and effort are required to determine and optimize many macromolecular structures because of the need for manual interpretation of complex numerical data, often using many different software packages, and the repeated use of interactive three-dimensional graphics. The Phenix software package has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on automation. This has required the development of new algorithms that minimize or eliminate subjective input in favor of built-in expert-systems knowledge, the automation of procedures that are traditionally performed by hand, and the development of a computational framework that allows a tight integration between the algorithms. The application of automated methods is particularly appropriate in the field of structural proteomics, where high throughput is desired. Features in Phenix for the automation of experimental phasing with subsequent model building, molecular replacement, structure refinement and validation are described and examples given of running Phenix from both the command line and graphical user interface. Copyright © 2011 Elsevier Inc. All rights reserved.

  5. Control assembly for controlling a fuel cell system during shutdown and restart

    Science.gov (United States)

    Venkataraman, Ramki; Berntsen, George; Carlson, Glenn L.; Farooque, Mohammad; Beachy, Dan; Peterhans, Stefan; Bischoff, Manfred

    2010-06-15

    A fuel cell system and method in which the fuel cell system receives and an input oxidant gas and an input fuel gas, and in which a fuel processing assembly is provided and is adapted to at least humidify the input fuel gas which is to be supplied to the anode of the fuel cell of the system whose cathode receives the oxidant input gas via an anode oxidizing assembly which is adapted to couple the output of the anode of the fuel cell to the inlet of the cathode of the fuel cell during normal operation, shutdown and restart of the fuel cell system, and in which a control assembly is further provided and is adapted to respond to shutdown of the fuel cell system during which input fuel gas and input oxidant gas cease to be received by the fuel cell system, the control assembly being further adapted to, when the fuel cell system is shut down: control the fuel cell system so as to enable a purging gas to be able to flow through the fuel processing assembly to remove humidified fuel gas from the processing assembly and to enable a purging gas to be able to flow through the anode of the fuel cell.

  6. In situ macromolecular crystallography using microbeams.

    Science.gov (United States)

    Axford, Danny; Owen, Robin L; Aishima, Jun; Foadi, James; Morgan, Ann W; Robinson, James I; Nettleship, Joanne E; Owens, Raymond J; Moraes, Isabel; Fry, Elizabeth E; Grimes, Jonathan M; Harlos, Karl; Kotecha, Abhay; Ren, Jingshan; Sutton, Geoff; Walter, Thomas S; Stuart, David I; Evans, Gwyndaf

    2012-05-01

    Despite significant progress in high-throughput methods in macromolecular crystallography, the production of diffraction-quality crystals remains a major bottleneck. By recording diffraction in situ from crystals in their crystallization plates at room temperature, a number of problems associated with crystal handling and cryoprotection can be side-stepped. Using a dedicated goniometer installed on the microfocus macromolecular crystallography beamline I24 at Diamond Light Source, crystals have been studied in situ with an intense and flexible microfocus beam, allowing weakly diffracting samples to be assessed without a manual crystal-handling step but with good signal to noise, despite the background scatter from the plate. A number of case studies are reported: the structure solution of bovine enterovirus 2, crystallization screening of membrane proteins and complexes, and structure solution from crystallization hits produced via a high-throughput pipeline. These demonstrate the potential for in situ data collection and structure solution with microbeams. © 2012 International Union of Crystallography

  7. Ceramic Composite Mechanical Fastener System for High-Temperature Structural Assemblies Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Under Phase I, the feasibility of a novel thermal stress-free ceramic composite mechanical fastener system suitable for assembly of high-temperature composite...

  8. Docking System Design and Self-Assembly Control of Distributed Swarm Flying Robots

    Directory of Open Access Journals (Sweden)

    Hongxing Wei

    2012-11-01

    Full Text Available This paper presents a novel docking system design and the distributed self-assembly control strategy for a Distributed Swarm Flying Robot (DSFR. The DSFR is a swarm robot comprising many identical robot modules that are able to move on the ground, dock with each other and fly coordinately once self-assembled into a robotic structure. A generalized adjacency matrix method is proposed to describe the configurations of robotic structures. Based on the docking system and the adjacency matrix, experiments are performed to demonstrate and verify the self-assembly control strategy.

  9. Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage.

    Directory of Open Access Journals (Sweden)

    Ines Thiele

    Full Text Available Biological systems are inherently hierarchal and multiscale in time and space. A major challenge of systems biology is to describe biological systems as a computational model, which can be used to derive novel hypothesis and drive experiments leading to new knowledge. The constraint-based reconstruction and analysis approach has been successfully applied to metabolism and to the macromolecular synthesis machinery assembly. Here, we present the first integrated stoichiometric multiscale model of metabolism and macromolecular synthesis for Escherichia coli K12 MG1655, which describes the sequence-specific synthesis and function of almost 2000 gene products at molecular detail. We added linear constraints, which couple enzyme synthesis and catalysis reactions. Comparison with experimental data showed improvement of growth phenotype prediction with the multiscale model over E. coli's metabolic model alone. Many of the genes covered by this integrated model are well conserved across enterobacters and other, less related bacteria. We addressed the question of whether the bias in synonymous codon usage could affect the growth phenotype and environmental niches that an organism can occupy. We created two classes of in silico strains, one with more biased codon usage and one with more equilibrated codon usage than the wildtype. The reduced growth phenotype in biased strains was caused by tRNA supply shortage, indicating that expansion of tRNA gene content or tRNA codon recognition allow E. coli to respond to changes in codon usage bias. Our analysis suggests that in order to maximize growth and to adapt to new environmental niches, codon usage and tRNA content must co-evolve. These results provide further evidence for the mutation-selection-drift balance theory of codon usage bias. This integrated multiscale reconstruction successfully demonstrates that the constraint-based modeling approach is well suited to whole-cell modeling endeavors.

  10. Macromolecular scaffolding: the relationship between nanoscale architecture and function in multichromophoric arrays for organic electronics.

    Science.gov (United States)

    Palermo, Vincenzo; Schwartz, Erik; Finlayson, Chris E; Liscio, Andrea; Otten, Matthijs B J; Trapani, Sara; Müllen, Klaus; Beljonne, David; Friend, Richard H; Nolte, Roeland J M; Rowan, Alan E; Samorì, Paolo

    2010-02-23

    The optimization of the electronic properties of molecular materials based on optically or electrically active organic building blocks requires a fine-tuning of their self-assembly properties at surfaces. Such a fine-tuning can be obtained on a scale up to 10 nm by mastering principles of supramolecular chemistry, i.e., by using suitably designed molecules interacting via pre-programmed noncovalent forces. The control and fine-tuning on a greater length scale is more difficult and challenging. This Research News highlights recent results we obtained on a new class of macromolecules that possess a very rigid backbone and side chains that point away from this backbone. Each side chain contains an organic semiconducting moiety, whose position and electronic interaction with neighboring moieties are dictated by the central macromolecular scaffold. A combined experimental and theoretical approach has made it possible to unravel the physical and chemical properties of this system across multiple length scales. The (opto)electronic properties of the new functional architectures have been explored by constructing prototypes of field-effect transistors and solar cells, thereby providing direct insight into the relationship between architecture and function.

  11. Sag Compensation System for Assembly of MDT-Chambers for the ATLAS Experiment

    CERN Document Server

    Barashkou, A V; Chepurnov, V F; Evtoukhovitch, P G; Glonti, G L; Gongadze, A L; Ilyushenka, Y N; Kotov, S A; Kruchonak, V G; Tskhadadze, E G

    2005-01-01

    The description of a system of the devices created for compensation of the gravitational deflection of the drift chamber during its assembly is presented. By means of this system during stage-by-stage gluing of layers of tube drift detectors to the chamber the transversal deflection considerably decreases and by that high accuracy of mutual position of separate tubes is provided. The devices were applied at assembly of 74 MDT-chambers of the ATLAS experiment. Design values of deformation of the chambers as well as the results of measurement of transversal deflections obtained during the assembly with the use of the system of sag compensation are given. Testing of chambers on the X-ray tomograph at CERN has shown that the accuracy of the positions of separate signal wires inside the assembled chambers is within the limits of the required 20 $\\mu$m.

  12. Effect of macromolecular crowding on the rate of diffusion-limited ...

    Indian Academy of Sciences (India)

    on percolation and diffusion in disordered systems to study the effect of macromolecular crowding on the enzymatic reaction rates. The model qualitatively explains some of the experimental observations. Keywords. Enzyme kinetics; Monte Carlo; percolation; random walk; obstacle. PACS Nos 02.50.Ey; 05.40.Jc; 05.60.Cd.

  13. A vibrating membrane bioreactor (VMBR): Macromolecular transmission-influence of extracellular polymeric substances

    DEFF Research Database (Denmark)

    Beier, Søren; Jonsson, Gunnar Eigil

    2009-01-01

    The vibrating membrane bioreactor (VMBR) system facilitates the possibility of conducting a separation of macromolecules (BSA) from larger biological components (yeast cells) with a relatively high and stable macromolecular transmission at sub-critical flux. This is not possible to achieve...

  14. Effect of macromolecular crowding on the rate of diffusion-limited ...

    Indian Academy of Sciences (India)

    The enzymatic reaction rate has been shown to be affected by the presence of such macromolecules. A simple numerical model is proposed here based on percolation and diffusion in disordered systems to study the effect of macromolecular crowding on the enzymatic reaction rates. The model qualitatively explains some ...

  15. Autonomous intelligent assembly systems LDRD 105746 final report.

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Robert J.

    2013-04-01

    This report documents a three-year to develop technology that enables mobile robots to perform autonomous assembly tasks in unstructured outdoor environments. This is a multi-tier problem that requires an integration of a large number of different software technologies including: command and control, estimation and localization, distributed communications, object recognition, pose estimation, real-time scanning, and scene interpretation. Although ultimately unsuccessful in achieving a target brick stacking task autonomously, numerous important component technologies were nevertheless developed. Such technologies include: a patent-pending polygon snake algorithm for robust feature tracking, a color grid algorithm for uniquely identification and calibration, a command and control framework for abstracting robot commands, a scanning capability that utilizes a compact robot portable scanner, and more. This report describes this project and these developed technologies.

  16. Dendrimer-like assemblies based on organoclays as multi-host system for sustained drug delivery.

    Science.gov (United States)

    Li, Wei; Sun, Lili; Pan, Lijun; Lan, Zuopin; Jiang, Tao; Yang, Xiaolan; Luo, Jianchun; Li, Ronghua; Tan, Liqing; Zhang, Shurong; Yu, Mingan

    2014-11-01

    Chemical modification of nanoclay will ensure further progress on these materials. In this work, we show that montmorillonite (MTM) nanosheets can be modified with β-cyclodextrin (CD) via a nucleophilic substitution reaction between mono-6-(p-toluenesulfonyl)-6-deoxy-β-CD and an amino group of 3-aminopropyltriethoxysilane (APTES)-functionalized MTM. The resulting MTM-APTES-CD can be further self-assembled into dendrimer-like assemblies, exhibit a well-dispersed property even in Dulbecco's phosphate-buffered saline and do not aggregate for a period of at least 20days. The structure, morphology and assembly mechanism are systematically studied by (29)Si MAS NMR, FT-IR, (1)H NMR, SEM, FE-TEM, DLS and AFM, and the change in assemblies during the drug release is monitored using FE-TEM images. MTT assays indicate that the assemblies only have low cytotoxicity, while CLSM and TEM observations reveal that the assemblies can easily penetrate cultured human endothelial cells. When clopidogrel is used as a guest molecule, the assemblies show not only much higher loading capacities compared to MTM and other containing β-CD assemblies or nanoparticles, but also a sustained release of clopidogrel up to 30days. This is attributed to the fact that the guest molecule is both supramolecularly complexed within the dendritic scaffold and intercalated into CD and MTM hosts. Host-guest systems between assemblies and various guests hold promising applications in drug delivery system and in the biomedical fields. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Advances in Macromolecular Data Storage

    CERN Document Server

    Mansuripur, Masud

    2014-01-01

    We propose to develop a new method of information storage to replace magnetic hard disk drives and other instruments of secondary/backup data storage. The proposed method stores petabytes of user-data in a sugar cube (1 cm3), and can read/write that information at hundreds of megabits/sec. Digital information is recorded and stored in the form of a long macromolecule consisting of at least two bases, A and B. (This would be similar to DNA strands constructed from the four nucleic acids G,C,A,T.) The macromolecules initially enter the system as blank slates. A macromolecule with, say, 10,000 identical bases in the form of AAAAA....AAA may be used to record a kilobyte block of user-data (including modulation and error-correction coding), although, in this blank state, it can only represent the null sequence 00000....000. Suppose this blank string of A's is dragged before an atomically-sharp needle of a scanning tunneling microscope (STM). When electric pulses are applied to the needle in accordance with the seq...

  18. Towards Robust Predictive Fault–Tolerant Control for a Battery Assembly System

    Directory of Open Access Journals (Sweden)

    Seybold Lothar

    2015-12-01

    Full Text Available The paper deals with the modeling and fault-tolerant control of a real battery assembly system which is under implementation at the RAFI GmbH company (one of the leading electronic manufacturing service providers in Germany. To model and control the battery assembly system, a unified max-plus algebra and model predictive control framework is introduced. Subsequently, the control strategy is enhanced with fault-tolerance features that increase the overall performance of the production system being considered. In particular, it enables tolerating (up to some degree mobile robot, processing and transportation faults. The paper discusses also robustness issues, which are inevitable in real production systems. As a result, a novel robust predictive fault-tolerant strategy is developed that is applied to the battery assembly system. The last part of the paper shows illustrative examples, which clearly exhibit the performance of the proposed approach.

  19. ULtiMATE system for rapid assembly of customized TAL effectors.

    Directory of Open Access Journals (Sweden)

    Junjiao Yang

    Full Text Available Engineered TAL-effector nucleases (TALENs and TALE-based constructs have become powerful tools for eukaryotic genome editing. Although many methods have been reported, it remains a challenge for the assembly of designer-based TALE repeats in a fast, precise and cost-effective manner. We present an ULtiMATE (USER-based Ligation Mediated Assembly of TAL Effector system for speedy and accurate assembly of customized TALE constructs. This method takes advantage of uracil-specific excision reagent (USER to create multiple distinct sticky ends between any neighboring DNA fragments for specific ligation. With pre-assembled templates, multiple TALE DNA-binding domains could be efficiently assembled in order within hours with minimal manual operation. This system has been demonstrated to produce both functional TALENs for effective gene knockout and TALE-mediated gene-specific transcription activation (TALE-TA. The feature of both ease-of-operation and high efficiency of ULtiMATE system makes it not only an ideal method for biologic labs, but also an approach well suited for large-scale assembly of TALENs and any other TALE-based constructions.

  20. Adaptation of a Filter Assembly to Assess Microbial Bioburden of Pressurant Within a Propulsion System

    Science.gov (United States)

    Benardini, James N.; Koukol, Robert C.; Schubert, Wayne W.; Morales, Fabian; Klatte, Marlin F.

    2012-01-01

    A report describes an adaptation of a filter assembly to enable it to be used to filter out microorganisms from a propulsion system. The filter assembly has previously been used for particulates greater than 2 micrometers. Projects that utilize large volumes of nonmetallic materials of planetary protection concern pose a challenge to their bioburden budget, as a conservative specification value of 30 spores per cubic centimeter is typically used. Helium was collected utilizing an adapted filtration approach employing an existing Millipore filter assembly apparatus used by the propulsion team for particulate analysis. The filter holder on the assembly has a 47-mm diameter, and typically a 1.2-5 micrometer pore-size filter is used for particulate analysis making it compatible with commercially available sterilization filters (0.22 micrometers) that are necessary for biological sampling. This adaptation to an existing technology provides a proof-of-concept and a demonstration of successful use in a ground equipment system. This adaptation has demonstrated that the Millipore filter assembly can be utilized to filter out microorganisms from a propulsion system, whereas in previous uses the filter assembly was utilized for particulates greater than 2 micrometers.

  1. Inclinometer Assembly Error Calibration and Horizontal Image Correction in Photoelectric Measurement Systems

    Directory of Open Access Journals (Sweden)

    Xiaofang Kong

    2018-01-01

    Full Text Available Inclinometer assembly error is one of the key factors affecting the measurement accuracy of photoelectric measurement systems. In order to solve the problem of the lack of complete attitude information in the measurement system, this paper proposes a new inclinometer assembly error calibration and horizontal image correction method utilizing plumb lines in the scenario. Based on the principle that the plumb line in the scenario should be a vertical line on the image plane when the camera is placed horizontally in the photoelectric system, the direction cosine matrix between the geodetic coordinate system and the inclinometer coordinate system is calculated firstly by three-dimensional coordinate transformation. Then, the homography matrix required for horizontal image correction is obtained, along with the constraint equation satisfying the inclinometer-camera system requirements. Finally, the assembly error of the inclinometer is calibrated by the optimization function. Experimental results show that the inclinometer assembly error can be calibrated only by using the inclination angle information in conjunction with plumb lines in the scenario. Perturbation simulation and practical experiments using MATLAB indicate the feasibility of the proposed method. The inclined image can be horizontally corrected by the homography matrix obtained during the calculation of the inclinometer assembly error, as well.

  2. Celebrating macromolecular crystallography: A personal perspective

    Directory of Open Access Journals (Sweden)

    Abad-Zapatero, Celerino

    2015-04-01

    Full Text Available The twentieth century has seen an enormous advance in the knowledge of the atomic structures that surround us. The discovery of the first crystal structures of simple inorganic salts by the Braggs in 1914, using the diffraction of X-rays by crystals, provided the critical elements to unveil the atomic structure of matter. Subsequent developments in the field leading to macromolecular crystallography are presented with a personal perspective, related to the cultural milieu of Spain in the late 1950’s. The journey of discovery of the author, as he developed professionally, is interwoven with the expansion of macromolecular crystallography from the first proteins (myoglobin, hemoglobin to the ‘coming of age’ of the field in 1971 and the discoveries that followed, culminating in the determination of the structure of the ribosomes at the turn of the century. A perspective is presented exploring the future of the field and also a reflection about the future generations of Spanish scientists.El siglo XX ha sido testigo del increíble avance que ha experimentado el conocimiento de la estructura atómica de la materia que nos rodea. El descubrimiento de las primeras estructuras atómicas de sales inorgánicas por los Bragg en 1914, empleando difracción de rayos X con cristales, proporcionó los elementos clave para alcanzar tal conocimiento. Posteriores desarrollos en este campo, que condujeron a la cristalografía macromolecular, se presentan aquí desde una perspectiva personal, relacionada con el contexto cultural de la España de la década de los 50. La experiencia del descubrimiento científico, durante mi desarrollo profesional, se integra en el desarrollo de la cristalografía macromolecular, desde las primeras proteínas (míoglobina y hemoglobina, hasta su madurez en 1971 que, con los posteriores descubrimientos, culmina con la determinación del la estructura del ribosoma. Asimismo, se explora el futuro de esta disciplina y se

  3. A Single Stereodynamic Center Modulates the Rate of Self-Assembly in a Biomolecular System.

    Science.gov (United States)

    Zhang, Yitao; Malamakal, Roy M; Chenoweth, David M

    2015-09-07

    Chirality is a property of asymmetry important to both physical and abstract systems. Understanding how molecular systems respond to perturbations in their chiral building blocks can provide insight into diverse areas such as biomolecular self-assembly, protein folding, drug design, materials, and catalysis. Despite the fundamental importance of stereochemical preorganization in nature and designed materials, the ramifications of replacing chiral centers with stereodynamic atomic mimics in the context of biomolecular systems is unknown. Herein, we demonstrate that replacement of a single amino acid stereocenter with a stereodynamic nitrogen atom has profound consequences on the self-assembly of a biomolecular system. Our results provide insight into how the fundamental biopolymers of life would behave if their chiral centers were not configurationally stable, highlighting the vital importance of stereochemistry as a pre-organizing element in biomolecular folding and assembly events. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Smart self-assembled hybrid hydrogel biomaterials.

    Science.gov (United States)

    Kopeček, Jindřich; Yang, Jiyuan

    2012-07-23

    Hybrid biomaterials are systems created from components of at least two distinct classes of molecules, for example, synthetic macromolecules and proteins or peptide domains. The synergistic combination of two types of structures may produce new materials that possess unprecedented levels of structural organization and novel properties. This Review focuses on biorecognition-driven self-assembly of hybrid macromolecules into functional hydrogel biomaterials. First, basic rules that govern the secondary structure of peptides are discussed, and then approaches to the specific design of hybrid systems with tailor-made properties are evaluated, followed by a discussion on the similarity of design principles of biomaterials and macromolecular therapeutics. Finally, the future of the field is briefly outlined. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. The assembly and use of continuous flow systems for chemical synthesis.

    Science.gov (United States)

    Britton, Joshua; Jamison, Timothy F

    2017-11-01

    The adoption of and opportunities in continuous flow synthesis ('flow chemistry') have increased significantly over the past several years. Continuous flow systems provide improved reaction safety and accelerated reaction kinetics, and have synthesised several active pharmaceutical ingredients in automated reconfigurable systems. Although continuous flow platforms are commercially available, systems constructed 'in-lab' provide researchers with a flexible, versatile, and cost-effective alternative. Herein, we describe the assembly and use of a modular continuous flow apparatus from readily available and affordable parts in as little as 30 min. Once assembled, the synthesis of a sulfonamide by reacting 4-chlorobenzenesulfonyl chloride with dibenzylamine in a single reactor coil with an in-line quench is presented. This example reaction offers the opportunity to learn several important skills including reactor construction, charging of a back-pressure regulator, assembly of stainless-steel syringes, assembly of a continuous flow system with multiple junctions, and yield determination. From our extensive experience of single-step and multistep continuous flow synthesis, we also describe solutions to commonly encountered technical problems such as precipitation of solids ('clogging') and reactor failure. Following this protocol, a nonspecialist can assemble a continuous flow system from reactor coils, syringes, pumps, in-line liquid-liquid separators, drying columns, back-pressure regulators, static mixers, and packed-bed reactors.

  6. The analysis of macromolecular interactions by sedimentation equilibrium.

    Science.gov (United States)

    Ghirlando, Rodolfo

    2011-05-01

    The study of macromolecular interactions by sedimentation equilibrium is a highly technical method that requires great care in both the experimental design and data analysis. The complexity of the interacting system that can be analyzed is only limited by the ability to deconvolute the exponential contributions of each of the species to the overall concentration gradient. This is achieved in part through the use of multi-signal data collection and the implementation of soft mass conservation. We illustrate the use of these constraints in SEDPHAT through the study of an A+B+B⇌AB+B⇌ABB system and highlight some of the technical challenges that arise. We show that both the multi-signal analysis and mass conservation result in a precise and robust data analysis and discuss improvements that can be obtained through the inclusion of data from other methods such as sedimentation velocity and isothermal titration calorimetry. Published by Elsevier Inc.

  7. The analysis of macromolecular interactions by sedimentation equilibrium

    Science.gov (United States)

    Ghirlando, Rodolfo

    2010-01-01

    The study of macromolecular interactions by sedimentation equilibrium is a highly technical method that requires great care in both the experimental design and data analysis. The complexity of the interacting system that can be analyzed is only limited by the ability to deconvolute the exponential contributions of each of the species to the overall concentration gradient. This is achieved in part through the use of multi-signal data collection and the implementation of soft mass conservation. We illustrate the use of these constraints in SEDPHAT through the study of an A + B + B ⇌ AB + B ⇌ ABB system and highlight some of the technical challenges that arise. We show that both the multi-signal analysis and mass conservation result in a precise and robust data analysis and discuss improvements that can be obtained through the inclusion of data from other methods such as sedimentation velocity and isothermal titration calorimetry. PMID:21167941

  8. Type IV kerogens as analogues for organic macromolecular materials in aqueously altered carbonaceous chondrites.

    Science.gov (United States)

    Matthewman, Richard; Martins, Zita; Sephton, Mark A

    2013-04-01

    Understanding the processes involved in the evolution of organic matter in the early Solar System requires extensive experimental work. The scientifically valuable carbonaceous chondrites are principal targets for organic analyses, but these meteorites are rare. Meteoritic analog materials available in larger quantities, on which experiments can be performed, would be highly beneficial. The bulk of the organic inventory of carbonaceous chondrites is made up of solvent-insoluble macromolecular material. This high-molecular-weight entity provides a record of thermal and aqueous parent-body alteration of precursor organic structures present at the birth of the Solar System. To identify an effective analogue for this macromolecular material, we analyzed a series of terrestrial kerogens by pyrolysis-gas chromatography-mass spectrometry. Type I and II kerogens are unsuitable analogues owing to their highly aliphatic nature. Type III kerogens show some similarities to meteoritic macromolecular materials but display a substantial biological heritage. Type IV kerogens, in this study derived from Mesozoic paleosols and produced by the reworking and oxidation of organic matter, represent an effective analogue. Some isomeric differences exist between meteoritic macromolecular materials and type IV kerogens, and stepped pyrolysis indicates variations in thermal stability. In addition to being a suitable material for novel experimentation, type IV kerogens also have the potential to aid in the optimization of instruments for deployment on Mars.

  9. GoldenBraid: an iterative cloning system for standardized assembly of reusable genetic modules.

    Directory of Open Access Journals (Sweden)

    Alejandro Sarrion-Perdigones

    Full Text Available Synthetic Biology requires efficient and versatile DNA assembly systems to facilitate the building of new genetic modules/pathways from basic DNA parts in a standardized way. Here we present GoldenBraid (GB, a standardized assembly system based on type IIS restriction enzymes that allows the indefinite growth of reusable gene modules made of standardized DNA pieces. The GB system consists of a set of four destination plasmids (pDGBs designed to incorporate multipartite assemblies made of standard DNA parts and to combine them binarily to build increasingly complex multigene constructs. The relative position of type IIS restriction sites inside pDGB vectors introduces a double loop ("braid" topology in the cloning strategy that allows the indefinite growth of composite parts through the succession of iterative assembling steps, while the overall simplicity of the system is maintained. We propose the use of GoldenBraid as an assembly standard for Plant Synthetic Biology. For this purpose we have GB-adapted a set of binary plasmids for A. tumefaciens-mediated plant transformation. Fast GB-engineering of several multigene T-DNAs, including two alternative modules made of five reusable devices each, and comprising a total of 19 basic parts are also described.

  10. GoldenBraid: An Iterative Cloning System for Standardized Assembly of Reusable Genetic Modules

    Science.gov (United States)

    Sarrion-Perdigones, Alejandro; Falconi, Erica Elvira; Zandalinas, Sara I.; Juárez, Paloma; Fernández-del-Carmen, Asun; Granell, Antonio; Orzaez, Diego

    2011-01-01

    Synthetic Biology requires efficient and versatile DNA assembly systems to facilitate the building of new genetic modules/pathways from basic DNA parts in a standardized way. Here we present GoldenBraid (GB), a standardized assembly system based on type IIS restriction enzymes that allows the indefinite growth of reusable gene modules made of standardized DNA pieces. The GB system consists of a set of four destination plasmids (pDGBs) designed to incorporate multipartite assemblies made of standard DNA parts and to combine them binarily to build increasingly complex multigene constructs. The relative position of type IIS restriction sites inside pDGB vectors introduces a double loop (“braid”) topology in the cloning strategy that allows the indefinite growth of composite parts through the succession of iterative assembling steps, while the overall simplicity of the system is maintained. We propose the use of GoldenBraid as an assembly standard for Plant Synthetic Biology. For this purpose we have GB-adapted a set of binary plasmids for A. tumefaciens-mediated plant transformation. Fast GB-engineering of several multigene T-DNAs, including two alternative modules made of five reusable devices each, and comprising a total of 19 basic parts are also described. PMID:21750718

  11. Rotation-Induced Macromolecular Spooling of DNA

    Science.gov (United States)

    Shendruk, Tyler N.; Sean, David; Berard, Daniel J.; Wolf, Julian; Dragoman, Justin; Battat, Sophie; Slater, Gary W.; Leslie, Sabrina R.

    2017-07-01

    Genetic information is stored in a linear sequence of base pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we discover that rotation-induced macromolecular spooling of DNA around a rotating microwire can monotonically order genomic bases, overcoming this challenge. We use single-molecule fluorescence microscopy to directly visualize long DNA strands deforming and elongating in shear flow near a rotating microwire, in agreement with numerical simulations. While untethered DNA is observed to elongate substantially, in agreement with our theory and numerical simulations, strong extension of DNA becomes possible by introducing tethering. For the case of tethered polymers, we show that increasing the rotation rate can deterministically spool a substantial portion of the chain into a fully stretched, single-file conformation. When applied to DNA, the fraction of genetic information sequentially ordered on the microwire surface will increase with the contour length, despite the increased entropy. This ability to handle long strands of DNA is in contrast to modern DNA sample preparation technologies for sequencing and mapping, which are typically restricted to comparatively short strands, resulting in challenges in reconstructing the genome. Thus, in addition to discovering new rotation-induced macromolecular dynamics, this work inspires new approaches to handling genomic-length DNA strands.

  12. Creating 3D physical models to probe student understanding of macromolecular structure.

    Science.gov (United States)

    Cooper, A Kat; Oliver-Hoyo, M T

    2017-11-01

    The high degree of complexity of macromolecular structure is extremely difficult for students to process. Students struggle to translate the simplified two-dimensional representations commonly used in biochemistry instruction to three-dimensional aspects crucial in understanding structure-property relationships. We designed four different physical models to address student understanding of electrostatics and noncovalent interactions and their relationship to macromolecular structure. In this study, we have tested these models in classroom settings to determine if these models are effective in engaging students at an appropriate level of difficulty and focusing student attention on the principles of electrostatic attractions. This article describes how to create these unique models for four targeted areas related to macromolecular structure: protein secondary structure, protein tertiary structure, membrane protein solubility, and DNA structure. We also provide evidence that merits their use in classroom settings based on the analysis of assembled models and a behavioral assessment of students enrolled in an introductory biochemistry course. By providing students with three-dimensional models that can be physically manipulated, barriers to understanding representations of these complex structures can be lowered and the focus shifted to addressing the foundational concepts behind these properties. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(6):491-500, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

  13. The role of macromolecular stability in desiccation tolerance

    NARCIS (Netherlands)

    Wolkers, W.F.

    1998-01-01

    The work presented in this thesis concerns a study on the molecular interactions that play a role in the macromolecular stability of desiccation-tolerant higher plant organs. Fourier transform infrared microspectroscopy was used as the main experimental technique to assess macromolecular

  14. MATERIAL PROCESSING FOR SELF-ASSEMBLING MACHINE SYSTEMS

    Energy Technology Data Exchange (ETDEWEB)

    K. LACKNER; D. BUTT; C. WENDT

    1999-06-01

    We are developing an important aspect of a new technology based on self-reproducing machine systems. Such systems could overcome resource limitations and control the deleterious side effects of human activities on the environment. Machine systems capable of building themselves promise an increase in industrial productivity as dramatic as that of the industrial revolution. To operate successfully, such systems must procure necessary raw materials from their surroundings. Therefore, next to automation, most critical for this new technology is the ability to extract important chemicals from readily available soils. In contrast to conventional metallurgical practice, these extraction processes cannot make substantial use of rare elements. We have designed a thermodynamically viable process and experimentally demonstrated most steps that differ from common practice. To this end we had to develop a small, disposable vacuum furnace system. Our work points to a viable extraction process.

  15. Self-assembly in the systems of magnetic anisotropic nanoparticles

    Science.gov (United States)

    Gudkova, A. V.; Pyanzina, E. S.

    2017-11-01

    This paper presents the complex investigation of the system of magnetic anisotropic nanoparticles using computer simulations in a wide range of the system's parameters. The cluster analysis was made, various average characteristics of the formed clusters were calculated and the initial magnetic susceptibility and the radial distribution function were computed. It was shown that via changing the nanoparticles characteristics (their shape and the values of the magnetic moments) it's possible to change macroscopic response of the system, that implements the idea of tuning and design new materials with controllable properties.

  16. Baseline tests of an autonomous telerobotic system for assembly of space truss structures

    Science.gov (United States)

    Rhodes, Marvin D.; Will, Ralph W.; Quach, Coung

    1994-07-01

    Several proposed space missions include precision reflectors that are larger in diameter than any current or proposed launch vehicle. Most of these reflectors will require a truss structure to accurately position the reflector panels and these reflectors will likely require assembly in orbit. A research program has been conducted at the NASA Langley Research Center to develop the technology required for the robotic assembly of truss structures. The focus of this research has been on hardware concepts, computer software control systems, and operator interfaces necessary to perform supervised autonomous assembly. A special facility was developed and four assembly and disassembly tests of a 102-strut tetrahedral truss have been conducted. The test procedures were developed around traditional 'pick-and-place' robotic techniques that rely on positioning repeatability for successful operation. The data from two of the four tests were evaluated and are presented in this report. All operations in the tests were controlled by predefined sequences stored in a command file, and the operator intervened only when the system paused because of the failure of an actuator command. The tests were successful in identifying potential pitfalls in a telerobotic system, many of which would not have been readily anticipated or incurred through simulation studies. Addressing the total integrated task, instead of bench testing the component parts, forced all aspects of the task to be evaluated. Although the test results indicate that additional developments should be pursued, no problems were encountered that would preclude automated assembly in space as a viable construction method.

  17. Aqueous Two Phase System Assisted Self-Assembled PLGA Microparticles

    National Research Council Canada - National Science Library

    Yeredla, Nitish; Kojima, Taisuke; Yang, Yi; Takayama, Shuichi; Kanapathipillai, Mathumai

    2016-01-01

    Here, we produce poly(lactide-co-glycolide) (PLGA) based microparticles with varying morphologies, and temperature responsive properties utilizing a Pluronic F127/dextran aqueous two-phase system (ATPS...

  18. Architecture, Function, and Assembly of the Mouse Visual System.

    Science.gov (United States)

    Seabrook, Tania A; Burbridge, Timothy J; Crair, Michael C; Huberman, Andrew D

    2017-07-25

    Vision is the sense humans rely on most to navigate the world, make decisions, and perform complex tasks. Understanding how humans see thus represents one of the most fundamental and important goals of neuroscience. The use of the mouse as a model for parsing how vision works at a fundamental level started approximately a decade ago, ushered in by the mouse's convenient size, relatively low cost, and, above all, amenability to genetic perturbations. In the course of that effort, a large cadre of new and powerful tools for in vivo labeling, monitoring, and manipulation of neurons were applied to this species. As a consequence, a significant body of work now exists on the architecture, function, and development of mouse central visual pathways. Excitingly, much of that work includes causal testing of the role of specific cell types and circuits in visual perception and behavior-something rare to find in studies of the visual system of other species. Indeed, one could argue that more information is now available about the mouse visual system than any other sensory system, in any species, including humans. As such, the mouse visual system has become a platform for multilevel analysis of the mammalian central nervous system generally. Here we review the mouse visual system structure, function, and development literature and comment on the similarities and differences between the visual system of this and other model species. We also make it a point to highlight the aspects of mouse visual circuitry that remain opaque and that are in need of additional experimentation to enrich our understanding of how vision works on a broad scale.

  19. Hydrogen isotope distillation for the Tritium Systems Test Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Bartlit, J.R.; Denton, W.H.; Sherman, R.H.

    1978-01-01

    A system of four, interlinked, cryogenic fractional distillation columns has been designed as a prototype for fuel processing for fusion power reactors. The distillation system will continuously separate a feedstream of 360 g moles/day of roughly 50-50 deuterium-tritium containing approximately 1% H into four product streams: (1) a tritium-free stream of HD for waste disposal; (2) a stream of high-purity D/sub 2/ for simulated neutral beam injection; (3) a stream of DT for simulated reactor refueling; and (4) a stream of high purity T/sub 2/ for refueling and studies on properties of tritium and effects of tritium on materials.

  20. A Digital Interface for the Part Designers and the Fixture Designers for a Reconfigurable Assembly System

    Directory of Open Access Journals (Sweden)

    Vishwa V. Kumar

    2013-01-01

    Full Text Available This paper presents a web-based framework for interfacing product designers and fixture designers to fetch the benefits of early supplier involvement (ESI to a reconfigurable assembly system (RAS. The interfacing of the two members requires four steps, namely, collaboration chain, fixture supplier selection, knowledge share, and accommodation of service facilities so as to produce multiple products on a single assembly line. The interfacing not only provokes concurrency in the activities of product and fixture designer but also enables the assembly systems to tackle the spatial and generational variety. Among the four stages of interfacing, two steps are characterized by optimization issues, one from the product customer side and the other from the fixture designer side. To impart promptness in the optimization and hence the interaction, computationally economic tools are also presented in the paper for both of the supplier selection and fixture design optimization.

  1. An assembly system based on industrial robot with binocular stereo vision

    Science.gov (United States)

    Tang, Hong; Xiao, Nanfeng

    2017-01-01

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

  2. A Versatile Multiple Target Detection System Based on DNA Nano-assembled Linear FRET Arrays.

    Science.gov (United States)

    Li, Yansheng; Du, Hongwu; Wang, Wenqian; Zhang, Peixun; Xu, Liping; Wen, Yongqiang; Zhang, Xueji

    2016-05-27

    DNA molecules have been utilized both as powerful synthetic building blocks to create nanoscale architectures and as inconstant programmable templates for assembly of biosensors. In this paper, a versatile, scalable and multiplex detection system is reported based on an extending fluorescent resonance energy transfer (FRET) cascades on a linear DNA assemblies. Seven combinations of three kinds of targets are successfully detected through the changes of fluorescence spectra because of the three-steps FRET or non-FRET continuity mechanisms. This nano-assembled FRET-based nanowire is extremely significant for the development of rapid, simple and sensitive detection system. The method used here could be extended to a general platform for multiplex detection through more-step FRET process.

  3. Developing An Effective Strategy to Configure Assembly Systems Using Lean Concepts

    Directory of Open Access Journals (Sweden)

    M.Eswaramoorthi

    2010-12-01

    Full Text Available The manufacturing industry has been pushed to adopt more effective production strategies to meet the challenges of shorter life cycle, higher quality, lower cost and wider variety of customer demands. This increased emphasis on achieving highly adaptive manufacturing with reduction in manufacturing costs and better utilization of manufacturing resources force to implementing new and efficient management techniques in their manufacturing operations. Some of the established tools in this context are lean practices. In manufacturing, assembly is one of the major activities that combine the machined components into final product. Decision on appropriate facility layout and viable assembly sequence (line balancing adaptable to takt time requirement with cost benefit is a challenging task. This paper proposes an integrated cost model for a typical assembly process to determine cost per part more precisely by considering seven types of "contributing factors". This procedure is performed under different takt time conditions to configure the assembly system in terms of cost per piece and to decide the adaptable layout. A prototype assembly system is established in this research to demonstrate the effectiveness of the cost model. The results show that there are significant variations in cost per piece with respect to changes in layout configurations and takt time.

  4. IBM system/360 assembly language interval arithmetic software

    Science.gov (United States)

    Phillips, E. J.

    1972-01-01

    Computer software designed to perform interval arithmetic is described. An interval is defined as the set of all real numbers between two given numbers including or excluding one or both endpoints. Interval arithmetic consists of the various elementary arithmetic operations defined on the set of all intervals, such as interval addition, subtraction, union, etc. One of the main applications of interval arithmetic is in the area of error analysis of computer calculations. For example, it has been used sucessfully to compute bounds on sounding errors in the solution of linear algebraic systems, error bounds in numerical solutions of ordinary differential equations, as well as integral equations and boundary value problems. The described software enables users to implement algorithms of the type described in references efficiently on the IBM 360 system.

  5. Challenges and Perspectives in the Macromolecular Flatland.

    Science.gov (United States)

    Servalli, Marco

    2017-06-28

    Polymer chemistry has recently welcomed a new addition to its field: the planar macromolecules known as two-dimensional polymers (2DPs). These topologically planar and crystalline monolayer covalent sheets are reminiscent of molecular fishermen's nets and apart from being conceptually very interesting for the field of macro-molecular chemistry, they also show some potential applications as novel 2D materials. This article reviews how the field has developed five years after the first 2DP was synthesised in 2012. After a brief historical introduction, the main synthetic approaches will be discussed providing concrete examples of 2DPs and highlighting the challenges associated with the synthesis and especially structural characterisation of these fascinating macro-molecules. Finally an overview on their potential applications such as membranes for gas separation, rewritable molecular paper and miniaturisation of optical devices will be presented.

  6. Acid-induced assembly of a reconstituted silk protein system

    Science.gov (United States)

    Tabatabai, A. Pasha; Weigandt, Katie M.; Blair, Daniel L.

    2017-08-01

    Silk cocoons are reconstituted into an aqueous suspension, and protein stability is investigated by comparing the protein's response to hydrochloric acid and sodium chloride. Aggregation occurs for systems mixed with hydrochloric acid, while sodium chloride over the same range of concentrations does not cause aggregation. We measure the structures present on the protein and aggregate length scales in these solutions using both optical and small-angle neutron scattering, while mass spectrometry techniques shed light on a possible mechanism for aggregate formation. We find that the introduction of acid modulates the aggregate size and pervaded volume of the protein, an effect that is not observed with salt.

  7. Probing the Composition, Assembly and Activity of Protein Molecular Machines using Native Mass Spectrometry

    NARCIS (Netherlands)

    Waterbeemd, M.J. van de

    2017-01-01

    Native mass spectrometry and mass spectrometry in general, are powerful analytical tools for studying proteins and protein complexes. Native mass spectrometry may provide accurate mass measurements of large macromolecular assemblies enabling the investigation of their composition and stoichiometry.

  8. Duct System Flammability and Air Sealing Fire Separation Assemblies in the International Residential Code

    Energy Technology Data Exchange (ETDEWEB)

    Rudd, A. [ABT Systems, LLC, Annville, PA (United States); Prahl, D. [IBACOS, Inc., Pittsburgh, PA (United States)

    2014-12-01

    IBACOS identified two barriers that limit the ability of builders to cost-effectively achieve higher energy efficiency levels in housing. These are the use of duct system materials that inherently achieve airtightness and are appropriately sized for low-load houses and the ability to air seal fire separation assemblies. The issues identified fall into a gray area of the codes.

  9. Duct System Flammability and Air Sealing Fire Separation Assemblies in the International Residential Code

    Energy Technology Data Exchange (ETDEWEB)

    Rudd, A.; Prahl, D.

    2014-12-01

    IBACOS identified two barriers that limit the ability of builders to cost-effectively achieve higher energy efficiency levels in housing. These are (1) the use of duct system materials that inherently achieve airtightness and are appropriately sized for low-load houses and (2) the ability to air seal fire separation assemblies. The issues identified fall into a gray area of the codes.

  10. The Phantom National? Assembling National Teaching Standards in Australia's Federal System

    Science.gov (United States)

    Savage, Glenn C.; Lewis, Steven

    2018-01-01

    In this paper, we use the development of the Australian Professional Standards for Teachers (APST) as an illustrative case to examine how national schooling reforms are assembled in Australia's federal system. Drawing upon an emerging body of research on "policy assemblage" within the fields of policy sociology, anthropology and critical…

  11. Self-Assembly Strategies for Integrating Light Harvesting and Charge Separation in Artificial Photosynthetic Systems

    Energy Technology Data Exchange (ETDEWEB)

    Wasielewski, Michael R. (NWU)

    2017-02-15

    In natural photosynthesis, organisms optimize solar energy conversion through organized assemblies of photofunctional chromophores and catalysts within proteins that provide specifically tailored environments for chemical reactions. As with their natural counterparts, artificial photosynthetic systems for practical solar fuels production must collect light energy, separate charge, and transport charge to catalytic sites where multielectron redox processes will occur. While encouraging progress has been made on each aspect of this complex problem, researchers have not yet developed self-ordering and self-assembling components and the tailored environments necessary to realize a fully-functional artificial system. Previously researchers have used complex, covalent molecular systems comprised of chromophores, electron donors, and electron acceptors to mimic both the light-harvesting and the charge separation functions of photosynthetic proteins. These systems allow for study of the dependencies of electron transfer rate constants on donor?acceptor distance and orientation, electronic interaction, and the free energy of the reaction. The most useful and informative systems are those in which structural constraints control both the distance and the orientation between the electron donors and acceptors. Self-assembly provides a facile means for organizing large numbers of molecules into supramolecular structures that can bridge length scales from nanometers to macroscopic dimensions. The resulting structures must provide pathways for migration of light excitation energy among antenna chromophores, and from antennas to reaction centers. They also must incorporate charge conduits, that is, molecular 'wires' that can efficiently move electrons and holes between reaction centers and catalytic sites. The central scientific challenge is to develop small, functional building blocks with a minimum number of covalent linkages, which also have the appropriate molecular

  12. Assembly of a Pulmonary Artery Pressure Sensor System

    Directory of Open Access Journals (Sweden)

    J. Müntjes

    2010-01-01

    Full Text Available This paper presents an implantable system for telemonitoring the intravascular pressure in the pulmonary artery. By implanting a catheter-bound pressure and temperature sensor into the pulmonary artery, it is possible to monitor the actual value and the time variations of the intravascular pressure with a frequency of 128 Hz. Thus hospitalization of patients suffering from heart insufficiency can be avoided by early changes in therapy.Preliminary in vivo experiments have been conducted to verify the fixation mechanism and the positioning of the sensor at the right place in the pulmonary artery. It was shown that the proposed fixation mechanism and the packaging of the sensor promise to be stable.

  13. Surfaces wettability and morphology modulation in a fluorene derivative self-assembly system

    Energy Technology Data Exchange (ETDEWEB)

    Cao, Xinhua, E-mail: caoxhchem@163.com; Gao, Aiping; Zhao, Na; Yuan, Fangyuan; Liu, Chenxi; Li, Ruru

    2016-04-15

    Graphical abstract: - Highlights: • The different structures could be obtained in this self-assembly system. • A water-drop could freely roll on the xerogel film with the sliding angle of 15.0. • The superhydrophobic surface can be obtained via supramolecular self-assembly. - Abstract: A new organogelator based on fluorene derivative (gelator 1) was designed and synthesized. Organogels could be obtained via the self-assembly of the derivative in acetone, toluene, ethyl acetate, hexane, DMSO and petroleum ether. The self-assembly process was thoroughly characterized using field-emission scanning electron microscopy (FESEM), X-ray diffraction (XRD), UV–vis, FT-IR and the contact angle. Surfaces with different morphologies and wetting properties were formed via the self-assembly of gelator 1 in the six different solvents. Interestingly, a superhydrophobic surface with a contact angle of 150° was obtained from organogel 1 in DMSO and exhibited the lotus-effect. The sliding angle necessary for a water droplet to move on the glass was only 15°. Hydrogen bonding and van der Waals forces were attributed as the main driving forces for gel formation.

  14. Supramolecular assembling systems formed by heme-heme pocket interactions in hemoproteins.

    Science.gov (United States)

    Oohora, Koji; Onoda, Akira; Hayashi, Takashi

    2012-12-14

    A native protein in a biological system spontaneously produces large and elegant assemblies via self-assembly or assembly with various biomolecules which provide non-covalent interactions. In this context, the protein plays a key role in construction of a unique supramolecular structure operating as a functional system. Our group has recently highlighted the structure and function of hemoproteins reconstituted with artificially created heme analogs. The heme molecule is a replaceable cofactor of several hemoproteins. Here, we focus on the successive supramolecular protein assemblies driven by heme-heme pocket interactions to afford various examples of protein fibers, networks and three-dimensional clusters in which an artificial heme moiety is introduced onto the surface of a hemoprotein via covalent linkage and the native heme cofactor is removed from the heme pocket. This strategy is found to be useful for constructing hybrid materials with an electrode or with nanoparticles. The new systems described herein are expected to lead to the generation of various biomaterials with functions and characteristic physicochemical properties similar to those of hemoproteins.

  15. A Versatile System for USER Cloning-Based Assembly of Expression Vectors for Mammalian Cell Engineering

    DEFF Research Database (Denmark)

    Lund, Anne Mathilde; Kildegaard, Helene Faustrup; Petersen, Maja Borup Kjær

    2014-01-01

    A new versatile mammalian vector system for protein production, cell biology analyses, and cell factory engineering was developed. The vector system applies the ligation-free uracil-excision based technique – USER cloning – to rapidly construct mammalian expression vectors of multiple DNA fragments...... efficiency above 90%. The functionality of basic vectors for FAST assembly was tested and validated by transient expression of fluorescent model proteins in CHO, U-2-OS and HEK293 cell lines. In this test, we included many of the most common vector elements for heterologous gene expression in mammalian cells......, in addition the system is fully extendable by other users. The vector system is designed to facilitate high-throughput genome-scale studies of mammalian cells, such as the newly sequenced CHO cell lines, through the ability to rapidly generate high-fidelity assembly of customizable gene expression vectors....

  16. Collaborative Policy of the Supply-Hub for Assemble-to-Order Systems with Delivery Uncertainty

    Directory of Open Access Journals (Sweden)

    Guo Li

    2014-01-01

    Full Text Available This paper considers the collaborative mechanisms of the Supply-Hub in the Assemble-to-Order system (ATO system hereafter with upstream delivery uncertainty. We first propose a collaborative replenishment mechanism in the ATO system, and construct a replenishment model with delivery uncertainty in use of the Supply-Hub. After transforming the original model into a one-dimensional optimization problem, we derive the optimal assembly quantity and reorder point of each component. In order to enable the Supply-Hub to conduct collaborative replenishment with each supplier, the punishment and reward mechanisms are proposed. The numerical analysis illustrates that service level of the Supply-Hub is an increasing function of both punishment and reward factors. Therefore, by adjusting the two factors, suppliers’ incentives of collaborative replenishment can be significantly enhanced, and then the service level of whole ATO system can be improved.

  17. The Clouds and the Earth's Radiant Energy System Elevation Bearing Assembly Life Test

    Science.gov (United States)

    Brown, Phillip L.; Miller, James B.; Jones, William R., Jr.; Rasmussen, Kent; Wheeler, Donald R.; Rana, Mauro; Peri, Frank

    1999-01-01

    The Clouds and the Earth's Radiant Energy System (CERES) elevation scan bearings lubricated with Pennzane SHF X2000 and 2% lead naphthenate (PbNp) were life tested for a seven-year equivalent Low Earth Orbit (LEO) operation. The bearing life assembly was tested continuously at an accelerated and normal rate using the scanning patterns developed for the CERES Earth Observing System AM-1 mission. A post-life-test analysis was performed on the collected data, bearing wear, and lubricant behavior.

  18. Human Factors and Their Effects on Human-Centred Assembly Systems - A Literature Review-Based Study

    Science.gov (United States)

    Wang, Q.; Abubakar, M. I.

    2017-09-01

    If a product has more than one component, then it must be assembled. Assembly of products relies on assembly systems or lines in which assembly of each product is often carried out manually by human workers following assembly sequences in various forms. It is widely understood that efficiency of assembling a product by reducing assembly times (therefore costs) is vital particularly for small and medium-sized manufacturing companies to survive in an increasingly competitive market. Ideally, it is helpful for pre-determining efficiency or productivity of a human-centred assembly system at the early design stage. To date, most research on performance of an assembly system using modelling simulation methods is focused on its “operational functions”. The term used in a narrow sense always indicates the performance of the “operational system”, which does not incorporate the effect of human factors that may also affect the system performance. This paper presents a research outcome of findings through a literature review-based study by identifying possible human factors that mostly affect the performance on human-centred manufacturing systems as part of the research project incorporating parameters of human factors into a DES (discrete event simulation) tool.

  19. SpRoUTS (Space Robot Universal Truss System): Reversible Robotic Assembly of Deployable Truss Structures of Reconfigurable Length

    Science.gov (United States)

    Jenett, Benjamin; Cellucci, Daniel; Cheung, Kenneth

    2015-01-01

    Automatic deployment of structures has been a focus of much academic and industrial work on infrastructure applications and robotics in general. This paper presents a robotic truss assembler designed for space applications - the Space Robot Universal Truss System (SpRoUTS) - that reversibly assembles a truss from a feedstock of hinged andflat-packed components, by folding the sides of each component up and locking onto the assembled structure. We describe the design and implementation of the robot and show that the assembled truss compares favorably with prior truss deployment systems.

  20. Re-Assembled Botulinum Neurotoxin Inhibits CNS Functions without Systemic Toxicity

    Directory of Open Access Journals (Sweden)

    Bazbek Davletov

    2011-03-01

    Full Text Available The therapeutic potential of botulinum neurotoxin type A (BoNT/A has recently been widely recognized. BoNT/A acts to silence synaptic transmission via specific proteolytic cleavage of an essential neuronal protein, SNAP25. The advantages of BoNT/A-mediated synaptic silencing include very long duration, high potency and localized action. However, there is a fear of possible side-effects of BoNT/A due to its diffusible nature which may lead to neuromuscular blockade away from the injection site. We recently developed a “protein-stapling” technology which allows re-assembly of BoNT/A from two separate fragments. This technology allowed, for the first time, safe production of this popular neuronal silencing agent. Here we evaluated the re-assembled toxin in several CNS assays and assessed its systemic effects in an animal model. Our results show that the re-assembled toxin is potent in inhibiting CNS function at 1 nM concentration but surprisingly does not exhibit systemic toxicity after intraperitoneal injection even at 200 ng/kg dose. This shows that the re-assembled toxin represents a uniquely safe tool for neuroscience research and future medical applications.

  1. Re-Assembled Botulinum Neurotoxin Inhibits CNS Functions without Systemic Toxicity

    Science.gov (United States)

    Ferrari, Enrico; Maywood, Elizabeth S.; Restani, Laura; Caleo, Matteo; Pirazzini, Marco; Rossetto, Ornella; Hastings, Michael H.; Niranjan, Dhevahi; Schiavo, Giampietro; Davletov, Bazbek

    2011-01-01

    The therapeutic potential of botulinum neurotoxin type A (BoNT/A) has recently been widely recognized. BoNT/A acts to silence synaptic transmission via specific proteolytic cleavage of an essential neuronal protein, SNAP25. The advantages of BoNT/A-mediated synaptic silencing include very long duration, high potency and localized action. However, there is a fear of possible side-effects of BoNT/A due to its diffusible nature which may lead to neuromuscular blockade away from the injection site. We recently developed a “protein-stapling” technology which allows re-assembly of BoNT/A from two separate fragments. This technology allowed, for the first time, safe production of this popular neuronal silencing agent. Here we evaluated the re-assembled toxin in several CNS assays and assessed its systemic effects in an animal model. Our results show that the re-assembled toxin is potent in inhibiting CNS function at 1 nM concentration but surprisingly does not exhibit systemic toxicity after intraperitoneal injection even at 200 ng/kg dose. This shows that the re-assembled toxin represents a uniquely safe tool for neuroscience research and future medical applications. PMID:22069712

  2. DRUGAS: implantable telemetric system for measuring the portal venous pressure: assembly aspects

    Directory of Open Access Journals (Sweden)

    Fischer Roland

    2017-09-01

    Full Text Available Developing an implantable, telemetric pressure measuring system for venous applications makes a high degree of miniaturization necessary. Thus the influence on the measurement environment is minimized and the risk of thrombosis at small flow blood velocities is decreased. But these systems are limited in terms of accuracy and resolution. The asked system requirements could only be reached by optimising the assembly and encapsulation techniques. To achieve the high degree of miniaturization numerical simulations were performed on the shape and size of the implant and led to the development of a specific metal housing consisting of two main components. A small measuring chamber will be placed into the portal vein and is rigidly fixed to a flat circular part that contains the pressure sensor chip and a transponder board and will be located outside on top of the vein. The main focus of the assembly process was based on a stress-free design and mounting of the components.

  3. Beamline 08ID-1, the prime beamline of the Canadian Macromolecular Crystallography Facility.

    Science.gov (United States)

    Grochulski, Pawel; Fodje, Michel N; Gorin, James; Labiuk, Shaunivan L; Berg, Russ

    2011-07-01

    Beamline 08ID-1 is the prime macromolecular crystallography beamline at the Canadian Light Source. Based on a small-gap in-vacuum undulator, it is designed for challenging projects like small crystals and crystals with large cell dimensions. Beamline 08ID-1, together with a second bending-magnet beamline, constitute the Canadian Macromolecular Crystallography Facility (CMCF). This paper presents an overall description of the 08ID-1 beamline, including its specifications, beamline software and recent scientific highlights. The end-station of the beamline is equipped with a CCD X-ray detector, on-axis crystal visualization system, a single-axis goniometer and a sample automounter allowing remote access to the beamline. The general user program is guaranteed up to 55% of the useful beam time and is run under a peer-review proposal system. The CMCF staff provide `Mail-in' crystallography service to the users with the highest-scored proposals.

  4. Application of the Modular Automated Reconfigurable Assembly System (MARAS) concept to adaptable vision gauging and parts feeding

    Science.gov (United States)

    By, Andre Bernard; Caron, Ken; Rothenberg, Michael; Sales, Vic

    1994-01-01

    This paper presents the first phase results of a collaborative effort between university researchers and a flexible assembly systems integrator to implement a comprehensive modular approach to flexible assembly automation. This approach, named MARAS (Modular Automated Reconfigurable Assembly System), has been structured to support multiple levels of modularity in terms of both physical components and system control functions. The initial focus of the MARAS development has been on parts gauging and feeding operations for cylinder lock assembly. This phase is nearing completion and has resulted in the development of a highly configurable system for vision gauging functions on a wide range of small components (2 mm to 100 mm in size). The reconfigurable concepts implemented in this adaptive Vision Gauging Module (VGM) are now being extended to applicable aspects of the singulating, selecting, and orienting functions required for the flexible feeding of similar mechanical components and assemblies.

  5. Design and simulation of integration system between automated material handling system and manufacturing layout in the automotive assembly line

    Science.gov (United States)

    Seha, S.; Zamberi, J.; Fairu, A. J.

    2017-10-01

    Material handling system (MHS) is an important part for the productivity plant and has recognized as an integral part of today’s manufacturing system. Currently, MHS has growth tremendously with its technology and equipment type. Based on the case study observation, the issue involving material handling system contribute to the reduction of production efficiency. This paper aims to propose a new design of integration between material handling and manufacturing layout by investigating the influences of layout and material handling system. A method approach tool using Delmia Quest software is introduced and the simulation result is used to assess the influences of the integration between material handling system and manufacturing layout in the performance of automotive assembly line. The result show, the production of assembly line output increases more than 31% from the current system. The source throughput rate average value went up to 252 units per working hour in model 3 and show the effectiveness of the pick-to-light system as efficient storage equipment. Thus, overall result shows, the application of AGV and the pick-to-light system gave a large significant effect in the automotive assembly line. Moreover, the change of layout also shows a large significant improvement to the performance.

  6. Gold detector: modular CCD area detector for macromolecular crystallography

    Science.gov (United States)

    Naday, Istvan; Ross, Stephan W.; Kanyo, Miklos; Westbrook, Mary L.; Westbrook, Edwin M.; Phillips, Walter C.; Stanton, Martin J.; O'Mara, Daniel M.

    1995-04-01

    We have designed, fabricated, and tested a modular CCD area detector system for macromolecular crystallography at synchrotron x-ray sources, code-named the `gold' detector system. The sensitive area of the detector is 150 mm X 150 mm, with 3,072 X 3,072 pixel sampling, resulting in roughly a 50 micrometers pixel raster. The x-ray image formed on the face of the detector is converted to visible light by a thin phosphor layer. This image is transferred optically to nine CCD sensors by nine square fiberoptic tapers (one for each CCD), arranged in a 3 X 3 array. Each taper demagnifies the image by a factor of approximately 2. Each CCD has a 1,024 X 1,024 pixel raster and is read out through two independent data channels. After each x-ray exposure period the x-ray shutter is closed and the electronic image is digitized (16-bit) and read out in 1.8s. Alteratively, the image may be binned 2 X 2 during readout, resulting in a 1,536 X 1,536 raster of 100 micrometers pixels; this image can be read out in 0.4s. The CCD sensors are operated at -40 degree(s)C to reduce electronic noise. The detector is operated under full computer control: all operational parameters (readout rates, CCD temperature, etc.) can be adjusted from the console. The image data (18 MByte/image) are transferred via a fast VME system to a control processor and ultimately to disk storage. During April 1994 we carried out a complete set of measurements at the Stanford Synchrotron Radiation Laboratory (SSRL) for a full characterization of the gold detector. Characterization includes quantitative evaluation of the instrument's conversion gain (signal level/x-ray photon); detective quantum efficiency (DQE); point-spread function; sensitivity as a function of x-ray energy; geometrical distortion of images; spatial uniformity; read noise; and dark image and dark image noise. Characterization parameters derived from these measurements show that this detector will be extraordinarily valuable for macromolecular

  7. Fluorescent nanoparticles based on self-assembled pi-conjugated systems.

    Science.gov (United States)

    Kaeser, Adrien; Schenning, Albertus P H J

    2010-07-27

    pi-Conjugated molecules are interesting components to prepare fluorescent nanoparticles. From the use of polymer chains that form small aggregates in water to the self-assembly of small chromophoric segments into highly ordered structures, the preparation of these materials allows to develop systems with applications as sensors or biolabels. The potential functionalization of the nanoparticles can lead to specific probing. This progress report describes the recent advances in the preparation of such emittive organic nanoparticles.

  8. Development of 3-D Flow Analysis Code for Fuel Assembly using Unstructured Grid System

    Energy Technology Data Exchange (ETDEWEB)

    Myong, Hyon Kook; Kim, Jong Eun; Ahn, Jong Ki; Yang, Seung Yong [Kookmin Univ., Seoul (Korea, Republic of)

    2007-03-15

    The flow through a nuclear rod bundle with mixing vanes are very complex and required a suitable turbulence model to be predicted accurately. Final objective of this study is to develop a CFD code for fluid flow and heat transfer analysis in a nuclear fuel assembly using unstructured grid system. In order to develop a CFD code for fluid flow and heat transfer analysis in a nuclear fuel assembly using unstructured grid system, the following researches are made: - Development of numerical algorithm for CFD code's solver - Grid and geometric connectivity data - Development of software(PowerCFD code) for fluid flow and heat transfer analysis in a nuclear fuel assembly using unstructured grid system - Modulation of software(PowerCFD code) - Development of turbulence model - Development of analysis module of RANS/LES hybrid models - Analysis of turbulent flow and heat transfer - Basic study on LES analysis - Development of main frame on pre/post processors based on GUI - Algorithm for fully-developed flow.

  9. Fiber-Based, Injection-Molded Optofluidic Systems: Improvements in Assembly and Applications

    Directory of Open Access Journals (Sweden)

    Marco Matteucci

    2015-12-01

    Full Text Available We present a method to fabricate polymer optofluidic systems by means of injection molding that allow the insertion of standard optical fibers. The chip fabrication and assembly methods produce large numbers of robust optofluidic systems that can be easily assembled and disposed of, yet allow precise optical alignment and improve delivery of optical power. Using a multi-level chip fabrication process, complex channel designs with extremely vertical sidewalls, and dimensions that range from few tens of nanometers to hundreds of microns can be obtained. The technology has been used to align optical fibers in a quick and precise manner, with a lateral alignment accuracy of 2.7 ± 1.8 μm. We report the production, assembly methods, and the characterization of the resulting injection-molded chips for Lab-on-Chip (LoC applications. We demonstrate the versatility of this technology by carrying out two types of experiments that benefit from the improved optical system: optical stretching of red blood cells (RBCs and Raman spectroscopy of a solution loaded into a hollow core fiber. The advantages offered by the presented technology are intended to encourage the use of LoC technology for commercialization and educational purposes.

  10. Assembly and Characterization of a Prototype Laser-Optical Firing System

    Energy Technology Data Exchange (ETDEWEB)

    Morelli, Gregg L

    2009-08-03

    The design, assembly and characterization of the latest generation of a small, ruggedized laser-optical firing system will be discussed. This work builds upon earlier results in an effort to continue the development of robust fiber-coupled laseroptical firing systems.[1][2] This newest prototype strives to improve on earlier designs, while continuing to utilize many of the environmentally proven opto-mechanical sub-assemblies.[2][3] One area of improvement involves the implementation of a second optical safing and arming component. Several additional design improvements were also incorporated to address shortcomings uncovered during environmental testing.[4][5] These tests and the subsequent failure analysis were performed at the laser sub-system level. Four identical prototypes were assembled and characterized. The performance of the units were evaluated by comparing a number of parameters including laser output energy, slope efficiency, beam divergence, spatial intensity profile, fiber injection and splitter-coupler transmission efficiency. Other factors evaluated were the ease of alignment, repeatability of the alignment process and the fabrication of the fiberoptical cables. The experimentally obtained results will be compared and contrasted to the performance of earlier prototypes.

  11. Concept and implementation of an agent-based control architecture for a cyber-physical assembly system

    Directory of Open Access Journals (Sweden)

    Müller Rainer

    2016-01-01

    Full Text Available Today’s production companies are challenged with: the assembly of different product variants with lot size of one on a single assembly line and the increase of product variants. The implementation of reconfigurable assembly systems with a modular design is a solution, which allows a flexible adaptation to different product variants. However, handling different assembly modules via specific communication protocols is limited by the current centralized control concepts. Therefore, this paper presents a concept for an agent-based control architecture. This concept uses coherent information starting from the planning process of the assembly system until the system is put into operation allowing a decentralized control. The decentralized agents in each station act as mediators between the modules and the assembly memory database enabling the product autonomous control throughout the assembly system. Moreover, the agent manages the data transfer for the modules with different specific syntaxes via respective communication protocols since a standardized communication protocol does not exist in industry. The concept is verified in a test assembly line for the production of small electronic components.

  12. Synthesis and characterization of macromolecular layers grafted to polymer surfaces

    Science.gov (United States)

    Burtovyy, Oleksandr

    The composition and behavior of surfaces and interfaces play a pivotal role in dictating the overall efficiency of the majority of polymeric materials and devices. Surface properties of the materials can be altered using surface modification techniques. It is necessary to highlight that successful methods of surface modification should affect only the upper layer of the polymer material without changing bulk properties. The processes must introduce new functionalities to the surface, optimize surface roughness, lubrication, hydrophobicity, hydrophilicity, adhesion, conductivity, and/or biocompatibility. Research presented in this dissertation is dedicated to the synthesis, characterization, and application of thin macromolecular layers anchored to polymer substrates. Specifically, attachment of functional polymers via a "grafting to" approach has been extensively studied using PET and nylon model substrates. First, poly(glycidyl methacrylate) was used to introduce permanent functionalities to the model substrates by anchoring it to model films. Then, three different functional polymers were grafted on top of the previous layer. As one part of this study, the temperature and time dependence of grafting functional layers were studied. The surface coverage by hydrophobic polymer was determined from experimental data and predicted by a model. In general, the model has a high degree of predictive capability. Next, surface modification of polymeric fibers and membranes is presented as an important application of the polymer thin layers targeted in the study. Specifically, the procedures developed for surface modification of model substrates was employed for modification of PET, nylon, and cotton fabrics as well as PET track-etched membranes. Since epoxy groups are highly reactive in various chemical reactions, the approach becomes virtually universal, allowing both various surfaces and end-functionalized macromolecules to be used in the grafted layer synthesis. PET

  13. Research on multi - channel interactive virtual assembly system for power equipment under the “VR+” era

    Science.gov (United States)

    Ren, Yilong; Duan, Xitong; Wu, Lei; He, Jin; Xu, Wu

    2017-06-01

    With the development of the “VR+” era, the traditional virtual assembly system of power equipment has been unable to satisfy our growing needs. In this paper, based on the analysis of the traditional virtual assembly system of electric power equipment and the application of VR technology in the virtual assembly system of electric power equipment in our country, this paper puts forward the scheme of establishing the virtual assembly system of power equipment: At first, we should obtain the information of power equipment, then we should using OpenGL and multi texture technology to build 3D solid graphics library. After the completion of three-dimensional modeling, we can use the dynamic link library DLL package three-dimensional solid graphics generation program to realize the modularization of power equipment model library and power equipment model library generated hidden algorithm. After the establishment of 3D power equipment model database, we set up the virtual assembly system of 3D power equipment to separate the assembly operation of the power equipment from the space. At the same time, aiming at the deficiency of the traditional gesture recognition algorithm, we propose a gesture recognition algorithm based on improved PSO algorithm for BP neural network data glove. Finally, the virtual assembly system of power equipment can really achieve multi-channel interaction function.

  14. Macromolecular networks and intelligence in microorganisms

    Directory of Open Access Journals (Sweden)

    Hans V Westerhoff

    2014-07-01

    Full Text Available Living organisms persist by virtue of complex interactions among many components organized into dynamic, environment-responsive networks that span multiple scales and dimensions. Biological networks constitute a type of Information and Communication Technology (ICT: they receive information from the outside and inside of cells, integrate and interpret this information, and then activate a response. Biological networks enable molecules within cells, and even cells themselves, to communicate with each other and their environment. We have become accustomed to associating brain activity – particularly activity of the human brain – with a phenomenon we call intelligence. Yet, four billion years of evolution could have selected networks with topologies and dynamics that confer traits analogous to this intelligence, even though they were outside the intercellular networks of the brain. Here, we explore how macromolecular networks in microbes confer intelligent characteristics, such as memory, anticipation, adaptation and reflection and we review current understanding of how network organization reflects the type of intelligence required for the environments in which they were selected. We propose that, if we were to leave terms such as human and brain out of the defining features of intelligence, all forms of life – from microbes to humans – exhibit some or all characteristics consistent with intelligence. We then review advances in genome-wide data production and analysis, especially in microbes, that provide a lens into microbial intelligence and propose how the insights derived from quantitatively characterizing biomolecular networks may enable synthetic biologists to create intelligent molecular networks for biotechnology, possibly generating new forms of intelligence, first in silico and then in vivo.

  15. Nuclear reactor fuel assembly duct-tube-to-inlet-nozzle attachment system

    Science.gov (United States)

    Christiansen, David W.; Smith, Bob G.

    1982-01-01

    A reusable system for removably attaching the lower end 21 of a nuclear reactor fuel assembly duct tube to an upper end 11 of a nuclear reactor fuel assembly inlet nozzle. The duct tube's lower end 21 has sides terminating in locking tabs 22 which end in inwardly-extending flanges 23. The flanges 23 engage recesses 13 in the top section 12 of the inlet nozzle's upper end 11. A retaining collar 30 slides over the inlet nozzle's upper end 11 to restrain the flanges 23 in the recesses 13. A locking nut 40 has an inside threaded portion 41 which engages an outside threaded portion 15 of the inlet nozzle's upper end 11 to secure the retaining collar 30 against protrusions 24 on the duct tube's sides.

  16. Experimental investigation of a two-phase closed thermosyphon assembly for passive containment cooling system

    Energy Technology Data Exchange (ETDEWEB)

    Nam, Kyung Ho [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of); Kim, Sang Nyung [Kyunghee Univ., Gyeonggi-do (Korea, Republic of)

    2017-06-15

    After the Fukushima accident, increasing interest has been raised in passive safety systems that maintain the integrity of the containment building. To improve the reliability and safety of nuclear power plants, long-term passive cooling concepts have been developed for advanced reactors. In a previous study, the proposed design was based on an ordinary cylindrical Two-Phase Closed Thermosyphon (TPCT). The exact assembly size and number of TPCTs should be elaborated upon through accurate calculations based on experiments. While the ultimate goal is to propose an effective MPHP design for the PCCS and experimentally verify its performance, a TPCT assembly that was manufactured based on the conceptual design in this paper was tested.

  17. Golden Gate Assembly system dedicated to complex pathway manipulation in Yarrowia lipolytica.

    Science.gov (United States)

    Celińska, Ewelina; Ledesma-Amaro, Rodrigo; Larroude, Macarena; Rossignol, Tristan; Pauthenier, Cyrille; Nicaud, Jean-Marc

    2017-03-01

    In this study, we have adopted Golden Gate modular cloning strategy to develop a robust and versatile DNA assembly platform for the nonconventional yeast Yarrowia lipolytica. To this end, a broad set of destination vectors and interchangeable building blocks have been constructed. The DNA modules were assembled on a scaffold of predesigned 4 nt overhangs covering three transcription units (each bearing promoter, gene and terminator), selection marker gene and genomic integration targeting sequences, constituting altogether thirteen elements. Previously validated DNA modules (regulatory elements and selection markers) were adopted as the Golden Gate bricks. The system's operability was demonstrated based on synthetic pathway of carotenoid production. This technology greatly enriches a molecular biology toolbox dedicated to this industrially relevant microorganism enabling fast combinatorial cloning of complex synthetic pathways. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  18. Macromolecular Crystallography for Synthetic Abiological Molecules: Combining xMDFF and PHENIX for Structure Determination of Cyanostar Macrocycles.

    Science.gov (United States)

    Singharoy, Abhishek; Venkatakrishnan, Balasubramanian; Liu, Yun; Mayne, Christopher G; Lee, Semin; Chen, Chun-Hsing; Zlotnick, Adam; Schulten, Klaus; Flood, Amar H

    2015-07-15

    Crystal structure determination has long provided insight into structure and bonding of small molecules. When those same small molecules are designed to come together in multimolecular assemblies, such as in coordination cages, supramolecular architectures and organic-based frameworks, their crystallographic characteristics closely resemble biological macromolecules. This resemblance suggests that biomacromolecular refinement approaches be used for structure determination of abiological molecular complexes that arise in an aggregate state. Following this suggestion we investigated the crystal structure of a pentagonal macrocycle, cyanostar, by means of biological structure analysis methods and compared results to traditional small molecule methods. Cyanostar presents difficulties seen in supramolecular crystallography including whole molecule disorder and highly flexible solvent molecules sitting in macrocyclic and intermolecule void spaces. We used the force-field assisted refinement method, molecular dynamics flexible fitting algorithm for X-ray crystallography (xMDFF), along with tools from the macromolecular structure determination suite PHENIX. We found that a standard implementation of PHENIX, namely one without xMDFF, either fails to produce a solution by molecular replacement alone or produces an inaccurate structure when using generic geometry restraints, even at a very high diffraction data resolution of 0.84 Å. The problems disappear when taking advantage of xMDFF, which applies an optimized force field to realign molecular models during phasing by providing accurate restraints. The structure determination for this model system shows excellent agreement with the small-molecule methods. Therefore, the joint xMDFF-PHENIX refinement protocol provides a new strategy that uses macromolecule methods for structure determination of small molecules and their assemblies.

  19. Overview of CMS robotic silicon module assembly hardware based on Aerotech Gantry Positioning system.

    CERN Multimedia

    Honma, Alan

    1999-01-01

    The goal of the robotic silicon module assembly pilot project is to fully automate the gluing and pick and placement of silicon sensors and front-end hybrid onto a carbon-fibre frame. The basis for thesystem is the Aerotech Gantry Positioning System (AGS10000) machineshown in the centre of the picture. To the left is the PC which contains the controller card and runs the user interface. To the rightis the rack of associated electronics which interfaces with the CERNbuilt tooling and vacuum chuck system.

  20. Arrangement of constituencies in electoral system used for the elections to the National Assembly of Slovenia

    Directory of Open Access Journals (Sweden)

    Boštjan Rogelj

    2012-12-01

    Full Text Available The frst part of this article presents some aspects of creating constituencies in electoral systems based on proportional electoral formula. The second part is an analysis of the con-stituencies in the electoral system that selects representatives for the National Assembly. Emphasized are the factors that engendered Slovenia’s specifc three-level organization of constituencies. The last part is an analysis of the organization of constituencies and electoral districts in light of fulflling the principles of voter equality, homogeneity and compactness.

  1. Hybrid Materials Prepared from Polymers and Self-assembled Systems by Physical Processes

    Institute of Scientific and Technical Information of China (English)

    Jean-Michel; Guenet

    2007-01-01

    1 Results A new type of hybrid materails prepared from ternary systems polymer/bicopper organic complex/solvent is presented.Each binary system displays differing types of behaviour: The polymer solutions produce thermoreversible gels while the bicopper organic complex (designated as CuS8) forms randomly-dispersed,self-assembling threads in organic solvents (See Fig.1(a),(b)).Fig.1 The CuS8 and ips thermoreversible gels Thermoreversible gels possess a fibrillar morphology with a typical mesh size ra...

  2. Development of next-generation macromolecular drugs based on the EPR effect: challenges and pitfalls.

    Science.gov (United States)

    Nakamura, Hideaki; Fang, Jun; Jun, Fang; Maeda, Hiroshi

    2015-01-01

    A major problem with conventional antitumor therapeutics is nonselective delivery of cytotoxic drugs to normal vital organs and tissues but little delivery to tumor tissues. Here, the authors describe the tumor selective delivery of antitumor drugs by taking advantage of nano-sized drugs and the means to augment it further. Based on the enhanced permeability and retention (EPR) effect, the mechanism for more efficient universal tumor delivery using macromolecular drugs to cover wider tumor types than single molecular target is discussed. Unique properties of solid tumor vasculature in the tumor tissue are discussed, especially leakiness of the blood vessels and factors involved and impaired clearance of macromolecular drugs from the tumor interstitium via the lymphatic system. The criteria for such macromolecular drugs or nanomedicines for effective accumulation at tumor sites is commented on as well as the importance of long plasma retention time of such drugs and a need to release active principles from nanoparticles at target sites. Methods to augment the EPR effect and tumor delivery (2 - 3 times) and its application to photodynamic therapy are also discussed. Tumor selective delivery of antitumor drugs based on the EPR effect can be accomplished and augmented by modulating the tumor environment. This methodology is favorable not only for tumor therapy but also for tumor imaging.

  3. Macromolecular Antioxidants and Dietary Fiber in Edible Seaweeds.

    Science.gov (United States)

    Sanz-Pintos, Nerea; Pérez-Jiménez, Jara; Buschmann, Alejandro H; Vergara-Salinas, José Rodrigo; Pérez-Correa, José Ricardo; Saura-Calixto, Fulgencio

    2017-02-01

    Seaweeds are rich in different bioactive compounds with potential uses in drugs, cosmetics and the food industry. The objective of this study was to analyze macromolecular antioxidants or nonextractable polyphenols, in several edible seaweed species collected in Chile (Gracilaria chilensis, Callophyllis concepcionensis, Macrocystis pyrifera, Scytosyphon lomentaria, Ulva sp. and Enteromorpha compressa), including their 1st HPLC characterization. Macromolecular antioxidants are commonly ignored in studies of bioactive compounds. They are associated with insoluble dietary fiber and exhibit significant biological activity, with specific features that are different from those of both dietary fiber and extractable polyphenols. We also evaluated extractable polyphenols and dietary fiber, given their relationship with macromolecular antioxidants. Our results show that macromolecular antioxidants are a major polyphenol fraction (averaging 42% to total polyphenol content), with hydroxycinnamic acids, hydroxybenzoic acids and flavonols being the main constituents. This fraction also showed remarkable antioxidant capacity, as determined by 2 complementary assays. The dietary fiber content was over 50% of dry weight, with some samples exhibiting the target proportionality between soluble and insoluble dietary fiber for adequate nutrition. Overall, our data show that seaweed could be an important source of commonly ignored macromolecular antioxidants. © 2017 Institute of Food Technologists®.

  4. Simulating New Drop Test Vehicles and Test Techniques for the Orion CEV Parachute Assembly System

    Science.gov (United States)

    Morris, Aaron L.; Fraire, Usbaldo, Jr.; Bledsoe, Kristin J.; Ray, Eric; Moore, Jim W.; Olson, Leah M.

    2011-01-01

    The Crew Exploration Vehicle Parachute Assembly System (CPAS) project is engaged in a multi-year design and test campaign to qualify a parachute recovery system for human use on the Orion Spacecraft. Test and simulation techniques have evolved concurrently to keep up with the demands of a challenging and complex system. The primary simulations used for preflight predictions and post-test data reconstructions are Decelerator System Simulation (DSS), Decelerator System Simulation Application (DSSA), and Drop Test Vehicle Simulation (DTV-SIM). The goal of this paper is to provide a roadmap to future programs on the test technique challenges and obstacles involved in executing a large-scale, multi-year parachute test program. A focus on flight simulation modeling and correlation to test techniques executed to obtain parachute performance parameters are presented.

  5. A translator writing system for microcomputer high-level languages and assemblers

    Science.gov (United States)

    Collins, W. R.; Knight, J. C.; Noonan, R. E.

    1980-01-01

    In order to implement high level languages whenever possible, a translator writing system of advanced design was developed. It is intended for routine production use by many programmers working on different projects. As well as a fairly conventional parser generator, it includes a system for the rapid generation of table driven code generators. The parser generator was developed from a prototype version. The translator writing system includes various tools for the management of the source text of a compiler under construction. In addition, it supplies various default source code sections so that its output is always compilable and executable. The system thereby encourages iterative enhancement as a development methodology by ensuring an executable program from the earliest stages of a compiler development project. The translator writing system includes PASCAL/48 compiler, three assemblers, and two compilers for a subset of HAL/S.

  6. A new paradigm for macromolecular crystallography beamlines derived from high-pressure methodology and results

    Energy Technology Data Exchange (ETDEWEB)

    Fourme, Roger, E-mail: roger.fourme@synchrotron-soleil.fr [Synchrotron SOLEIL, BP 48, Saint Aubin, 91192 Gif-sur-Yvette (France); Girard, Eric [IBS (UMR 5075 CEA-CNRS-UJF-PSB), 41 rue Jules Horowitz, 38027 Grenoble Cedex (France); Dhaussy, Anne-Claire [CRISMAT, ENSICAEN, 6 Boulevard du Maréchal Juin, 14000 Caen (France); Medjoubi, Kadda [Synchrotron SOLEIL, BP 48, Saint Aubin, 91192 Gif-sur-Yvette (France); Prangé, Thierry [LCRB (UMR 8015 CNRS), Université Paris Descartes, Faculté de Pharmacie, 4 avenue de l’Observatoire, 75270 Paris (France); Ascone, Isabella [ENSCP (UMR CNRS 7223), 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05 (France); Mezouar, Mohamed [ESRF, BP 220, 38043 Grenoble (France); Kahn, Richard [IBS (UMR 5075 CEA-CNRS-UJF-PSB), 41 rue Jules Horowitz, 38027 Grenoble Cedex (France)

    2011-01-01

    Macromolecular crystallography at high pressure (HPMX) is a mature technique. Shorter X-ray wavelengths increase data collection efficiency on cryocooled crystals. Extending applications and exploiting spin-off of HPMX will require dedicated synchrotron radiation beamlines based on a new paradigm. Biological structures can now be investigated at high resolution by high-pressure X-ray macromolecular crystallography (HPMX). The number of HPMX studies is growing, with applications to polynucleotides, monomeric and multimeric proteins, complex assemblies and even a virus capsid. Investigations of the effects of pressure perturbation have encompassed elastic compression of the native state, study of proteins from extremophiles and trapping of higher-energy conformers that are often of biological interest; measurements of the compressibility of crystals and macromolecules were also performed. HPMX results were an incentive to investigate short and ultra-short wavelengths for standard biocrystallography. On cryocooled lysozyme crystals it was found that the data collection efficiency using 33 keV photons is increased with respect to 18 keV photons. This conclusion was extended from 33 keV down to 6.5 keV by exploiting previously published data. To be fully exploited, the potential of higher-energy photons requires detectors with a good efficiency. Accordingly, a new paradigm for MX beamlines was suggested, using conventional short and ultra-short wavelengths, aiming at the collection of very high accuracy data on crystals under standard conditions or under high pressure. The main elements of such beamlines are outlined.

  7. De novo assembly of the Carcinus maenas transcriptome and characterization of innate immune system pathways.

    Science.gov (United States)

    Verbruggen, Bas; Bickley, Lisa K; Santos, Eduarda M; Tyler, Charles R; Stentiford, Grant D; Bateman, Kelly S; van Aerle, Ronny

    2015-06-16

    The European shore crab, Carcinus maenas, is used widely in biomonitoring, ecotoxicology and for studies into host-pathogen interactions. It is also an important invasive species in numerous global locations. However, the genomic resources for this organism are still sparse, limiting research progress in these fields. To address this resource shortfall we produced a C. maenas transcriptome, enabled by the progress in next-generation sequencing technologies, and applied this to assemble information on the innate immune system in this species. We isolated and pooled RNA for twelve different tissues and organs from C. maenas individuals and sequenced the RNA using next generation sequencing on an Illumina HiSeq 2500 platform. After de novo assembly a transcriptome was generated encompassing 212,427 transcripts (153,699 loci). The transcripts were filtered, annotated and characterised using a variety of tools (including BLAST, MEGAN and RSEM) and databases (including NCBI, Gene Ontology and KEGG). There were differential patterns of expression for between 1,223 and 2,741 transcripts across tissues and organs with over-represented Gene Ontology terms relating to their specific function. Based on sequence homology to immune system components in other organisms, we show both the presence of transcripts for a series of known pathogen recognition receptors and response proteins that form part of the innate immune system, and transcripts representing the RNAi, Toll-like receptor signalling, IMD and JAK/STAT pathways. We have produced an assembled transcriptome for C. maenas that provides a significant molecular resource for wide ranging studies in this species. Analysis of the transcriptome has revealed the presence of a series of known targets and functional pathways that form part of their innate immune system and illustrate tissue specific differences in their expression patterns.

  8. Development of numerical simulation system for thermal-hydraulic analysis in fuel assembly of sodium-cooled fast reactor

    Energy Technology Data Exchange (ETDEWEB)

    Ohshima, Hiroyuki; Uwaba, Tomoyuki [Japan Atomic Energy Agency (4002 Narita, O-arai, Ibaraki 311-1393, Japan) (Japan); Hashimoto, Akihiko; Imai, Yasutomo [NDD Corporation (1-1-6 Jounan, Mito, Ibaraki 310-0803, Japan) (Japan); Ito, Masahiro [NESI Inc. (4002 Narita, O-arai, Ibaraki 311-1393, Japan) (Japan)

    2015-12-31

    A numerical simulation system, which consists of a deformation analysis program and three kinds of thermal-hydraulics analysis programs, is being developed in Japan Atomic Energy Agency in order to offer methodologies to clarify thermal-hydraulic phenomena in fuel assemblies of sodium-cooled fast reactors under various operating conditions. This paper gives the outline of the system and its applications to fuel assembly analyses as a validation study.

  9. RECENT ADVANCES IN MACROMOLECULAR HYDRODYNAMIC MODELING

    Science.gov (United States)

    Aragon, Sergio R.

    2010-01-01

    The modern implementation of the boundary element method (S.R. Aragon, J. Comput. Chem. 25(2004)1191–12055) has ushered unprecedented accuracy and precision for the solution of the Stokes equations of hydrodynamics with stick boundary conditions. This article begins by reviewing computations with the program BEST of smooth surface objects such as ellipsoids, the dumbbell, and cylinders that demonstrate that the numerical solution of the integral equation formulation of hydrodynamics yields very high precision and accuracy. When BEST is used for macromolecular computations, the limiting factor becomes the definition of the molecular hydrodynamic surface and the implied effective solvation of the molecular surface. Studies on 49 different proteins, ranging in molecular weight from 9 to over 400 kDa, have shown that a model using a 1.1 A thick hydration layer describes all protein transport properties very well for the overwhelming majority of them. In addition, this data implies that the crystal structure is an excellent representation of the average solution structure for most of them. In order to investigate the origin of a handful of significant discrepancies in some multimeric proteins (over −20% observed in the intrinsic viscosity), the technique of Molecular Dynamics simulation (MD) has been incorporated into the research program. A preliminary study of dimeric α-chymotrypsin using approximate implicit water MD is presented. In addition I describe the successful validation of modern protein force fields, ff03 and ff99SB, for the accurate computation of solution structure in explicit water simulation by comparison of trajectory ensemble average computed transport properties with experimental measurements. This work includes small proteins such as lysozyme, ribonuclease and ubiquitin using trajectories around 10 ns duration. We have also studied a 150 kDa flexible monoclonal IgG antibody, trastuzumab, with multiple independent trajectories encompassing over

  10. Complex Macromolecular Architectures by Living Cationic Polymerization

    KAUST Repository

    Alghamdi, Reem D.

    2015-05-01

    Poly (vinyl ether)-based graft polymers have been synthesized by the combination of living cationic polymerization of vinyl ethers with other living or controlled/ living polymerization techniques (anionic and ATRP). The process involves the synthesis of well-defined homopolymers (PnBVE) and co/terpolymers [PnBVE-b-PCEVE-b-PSiDEGVE (ABC type) and PSiDEGVE-b-PnBVE-b-PSiDEGVE (CAC type)] by sequential living cationic polymerization of n-butyl vinyl ether (nBVE), 2-chloroethyl vinyl ether (CEVE) and tert-butyldimethylsilyl ethylene glycol vinyl ether (SiDEGVE), using mono-functional {[n-butoxyethyl acetate (nBEA)], [1-(2-chloroethoxy) ethyl acetate (CEEA)], [1-(2-(2-(t-butyldimethylsilyloxy)ethoxy) ethoxy) ethyl acetate (SiDEGEA)]} or di-functional [1,4-cyclohexanedimethanol di(1-ethyl acetate) (cHMDEA), (VEMOA)] initiators. The living cationic polymerizations of those monomers were conducted in hexane at -20 0C using Et3Al2Cl3 (catalyst) in the presence of 1 M AcOEt base.[1] The PCEVE segments of the synthesized block terpolymers were then used to react with living macroanions (PS-DPE-Li; poly styrene diphenyl ethylene lithium) to afford graft polymers. The quantitative desilylation of PSiDEGVE segments by n-Bu4N+F- in THF at 0 °C led to graft co- and terpolymers in which the polyalcohol is the outer block. These co-/terpolymers were subsequently subjected to “grafting-from” reactions by atom transfer radical polymerization (ATRP) of styrene to afford more complex macromolecular architectures. The base assisted living cationic polymerization of vinyl ethers were also used to synthesize well-defined α-hydroxyl polyvinylether (PnBVE-OH). The resulting polymers were then modified into an ATRP macro-initiator for the synthesis of well-defined block copolymers (PnBVE-b-PS). Bifunctional PnBVE with terminal malonate groups was also synthesized and used as a precursor for more complex architectures such as H-shaped block copolymer by “grafting-from” or

  11. Assembly and Testing of a Radioisotope Power System for the New Horizons Spacecraft

    Energy Technology Data Exchange (ETDEWEB)

    Kenneth E. Rosenberg; Stephen G. Johnson

    2006-06-01

    The Idaho National Laboratory (INL) recently fueled and assembled a radioisotope power system (RPS) that was used upon the New Horizons spacecraft which was launched in January 2006. New Horizons is the first mission to the last planet - the initial reconnaissance of Pluto-Charon and the Kuiper Belt, exploring the mysterious worlds at the edge of our solar system. The RPS otherwise known as a "space battery" converts thermal heat into electrical energy. The thermal heat source contains plutonium dioxide in the form of ceramic pellets encapsulated in iridium metal. The space battery was assembled in a new facility at the Idaho National Laboratory site near Idaho Falls, Idaho. The new facility has all the fueling and testing capabilities including the following: the ability to handle all the shipping containers currently certified to ship Pu-238, the ability to fuel a variety of RPS designs, the ability to perform vibrational testing to simulate transportation and launch environments, welding systems, a center of mass determination device, and various other support systems.

  12. NASA Wrangler: Automated Cloud-Based Data Assembly in the RECOVER Wildfire Decision Support System

    Science.gov (United States)

    Schnase, John; Carroll, Mark; Gill, Roger; Wooten, Margaret; Weber, Keith; Blair, Kindra; May, Jeffrey; Toombs, William

    2017-01-01

    NASA Wrangler is a loosely-coupled, event driven, highly parallel data aggregation service designed to take advantageof the elastic resource capabilities of cloud computing. Wrangler automatically collects Earth observational data, climate model outputs, derived remote sensing data products, and historic biophysical data for pre-, active-, and post-wildfire decision making. It is a core service of the RECOVER decision support system, which is providing rapid-response GIS analytic capabilities to state and local government agencies. Wrangler reduces to minutes the time needed to assemble and deliver crucial wildfire-related data.

  13. Control of Macromolecular Architectures for Renewable Polymers: Case Studies

    Science.gov (United States)

    Tang, Chuanbing

    The development of sustainable polymers from nature biomass is growing, but facing fierce competition from existing petrochemical-based counterparts. Controlling macromolecular architectures to maximize the properties of renewable polymers is a desirable approach to gain advantages. Given the complexity of biomass, there needs special consideration other than traditional design. In the presentation, I will talk about a few case studies on how macromolecular architectures could tune the properties of sustainable bioplastics and elastomers from renewable biomass such as resin acids (natural rosin) and plant oils.

  14. Macromolecular crystallography beamline X25 at the NSLS.

    Science.gov (United States)

    Héroux, Annie; Allaire, Marc; Buono, Richard; Cowan, Matthew L; Dvorak, Joseph; Flaks, Leon; Lamarra, Steven; Myers, Stuart F; Orville, Allen M; Robinson, Howard H; Roessler, Christian G; Schneider, Dieter K; Shea-McCarthy, Grace; Skinner, John M; Skinner, Michael; Soares, Alexei S; Sweet, Robert M; Berman, Lonny E

    2014-05-01

    Beamline X25 at the NSLS is one of the five beamlines dedicated to macromolecular crystallography operated by the Brookhaven National Laboratory Macromolecular Crystallography Research Resource group. This mini-gap insertion-device beamline has seen constant upgrades for the last seven years in order to achieve mini-beam capability down to 20 µm × 20 µm. All major components beginning with the radiation source, and continuing along the beamline and its experimental hutch, have changed to produce a state-of-the-art facility for the scientific community.

  15. Macromolecular crystallography beamline X25 at the NSLS

    Science.gov (United States)

    Héroux, Annie; Allaire, Marc; Buono, Richard; Cowan, Matthew L.; Dvorak, Joseph; Flaks, Leon; LaMarra, Steven; Myers, Stuart F.; Orville, Allen M.; Robinson, Howard H.; Roessler, Christian G.; Schneider, Dieter K.; Shea-McCarthy, Grace; Skinner, John M.; Skinner, Michael; Soares, Alexei S.; Sweet, Robert M.; Berman, Lonny E.

    2014-01-01

    Beamline X25 at the NSLS is one of the five beamlines dedicated to macromolecular crystallography operated by the Brookhaven National Laboratory Macromolecular Crystallography Research Resource group. This mini-gap insertion-device beamline has seen constant upgrades for the last seven years in order to achieve mini-beam capability down to 20 µm × 20 µm. All major components beginning with the radiation source, and continuing along the beamline and its experimental hutch, have changed to produce a state-of-the-art facility for the scientific community. PMID:24763654

  16. Simulation and development of a multi-leg homogeniser concentrating assembly for concentrated photovoltaic (CPV) system with electrical rating analysis

    KAUST Repository

    Burhan, Muhammad

    2016-03-09

    Concentrated photovoltaic (CPV) system utilizing multi-junction solar cells, is the main focus for current research, offering highest efficiency among all photovoltaic systems. The main aspect of CPV system is the design and performance of concentrating assembly, as it determines the performance of whole CPV system. However, the conventional design of CPV concentrating assembly dedicates one concentrator for each solar cell, in which single concentrator is capable to concentrate solar radiation onto single solar cell. This paper proposes a novel concentrating assembly for CPV system, which is designed to concentrate solar radiation onto four multi-junction solar cells with a single set of concentrators. The proposed design not only can reduce the number of concentrators and assembly efforts for CPV systems, but also achieved an acceptance angle of 1°. In this paper, the proposed multi-leg homogeniser CPV concentrating assembly is designed, developed, experimentally tested and verified through ray tracing simulation. The paper also discuss the development of mini, precise and accurate but cost effective two axis solar tracker for CPV system, which can be installed at any location even at rooftop of residential buildings, unlike conventional large scale CPV systems. Moreover, through the electrical rating analysis of the developed CPV system, its performance can be accurately estimated in any region. © 2016 Elsevier Ltd. All rights reserved.

  17. INTRODUCTION: New trends in simulating colloids and self-assembling systems New trends in simulating colloids and self-assembling systems

    Science.gov (United States)

    Foffi, Giuseppe; Kahl, Gerhard

    2010-03-01

    relatively high number of contributions as an indicator that the topics presented at these workshops represent substantial scientific developments. The particular motivation to organize these two workshops came from the fact that experimental work in colloidal physics is advancing rapidly around the globe. In contrast, theoretical and simulation approaches to investigate the wide range of new and surprising physical phenomena of colloidal systems is lagging behind this experimental progress. This is the more deploring since theory and simulation might provide a more profound understanding of many phenomena in soft and bio-related physics, such as phase behaviour, self-assembly strategies, or rheological properties, to name but a few. Furthermore this insight might help to guide experiment to design new colloid-based materials with desired properties. The declared aim of the two workshops was thus to bring together scientists who have contributed in recent time to new developments in colloidal physics and to share and discuss their latest innovations. While CECAM workshops traditionally bring together scientists from the theoretical and simulator communities, from the very beginning the organizers considered it an indispensable necessity to invite experimentalists. And indeed, the organizers are happy to confirm that the participation of experimentalists, theoreticians, and simulators was highly fruitful and mutually inspiring: discussions between all communities did help to understand the possibilities and limitations imposed by experiment, theory, and simulations. Reuniting thus all forces, the workshop did contribute to a deeper understanding in colloidal physics and has helped to address future aspects that might lead to more applied problems of technological relevance. The first workshop, entitled 'Computer Simulation Approaches to Study Self-Assembly: From Patchy Nano-Colloids to Virus Capsides', (organized by Jonathan Doye—University Of Oxford, Ard A Louis

  18. Phototrophic Biofilm Assembly in Microbial-Mat-Derived Unicyanobacterial Consortia: Model Systems for the Study of Autotroph-Heterotroph Interactions

    Energy Technology Data Exchange (ETDEWEB)

    Cole, Jessica K.; Hutchison, Janine R.; Renslow, Ryan S.; Kim, Young-Mo; Chrisler, William B.; Engelmann, Heather E.; Dohnalkova, Alice; Hu, Dehong; Metz, Thomas O.; Fredrickson, Jim K.; Lindemann, Stephen R.

    2014-04-07

    Though microbial autotroph-heterotroph interactions influence biogeochemical cycles on a global scale, the diversity and complexity of natural systems and their intractability to in situ environmental manipulation makes elucidation of the principles governing these interactions challenging. Examination of primary succession during phototrophic biofilm assembly provides a robust means by which to elucidate the dynamics of such interactions and determine their influence upon recruitment and maintenance of phylogenetic and functional diversity in microbial communities. We isolated and characterized two unicyanobacterial consortia from the Hot Lake phototrophic mat, quantifying the structural and community composition of their assembling biofilms. The same heterotrophs were retained in both consortia and included members of Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes, taxa frequently reported as consorts of microbial photoautotrophs. Cyanobacteria led biofilm assembly, eventually giving way to a late heterotrophic bloom. The consortial biofilms exhibited similar patterns of assembly, with the relative abundances of members of Bacteroidetes and Alphaproteobacteria increasing and members of Gammaproteobacteria decreasing as colonization progressed. Despite similar trends in assembly at higher taxa, the consortia exhibited substantial differences in community structure at the species level. These similar patterns of assembly with divergent community structures suggest that, while similar niches are created by the metabolism of the cyanobacteria, the resultant webs of autotroph-heterotroph and heterotroph-heterotroph interactions driving metabolic exchange are specific to each primary producer. Altogether, our data support these Hot Lake unicyanobacterial consortia as generalizable model systems whose simplicity and tractability permit the deciphering of community assembly principles relevant to natural microbial communities.

  19. Analytical Kinematics and Coupled Vibrations Analysis of Mechanical System Operated by Solar Array Drive Assembly

    Science.gov (United States)

    Sattar, M.; Wei, C.; Jalali, A.; Sattar, R.

    2017-07-01

    To address the impact of solar array (SA) anomalies and vibrations on performance of precision space-based operations, it is important to complete its accurate jitter analysis. This work provides mathematical modelling scheme to approximate kinematics and coupled micro disturbance dynamics of rigid load supported and operated by solar array drive assembly (SADA). SADA employed in analysis provides a step wave excitation torque to activate the system. Analytical investigations into kinematics is accomplished by using generalized linear and Euler angle coordinates, applying multi-body dynamics concepts and transformations principles. Theoretical model is extended, to develop equations of motion (EoM), through energy method (Lagrange equation). The main emphasis is to research coupled frequency response by determining energies dissipated and observing dynamic behaviour of internal vibratory systems of SADA. The disturbance model captures discrete active harmonics of SADA, natural modes and vibration amplifications caused by interactions between active harmonics and structural modes of mechanical assembly. The proposed methodology can help to predict true micro disturbance nature of SADA operating rigid load. Moreover, performance outputs may be compared against actual mission requirements to assess precise spacecraft controller design to meet next space generation stringent accuracy goals.

  20. Managing bottlenecks in manual automobile assembly systems using discrete event simulation

    Directory of Open Access Journals (Sweden)

    Dewa, M.

    2013-08-01

    Full Text Available Batch model lines are quite handy when the demand for each product is moderate. However, they are characterised by high work-in-progress inventories, lost production time when changing over models, and reduced flexibility when it comes to altering production rates as product demand changes. On the other hand, mixed model lines can offer reduced work-in-progress inventory and increased flexibility. The object of this paper is to illustrate that a manual automobile assembling system can be optimised through managing bottlenecks by ensuring high workstation utilisation, reducing queue lengths before stations and reducing station downtime. A case study from the automobile industry is used for data collection. A model is developed through the use of simulation software. The model is then verified and validated before a detailed bottleneck analysis is conducted. An operational strategy is then proposed for optimal bottleneck management. Although the paper focuses on improving automobile assembly systems in batch mode, the methodology can also be applied in single model manual and automated production lines.

  1. Self-Assembly, Pattern Formation and Growth Phenomena in Nano-Systems

    CERN Document Server

    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...

  2. Analysis of sedimentation equilibrium distributions reflecting nonideal macromolecular associations.

    OpenAIRE

    Wills, Peter R.; Jacobsen, Michael P.; Winzor, Donald J.

    2000-01-01

    A rigorous statistical-mechanical approach is adopted to derive general quantitative expressions that allow for the effects of thermodynamic nonideality in equilibrium measurements reflecting interaction between dissimilar macromolecular reactants. An analytical procedure based on these expressions is then formulated for obtaining global estimates of equilibrium constants and the corresponding reference thermodynamic activities of the free reactants in each of several sedimentation equilibriu...

  3. Optimization of macromolecular prodrugs of the antitumor antibiotic adriamycin

    NARCIS (Netherlands)

    Hoes, C.J.T.; Potman, W.; Heeswijk, W.A.R.; Mud, J.; de Grooth, B.G.; Greve, Jan; Feijen, Jan

    1985-01-01

    In our earlier work [10] on aminoribosyl-bound prodrugs of adriamycin (ADR) using poly(α-l-glutamic acid) (PGA) grafted in high yield (90–100 mol.%) with various peptide spacers as a plasma-soluble macromolecular carrier we observed rather low cytotoxic activities in L1210 leukemia and B16 melanoma

  4. Efficient systemic DNA delivery to the tumor by self-assembled nanoparticle

    Science.gov (United States)

    Tang, Hailin; Xie, Xinhua; Guo, Jiaoli; Wei, Weidong; Wu, Minqing; Liu, Peng; Kong, Yanan; Yang, Lu; Hung, Mien-Chie; Xie, Xiaoming

    2014-01-01

    There are few delivery agents that could deliver gene with high efficiency and low toxicity, especially for animal experiments. Therefore, creating vectors with good delivery efficiency and safety profile is a meaningful work. We have developed a self-assembled gene delivery system (XM001), which can more efficiently deliver DNA to multiple cell lines and breast tumor, as compared to commercial delivery agents. In addition, systemically administrated XM001-BikDD (BikDD is a mutant form of proapoptotic gene Bik) significantly inhibited the growth of human breast cancer cells and prolonged the life span in implanted nude mice. This study demonstrates that XM001 is an efficient and widespread transfection agent, which could be a promising tumor delivery vector for cancer targeted therapy.

  5. Mechatronic Development and Vision Feedback Control of a Nanorobotics Manipulation System inside SEM for Nanodevice Assembly

    Directory of Open Access Journals (Sweden)

    Zhan Yang

    2016-09-01

    Full Text Available Carbon nanotubes (CNT have been developed in recent decades for nanodevices such as nanoradios, nanogenerators, carbon nanotube field effect transistors (CNTFETs and so on, indicating that the application of CNTs for nanoscale electronics may play a key role in the development of nanotechnology. Nanorobotics manipulation systems are a promising method for nanodevice construction and assembly. For the purpose of constructing three-dimensional CNTFETs, a nanorobotics manipulation system with 16 DOFs was developed for nanomanipulation of nanometer-scale objects inside the specimen chamber of a scanning electron microscope (SEM. Nanorobotics manipulators are assembled into four units with four DOFs (X-Y-Z-θ individually. The rotational one is actuated by a picomotor. That means a manipulator has four DOFs including three linear motions in the X, Y, Z directions and a 360-degree rotational one (X-Y-Z-θ stage, θ is along the direction rotating with X or Y axis. Manipulators are actuated by picomotors with better than 30 nm linear resolution and <1 micro-rad rotary resolution. Four vertically installed AFM cantilevers (the axis of the cantilever tip is vertical to the axis of electronic beam of SEM served as the end-effectors to facilitate the real-time observation of the operations. A series of kinematic derivations of these four manipulators based on the Denavit-Hartenberg (D-H notation were established. The common working space of the end-effectors is 2.78 mm by 4.39 mm by 6 mm. The manipulation strategy and vision feedback control for multi-manipulators operating inside the SEM chamber were been discussed. Finally, application of the designed nanorobotics manipulation system by successfully testing of the pickup-and-place manipulation of an individual CNT onto four probes was described. The experimental results have shown that carbon nanotubes can be successfully picked up with this nanorobotics manipulation system.

  6. Mechatronic Development and Vision Feedback Control of a Nanorobotics Manipulation System inside SEM for Nanodevice Assembly.

    Science.gov (United States)

    Yang, Zhan; Wang, Yaqiong; Yang, Bin; Li, Guanghui; Chen, Tao; Nakajima, Masahiro; Sun, Lining; Fukuda, Toshio

    2016-09-14

    Carbon nanotubes (CNT) have been developed in recent decades for nanodevices such as nanoradios, nanogenerators, carbon nanotube field effect transistors (CNTFETs) and so on, indicating that the application of CNTs for nanoscale electronics may play a key role in the development of nanotechnology. Nanorobotics manipulation systems are a promising method for nanodevice construction and assembly. For the purpose of constructing three-dimensional CNTFETs, a nanorobotics manipulation system with 16 DOFs was developed for nanomanipulation of nanometer-scale objects inside the specimen chamber of a scanning electron microscope (SEM). Nanorobotics manipulators are assembled into four units with four DOFs (X-Y-Z-θ) individually. The rotational one is actuated by a picomotor. That means a manipulator has four DOFs including three linear motions in the X, Y, Z directions and a 360-degree rotational one (X-Y-Z-θ stage, θ is along the direction rotating with X or Y axis). Manipulators are actuated by picomotors with better than 30 nm linear resolution and <1 micro-rad rotary resolution. Four vertically installed AFM cantilevers (the axis of the cantilever tip is vertical to the axis of electronic beam of SEM) served as the end-effectors to facilitate the real-time observation of the operations. A series of kinematic derivations of these four manipulators based on the Denavit-Hartenberg (D-H) notation were established. The common working space of the end-effectors is 2.78 mm by 4.39 mm by 6 mm. The manipulation strategy and vision feedback control for multi-manipulators operating inside the SEM chamber were been discussed. Finally, application of the designed nanorobotics manipulation system by successfully testing of the pickup-and-place manipulation of an individual CNT onto four probes was described. The experimental results have shown that carbon nanotubes can be successfully picked up with this nanorobotics manipulation system.

  7. Controlled assembly of SNAP-PNA-fluorophore systems on DNA templates to produce fluorescence resonance energy transfer.

    Science.gov (United States)

    Gholami, Zahra; Hanley, Quentin

    2014-10-15

    The SNAP protein is a widely used self-labeling tag that can be used for tracking protein localization and trafficking in living systems. A model system providing controlled alignment of SNAP-tag units can provide a new way to study clustering of fusion proteins. In this work, fluorescent SNAP-PNA conjugates were controllably assembled on DNA frameworks, forming dimers, trimers, and tetramers. Modification of peptide nucleic acid (PNA) with the O(6)-benzyl guanine (BG) group allowed the generation of site-selective covalent links between PNA and the SNAP protein. The modified BG-PNAs were labeled with fluorescent Atto dyes and subsequently chemo-selectively conjugated to SNAP protein. Efficient assembly into dimer and oligomer forms was verified via size exclusion chromatography (SEC), electrophoresis (SDS-PAGE), and fluorescence spectroscopy. DNA-directed assembly of homo- and heterodimers of SNAP-PNA constructs induced homo- and hetero-FRET, respectively. Longer DNA scaffolds controllably aligned similar fluorescent SNAP-PNA constructs into higher oligomers exhibiting homo-FRET. The combined SEC and homo-FRET studies indicated the 1:1 and saturated assemblies of SNAP-PNA-fluorophore:DNA formed preferentially in this system. This suggested a kinetic/stoichiometric model of assembly rather than binomially distributed products. These BG-PNA-fluorophore building blocks allow facile introduction of fluorophores and/or assembly directing moieties onto any protein containing SNAP. Template-directed assembly of PNA-modified SNAP proteins may be used to investigate clustering behavior both with and without fluorescent labels, which may find use in the study of assembly processes in cells.

  8. Visualization of the Serratia Type VI Secretion System Reveals Unprovoked Attacks and Dynamic Assembly.

    Science.gov (United States)

    Gerc, Amy J; Diepold, Andreas; Trunk, Katharina; Porter, Michael; Rickman, Colin; Armitage, Judith P; Stanley-Wall, Nicola R; Coulthurst, Sarah J

    2015-09-29

    The Type VI secretion system (T6SS) is a bacterial nanomachine that fires toxic proteins into target cells. Deployment of the T6SS represents an efficient and widespread means by which bacteria attack competitors or interact with host organisms and may be triggered by contact from an attacking neighbor cell as a defensive strategy. Here, we use the opportunist pathogen Serratia marcescens and functional fluorescent fusions of key components of the T6SS to observe different subassemblies of the machinery simultaneously and on multiple timescales in vivo. We report that the localization and dynamic behavior of each of the components examined is distinct, revealing a multi-stage and dynamic assembly process for the T6SS machinery. We also show that the T6SS can assemble and fire without needing a cell contact trigger, defining an aggressive strategy that broadens target range and suggesting that activation of the T6SS is tailored to survival in specific niches. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  9. Visualization of the Serratia Type VI Secretion System Reveals Unprovoked Attacks and Dynamic Assembly

    Directory of Open Access Journals (Sweden)

    Amy J. Gerc

    2015-09-01

    Full Text Available The Type VI secretion system (T6SS is a bacterial nanomachine that fires toxic proteins into target cells. Deployment of the T6SS represents an efficient and widespread means by which bacteria attack competitors or interact with host organisms and may be triggered by contact from an attacking neighbor cell as a defensive strategy. Here, we use the opportunist pathogen Serratia marcescens and functional fluorescent fusions of key components of the T6SS to observe different subassemblies of the machinery simultaneously and on multiple timescales in vivo. We report that the localization and dynamic behavior of each of the components examined is distinct, revealing a multi-stage and dynamic assembly process for the T6SS machinery. We also show that the T6SS can assemble and fire without needing a cell contact trigger, defining an aggressive strategy that broadens target range and suggesting that activation of the T6SS is tailored to survival in specific niches.

  10. Fault Diagnosis of a High-Speed Cam-Driven Pin Assembly System

    Directory of Open Access Journals (Sweden)

    Chi-Cheng Cheng

    2016-01-01

    Full Text Available A cam-driven mechanical system applied for pin assembly of connectors of electrical devices is studied in this paper. Three cooperative cams are involved in the tasks of approaching, cutting, insertion, and restoring. In order to meet the demanded productivity growth, the operation speed tends to be elevated. However, high running speeds usually cause deficiencies of pin dropping and inaccurate positioning. Diagnosis is therefore conducted to explore their physical reasons so that modification of future mechanical design can be made. Frequency responses of experimental measurements show greater natural frequency and system stiffness caused by nonlinear dynamics for higher operation speed. It also appears that the clamping force is reduced and drift of the locked pin’s location is induced for higher running speed. In addition, separation of the fixture system induced by contact oscillation generates clearance larger than the thickness of the pin. Based on the mathematical models obtained from the technique of system identification, deeper insight of the mechanical system and future system improvement can be highly expected.

  11. Manufacturing of a Secretoneurin Drug Delivery System with Self-Assembled Protamine Nanoparticles by Titration.

    Directory of Open Access Journals (Sweden)

    Bernhard Scheicher

    Full Text Available Since therapeutic peptides and oligonucleotides are gathering interests as active pharmaceutical ingredients (APIs, nanoparticulate drug delivery systems are becoming of great importance. Thereby, the possibility to design drug delivery systems according to the therapeutic needs of APIs enhances clinical implementation. Over the last years, the focus of our group was laid on protamine-oligonucleotide-nanoparticles (so called proticles, however, the possibility to modify the size, zeta potential or loading efficiencies was limited. Therefore, at the present study we integrated a stepwise addition of protamine (titration into the formation process of proticles loaded with the angiogenic neuropeptide secretoneurin (SN. A particle size around 130 nm was determined when proticles were assembled by the commonly used protamine addition at once. Through application of the protamine titration process it was possible to modify and adjust the particle size between approx. 120 and 1200 nm (dependent on mass ratio without influencing the SN loading capacity. Dynamic light scattering pointed out that the difference in particle size was most probably the result of a secondary aggregation. Initially-formed particles of early stages in the titration process aggregated towards bigger assemblies. Atomic-force-microscopy images also revealed differences in morphology along with different particle size. In contrast, the SN loading was only influenced by the applied mass ratio, where a slight saturation effect was observable. Up to 65% of deployed SN could be imbedded into the proticle matrix. An in-vivo biodistribution study (i.m. showed a retarded distribution of SN from the site of injection after the application of a SN-proticle formulation. Further, it was demonstrated that SN loaded proticles can be successfully freeze-dried and resuspended afterwards. To conclude, the integration of the protamine titration process offers new possibilities for the formulation

  12. Manufacturing of a Secretoneurin Drug Delivery System with Self-Assembled Protamine Nanoparticles by Titration.

    Science.gov (United States)

    Scheicher, Bernhard; Lorenzer, Cornelia; Gegenbauer, Katrin; Partlic, Julia; Andreae, Fritz; Kirsch, Alexander H; Rosenkranz, Alexander R; Werzer, Oliver; Zimmer, Andreas

    2016-01-01

    Since therapeutic peptides and oligonucleotides are gathering interests as active pharmaceutical ingredients (APIs), nanoparticulate drug delivery systems are becoming of great importance. Thereby, the possibility to design drug delivery systems according to the therapeutic needs of APIs enhances clinical implementation. Over the last years, the focus of our group was laid on protamine-oligonucleotide-nanoparticles (so called proticles), however, the possibility to modify the size, zeta potential or loading efficiencies was limited. Therefore, at the present study we integrated a stepwise addition of protamine (titration) into the formation process of proticles loaded with the angiogenic neuropeptide secretoneurin (SN). A particle size around 130 nm was determined when proticles were assembled by the commonly used protamine addition at once. Through application of the protamine titration process it was possible to modify and adjust the particle size between approx. 120 and 1200 nm (dependent on mass ratio) without influencing the SN loading capacity. Dynamic light scattering pointed out that the difference in particle size was most probably the result of a secondary aggregation. Initially-formed particles of early stages in the titration process aggregated towards bigger assemblies. Atomic-force-microscopy images also revealed differences in morphology along with different particle size. In contrast, the SN loading was only influenced by the applied mass ratio, where a slight saturation effect was observable. Up to 65% of deployed SN could be imbedded into the proticle matrix. An in-vivo biodistribution study (i.m.) showed a retarded distribution of SN from the site of injection after the application of a SN-proticle formulation. Further, it was demonstrated that SN loaded proticles can be successfully freeze-dried and resuspended afterwards. To conclude, the integration of the protamine titration process offers new possibilities for the formulation of proticles in

  13. Manufacturing of a Secretoneurin Drug Delivery System with Self-Assembled Protamine Nanoparticles by Titration

    Science.gov (United States)

    Scheicher, Bernhard; Lorenzer, Cornelia; Gegenbauer, Katrin; Partlic, Julia; Andreae, Fritz; Kirsch, Alexander H.; Rosenkranz, Alexander R.; Werzer, Oliver

    2016-01-01

    Since therapeutic peptides and oligonucleotides are gathering interests as active pharmaceutical ingredients (APIs), nanoparticulate drug delivery systems are becoming of great importance. Thereby, the possibility to design drug delivery systems according to the therapeutic needs of APIs enhances clinical implementation. Over the last years, the focus of our group was laid on protamine-oligonucleotide-nanoparticles (so called proticles), however, the possibility to modify the size, zeta potential or loading efficiencies was limited. Therefore, at the present study we integrated a stepwise addition of protamine (titration) into the formation process of proticles loaded with the angiogenic neuropeptide secretoneurin (SN). A particle size around 130 nm was determined when proticles were assembled by the commonly used protamine addition at once. Through application of the protamine titration process it was possible to modify and adjust the particle size between approx. 120 and 1200 nm (dependent on mass ratio) without influencing the SN loading capacity. Dynamic light scattering pointed out that the difference in particle size was most probably the result of a secondary aggregation. Initially-formed particles of early stages in the titration process aggregated towards bigger assemblies. Atomic-force-microscopy images also revealed differences in morphology along with different particle size. In contrast, the SN loading was only influenced by the applied mass ratio, where a slight saturation effect was observable. Up to 65% of deployed SN could be imbedded into the proticle matrix. An in-vivo biodistribution study (i.m.) showed a retarded distribution of SN from the site of injection after the application of a SN-proticle formulation. Further, it was demonstrated that SN loaded proticles can be successfully freeze-dried and resuspended afterwards. To conclude, the integration of the protamine titration process offers new possibilities for the formulation of proticles in

  14. Autonomous electrochromic assembly

    Energy Technology Data Exchange (ETDEWEB)

    Berland, Brian Spencer; Lanning, Bruce Roy; Stowell, Jr., Michael Wayne

    2015-03-10

    This disclosure describes system and methods for creating an autonomous electrochromic assembly, and systems and methods for use of the autonomous electrochromic assembly in combination with a window. Embodiments described herein include an electrochromic assembly that has an electrochromic device, an energy storage device, an energy collection device, and an electrochromic controller device. These devices may be combined into a unitary electrochromic insert assembly. The electrochromic assembly may have the capability of generating power sufficient to operate and control an electrochromic device. This control may occur through the application of a voltage to an electrochromic device to change its opacity state. The electrochromic assembly may be used in combination with a window.

  15. Functionalization of polyoxometalates by carboxylato and azido ligands: macromolecular complexes and extended compounds.

    Science.gov (United States)

    Mialane, Pierre; Dolbecq, Anne; Sécheresse, Francis

    2006-09-07

    Polyoxometalate compounds continue to be widely studied due to their relevance in various fields such as catalysis or magnetochemistry. In this article, we will focus on two topics we recently developed, the functionalization of rare earth polyoxometalates by organic ligands, which has led to compounds ranging from magnetic macromolecular complexes to a 3D open-framework system, and the functionalization of first row transition metal substituted polyoxometalates by azido ligands, which has allowed the isolation of complexes exhibiting the largest ferromagnetic exchange couplings observed to date in polyoxometalate chemistry.

  16. Integrated software for macromolecular crystallography synchrotron beamlines II: revision, robots and a database.

    Science.gov (United States)

    Skinner, John M; Cowan, Matt; Buono, Rick; Nolan, William; Bosshard, Heinz; Robinson, Howard H; Héroux, Annie; Soares, Alexei S; Schneider, Dieter K; Sweet, Robert M

    2006-11-01

    This manuscript chronicles the evolution of software used originally to control a diffractometer at a macromolecular crystallography beamline. The system has been augmented and rewritten. A modular and carefully organized suite of programs now handles the whole experimental environment from a single vantage point. It provides automatic logging of the experiment and communication with the user, all the way from an initial proposal to perform the work to the end of data collection. This has included construction of a relational database to organize all details of the experiment and incorporation of a robotic specimen changer to provide automation for high-throughput applications.

  17. Nano-droplet systems by surfactant self-assembly and applications in the pharmaceutical industry.

    Science.gov (United States)

    Rodríguez-Abreu, Carlos; Vila, Ana

    2014-01-01

    Liquid systems containing droplets with size in the nanoscale range are attractive from both scientific and technological points of view as they have many current and potential applications in several industries and products. The formation and stabilization of nano-droplet systems are mostly based on the self-assembly of surfactant (amphiphilic) molecules at interfaces, driven by the solvophobic effect. Surfactants are involved in both top-bottom (high energy) and bottom- up (low energy) methods. Several devices have also been developed to aid in liquid fragmentation down to the nanometer scale. Nano-droplet systems can be both thermodynamically stable (microemulsions) or metastable (nanoemulsions), and appropriate formulation is a key for optimum product design in terms of droplet size, maximum solubilization, colloidal stability, and optical and rheological properties, among others. Such characteristics are determined by molecular packing, interfacial curvature, droplet-droplet interactions, film elasticity and nature of the dispersed and continuous phase. These properties can be engineered by proper understanding of the molecular structure and phase behavior of the multicomponent systems involved and by a range of experimental characterization techniques. Nano-droplet systems can help to solve specific issues in pharmaceutical products such as processing, limitations in drug solubility or stability, control on drug release, drug targeting and absorption; there are many examples to prove that. However, several practical aspects should be considered for preclinical and clinical tests and product development.

  18. Mini-channel evaporator/heat pipe assembly for a chip cooling vapor compression refrigeration system

    Energy Technology Data Exchange (ETDEWEB)

    Ribeiro, Guilherme B.; Barbosa, Jader R. Jr.; Prata, Alvaro T. [Polo - Research Laboratories for Emerging Technologies in Cooling and Thermophysics, Department of Mechanical Engineering, Campus Universitario, Trindade, Federal University of Santa Catarina, Florianopolis, SC 88040900 (Brazil)

    2010-11-15

    We investigate a novel evaporator design for a small-scale refrigeration system whose function is to assist the existing heat pipe technology currently used in chip cooling of portable computers. A heat transfer model for the evaporator/heat pipe assembly was devised specifically for sizing the evaporator in order to keep the chip surface temperature below a certain value. A prototype was tested with R-600a at saturation temperatures of 45 and 55 C, mass flow rates between 0.5 and 1.5 kg h{sup -1} and heat transfer rates between 30 and 60 W. The experimental results demonstrated that the average refrigerant-side heat transfer coefficient is more sensitive to a change in the refrigerant mass flux than to changes in the saturation temperature and heat transfer rate. The agreement between the calculated heat transfer coefficient and the data was within {+-}10% for the conditions evaluated. (author)

  19. Beamline AR-NW12A: high-throughput beamline for macromolecular crystallography at the Photon Factory.

    Science.gov (United States)

    Chavas, L M G; Matsugaki, N; Yamada, Y; Hiraki, M; Igarashi, N; Suzuki, M; Wakatsuki, S

    2012-05-01

    AR-NW12A is an in-vacuum undulator beamline optimized for high-throughput macromolecular crystallography experiments as one of the five macromolecular crystallography (MX) beamlines at the Photon Factory. This report provides details of the beamline design, covering its optical specifications, hardware set-up, control software, and the latest developments for MX experiments. The experimental environment presents state-of-the-art instrumentation for high-throughput projects with a high-precision goniometer with an adaptable goniometer head, and a UV-light sample visualization system. Combined with an efficient automounting robot modified from the SSRL SAM system, a remote control system enables fully automated and remote-access X-ray diffraction experiments.

  20. On the vibron dressing in the one-dimensional macromolecular chains caused by the interaction with acoustic phonon modes

    CERN Document Server

    Cevizovic, Dalibor; Galovic, Slobodanka; Ivic, Zoran

    2012-01-01

    We present a study of the physical properties of the vibrational excitation in the one-dimensional macromolecular chains, caused by the interaction with acoustical phonon modes. The influence of the temperature and the basic system parameters on the vibron dressing has been analyzed by employing the simple mean--field approach based on the variational extension of the Lang--Firsov unitary transformation. Applied approach predicts a region in system parameter space where it is possible of the coexistence of the partially dressed (light and mobile) and fully dressed (immobile) vibron states. We found that the boundary of this region depends on system temperature and type of bond among structure elements in macromolecular chain.

  1. A System for Measuring the Sway of the Vehicle Assembly Building

    Science.gov (United States)

    Youngquist, Robert; Starr, Stanley; Lane, John; Simmons, Stephen; Ihlefeld, Curtis

    2013-01-01

    A system was developed to measure the sway of the Vehicle Assembly Building (VAB) at Kennedy Space Center. This system was installed in the VAB and gathered more than one total year of data. The building movement was correlated with measurements provided by three wind towers in order to determine the maximum deflection of the building during high-wind events. The VAB owners were in the process of obtaining new platforms for use in assembling very tall rockets when analysis of the VAB showed that a high wind could move the building sufficiently that an upper platform might impact a rocket. The problem arises because safety requires a relatively small gap between the platform and the rocket, while a large enough gap is needed to ensure that stacking tolerances prevent contact between the rocket and the platform. This only leaves an inch or two (approximately 2 to 5 cm) of total clearance, so when the analysis showed that more than a couple of inches of motion could occur in a high wind, there was a potential for damaging the rocket. The KSC Applied Physics Laboratory was asked to install a system in the VAB that could measure the motion of the building in high winds to determine the actual building sway. The motion of the VAB roof under wind load was measured optically, and under analysis, it was determined that a relatively large-aperture optical system would be required to reduce diffraction effects to less than a small fraction of an inch (approximately mm) at a distance of 500 ft (˜150 m). A 10-in. (approximately 250 mm) telescope was placed on the floor of the building, looking at the ceiling. On the ceiling, a flat plate with three white LEDs was mounted in an "L" shape, such that the telescope was essentially looking at three stars. Software was written to track the motion of these three points using an image processing system. This provided a better than 1/10-in. (approximately 2.5-mm) 2D measurement faster than once a second. Data was downloaded once a

  2. Assembly Domain-Based Optogenetic System for the Efficient Control of Cellular Signaling.

    Science.gov (United States)

    Furuya, Akihiro; Kawano, Fuun; Nakajima, Takahiro; Ueda, Yoshibumi; Sato, Moritoshi

    2017-06-16

    We previously developed the Magnet system, which consists of two distinct Vivid protein variants, one positively and one negatively charged, designated the positive Magnet (pMag) and negative Magnet (nMag), respectively. These two proteins bind to each other through electrostatic interactions, preventing unwanted homodimerization and providing selective light-induced heterodimerization. The Magnet system enables the manipulation of cellular functions such as protein-protein interactions and genome editing, although the system could be improved further. To enhance the ability of pMagFast2 (a pMag variant with fast kinetics) to bind nMag, we introduced several pMagFast2 modules in tandem into a single construct, pMagFast2(3×). However, the expression level of this construct decreased drastically with increasing number of pMagFast2 molecules integrated into a single construct. In the present study, we applied a new approach to improve the Magnet system based on an assembly domain (AD). Among several ADs, the Ca2+/calmodulin-dependent protein kinase IIα association domain (CAD) most enhanced the Magnet system. The present CAD-Magnet system overcame a trade-off issue between the expression level and binding affinity. The CAD-converged 12 pMag photoswitches exhibited a stronger interaction with nMag after blue light irradiation compared with monomeric pMag. Additionally, the CAD played a key role in converging effector proteins as well in a single complex. Owing to these substantial improvements, the CAD-Magnet system combined with Tiam1 allowed us to robustly induce localized formation of vertical ruffles on the apical plasma membrane. The CAD-Magnet system combined with 4D imaging was instrumental in revealing the dynamics of ruffle formation.

  3. Non-contact luminescence lifetime cryothermometry for macromolecular crystallography.

    Science.gov (United States)

    Mykhaylyk, V B; Wagner, A; Kraus, H

    2017-05-01

    Temperature is a very important parameter when aiming to minimize radiation damage to biological samples during experiments that utilize intense ionizing radiation. A novel technique for remote, non-contact, in situ monitoring of the protein crystal temperature has been developed for the new I23 beamline at the Diamond Light Source, a facility dedicated to macromolecular crystallography (MX) with long-wavelength X-rays. The temperature is derived from the temperature-dependent decay time constant of luminescence from a minuscule scintillation sensor (<0.05 mm 3 ) located in very close proximity to the sample under test. In this work the underlying principle of cryogenic luminescence lifetime thermometry is presented, the features of the detection method and the choice of temperature sensor are discussed, and it is demonstrated how the temperature monitoring system was integrated within the viewing system of the endstation used for the visualization of protein crystals. The thermometry system was characterized using a Bi 4 Ge 3 O 12 crystal scintillator that exhibits good responsivity of the decay time constant as a function of temperature over a wide range (8-270 K). The scintillation sensor was calibrated and the uncertainty of the temperature measurements over the primary operation temperature range of the beamline (30-150 K) was assessed to be ±1.6 K. It has been shown that the temperature of the sample holder, measured using the luminescence sensor, agrees well with the expected value. The technique was applied to characterize the thermal performance of different sample mounts that have been used in MX experiments at the I23 beamline. The thickness of the mount is shown to have the greatest impact upon the temperature distribution across the sample mount. Altogether, these tests and findings demonstrate the usefulness of the thermometry system in highlighting the challenges that remain to be addressed for the in-vacuum MX experiment to become a

  4. A highly controllable protein self-assembly system with morphological versatility induced by reengineered host-guest interactions.

    Science.gov (United States)

    Li, Xiumei; Bai, Yushi; Huang, Zupeng; Si, Chengye; Dong, Zeyuan; Luo, Quan; Liu, Junqiu

    2017-06-14

    Manipulating proteins to self-assemble into highly ordered nanostructures not only provides insights into the natural protein assembly process but also allows access to advanced biomaterials. Host-guest interactions have been widely used in the construction of artificial protein assemblies in recent years. CB[8] can selectively associate with two tripeptide Phe-Gly-Gly (FGG) tags with an extraordinarily high binding affinity (Kter = 1.5 × 10(11) M(-2)). However, the FGG tags utilized before are all fixed to the N-termini via genetic fusion; this spatial limitation greatly confined the availability of the CB[8]/FGG pair in the construction of more sophisticated protein nanostructures. Here we first designed and synthesized a maleimide-functionalized Phe-Gly-Gly tag as a versatile site-specific protein modification tool; this designed tag can site-selectively introduce desired guest moieties onto protein surfaces for host-guest driven protein assembly. When regulating the self-assembly process of proteins and CB[8], the constructed protein nanosystem can exhibit distinctive morphological diversities ranging from nanorings, nanospirals, nanowires to superwires. This work developed a new strategy for site-specific protein modification of the CB[8] binding tag and provides a possible direction for the construction of 'smart', dynamic self-assembly systems.

  5. Aging changes of macromolecular synthesis in the digestive organs of mice as revealed by microscopic radioautography and X-ray microanalysis

    Energy Technology Data Exchange (ETDEWEB)

    Nagata, Tetsuji [Shinshu Univ., Matsumoto (Japan). School of Medicine. Dept. of Anatomy and Cell Biology]. E-mail: nagatas@po.cnet.ne.jp

    2002-07-01

    For the purpose of elucidating the aging changes of macromolecular synthesis such as DNA, RNA, proteins, glycoproteins, glycides and lipids in various organ systems of experimental animals, we have studied the digestive organs of aging mice and rats as a series of systematic studies using light and electron microscopic radioautography after incorporations with macromolecular precursors. The experimental animals mainly used were ddY strain mice at various aging groups from embryo to postnatal days 1 and 3, weeks 1 and 2, months 1, 2, 6, 12 up to 2 year senescent stages as well as several groups of adult Wistar rats. The animals were injected with such macromolecular precursors as {sup 3}H - thymidine for DNA, {sup 3}H-uridine for RNA, {sup 3}H-leucine and {sup 3}H proline for proteins, {sup 35}SO{sub 4} for glycoproteins, {sup 3} H-glucosamine for glucides and {sup 3}H-glycerol for lipids. The results demonstrated that these precursors were incorporated into various cell types in the oral cavity, the salivary glands, the esophagus, the stomach, the small and large intestines, the liver and the pancreas at various ages from perinatal to juvenile, mature and senescent stages, showing specific patterns of macromolecular synthesis. It is concluded that these specific patterns of macromolecular synthesis in respective cell types demonstrated the organ specificity of aging of animals. (author)

  6. Capacity planning and resource allocation in assembly systems consisting of dedicated and reconfigurable lines

    OpenAIRE

    Gyulai, D.; Kádár, B.; Monostori, L.

    2014-01-01

    Companies with diverse product portfolio often face capacity planning problems due to the diversity of the products and the fluctuation of the order stream. High volume products can be produced cost-efficiently in dedicated assembly lines, but the assembly of low-volume products in such lines involves high idle times and operation costs. Reconfigurable assembly lines offer reasonable solution for the problem; however, it is still complicated to identify the set of products which are worth to ...

  7. D3, the new diffractometer for the macromolecular crystallography beamlines of the Swiss Light Source

    Energy Technology Data Exchange (ETDEWEB)

    Fuchs, Martin R., E-mail: mfuchs@bnl.gov [Paul Scherrer Institute, 5232 Villigen PSI (Switzerland); Brookhaven National Laboratory, Mail Stop 745, Upton, NY 11973 (United States); Pradervand, Claude; Thominet, Vincent; Schneider, Roman; Panepucci, Ezequiel; Grunder, Marcel; Gabadinho, Jose; Dworkowski, Florian S. N.; Tomizaki, Takashi; Schneider, Jörg; Mayer, Aline; Curtin, Adrian; Olieric, Vincent; Frommherz, Uli; Kotrle, Goran; Welte, Jörg; Wang, Xinyu; Maag, Stephan [Paul Scherrer Institute, 5232 Villigen PSI (Switzerland); Schulze-Briese, Clemens [DECTRIS Ltd, Neuenhoferstrasse 107, 5400 Baden (Switzerland); Wang, Meitian [Paul Scherrer Institute, 5232 Villigen PSI (Switzerland)

    2014-02-04

    A new diffractometer for microcrystallography has been developed for the three macromolecular crystallography beamlines of the Swiss Light Source. A new diffractometer for microcrystallography has been developed for the three macromolecular crystallography beamlines of the Swiss Light Source. Building upon and critically extending previous developments realised for the high-resolution endstations of the two undulator beamlines X06SA and X10SA, as well as the super-bend dipole beamline X06DA, the new diffractometer was designed to the following core design goals. (i) Redesign of the goniometer to a sub-micrometer peak-to-peak cylinder of confusion for the horizontal single axis. Crystal sizes down to at least 5 µm and advanced sample-rastering and scanning modes are supported. In addition, it can accommodate the new multi-axis goniometer PRIGo (Parallel Robotics Inspired Goniometer). (ii) A rapid-change beam-shaping element system with aperture sizes down to a minimum of 10 µm for microcrystallography measurements. (iii) Integration of the on-axis microspectrophotometer MS3 for microscopic sample imaging with 1 µm image resolution. Its multi-mode optical spectroscopy module is always online and supports in situ UV/Vis absorption, fluorescence and Raman spectroscopy. (iv) High stability of the sample environment by a mineral cast support construction and by close containment of the cryo-stream. Further features are the support for in situ crystallization plate screening and a minimal achievable detector distance of 120 mm for the Pilatus 6M, 2M and the macromolecular crystallography group’s planned future area detector Eiger 16M.

  8. Assembling Large, Multi-Sensor Climate Datasets Using the SciFlo Grid Workflow System

    Science.gov (United States)

    Wilson, B.; Manipon, G.; Xing, Z.; Fetzer, E.

    2009-04-01

    NASA's Earth Observing System (EOS) is an ambitious facility for studying global climate change. The mandate now is to combine measurements from the instruments on the "A-Train" platforms (AIRS, AMSR-E, MODIS, MISR, MLS, and CloudSat) and other Earth probes to enable large-scale studies of climate change over periods of years to decades. However, moving from predominantly single-instrument studies to a multi-sensor, measurement-based model for long-duration analysis of important climate variables presents serious challenges for large-scale data mining and data fusion. For example, one might want to compare temperature and water vapor retrievals from one instrument (AIRS) to another instrument (MODIS), and to a model (ECMWF), stratify the comparisons using a classification of the "cloud scenes" from CloudSat, and repeat the entire analysis over years of AIRS data. To perform such an analysis, one must discover & access multiple datasets from remote sites, find the space/time "matchups" between instruments swaths and model grids, understand the quality flags and uncertainties for retrieved physical variables, assemble merged datasets, and compute fused products for further scientific and statistical analysis. To meet these large-scale challenges, we are utilizing a Grid computing and dataflow framework, named SciFlo, in which we are deploying a set of versatile and reusable operators for data query, access, subsetting, co-registration, mining, fusion, and advanced statistical analysis. SciFlo is a semantically-enabled ("smart") Grid Workflow system that ties together a peer-to-peer network of computers into an efficient engine for distributed computation. The SciFlo workflow engine enables scientists to do multi-instrument Earth Science by assembling remotely-invokable Web Services (SOAP or http GET URLs), native executables, command-line scripts, and Python codes into a distributed computing flow. A scientist visually authors the graph of operation in the Viz

  9. Macromolecular Crowding Studies of Amino Acids Using NMR Diffusion Measurements and Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Amninder S Virk

    2015-02-01

    Full Text Available Molecular crowding occurs when the total concentration of macromolecular species in a solution is so high that a considerable proportion of the volume is physically occupied and therefore not accessible to other molecules. This results in significant changes in the solution properties of the molecules in such systems. Macromolecular crowding is ubiquitous in biological systems due to the generally high intracellular protein concentrations. The major hindrance to understanding crowding is the lack of direct comparison of experimental data with theoretical or simulated data. Self-diffusion is sensitive to changes in the molecular weight and shape of the diffusing species, and the available diffusion space (i.e., diffusive obstruction. Consequently, diffusion measurements are a direct means for probing crowded systems including the self-association of molecules. In this work, nuclear magnetic resonance measurements of the self-diffusion of four amino acids (glycine, alanine, valine and phenylalanine up to their solubility limit in water were compared directly with molecular dynamics simulations. The experimental data were then analyzed using various models of aggregation and obstruction. Both experimental and simulated data revealed that the diffusion of both water and the amino acids were sensitive to the amino acid concentration. The direct comparison of the simulated and experimental data afforded greater insights into the aggregation and obstruction properties of each amino acid.

  10. Plasticity in the macromolecular-scale causal networks of cell migration.

    Science.gov (United States)

    Lock, John G; Mamaghani, Mehrdad Jafari; Shafqat-Abbasi, Hamdah; Gong, Xiaowei; Tyrcha, Joanna; Strömblad, Staffan

    2014-01-01

    Heterogeneous and dynamic single cell migration behaviours arise from a complex multi-scale signalling network comprising both molecular components and macromolecular modules, among which cell-matrix adhesions and F-actin directly mediate migration. To date, the global wiring architecture characterizing this network remains poorly defined. It is also unclear whether such a wiring pattern may be stable and generalizable to different conditions, or plastic and context dependent. Here, synchronous imaging-based quantification of migration system organization, represented by 87 morphological and dynamic macromolecular module features, and migration system behaviour, i.e., migration speed, facilitated Granger causality analysis. We thereby leveraged natural cellular heterogeneity to begin mapping the directionally specific causal wiring between organizational and behavioural features of the cell migration system. This represents an important advance on commonly used correlative analyses that do not resolve causal directionality. We identified organizational features such as adhesion stability and adhesion F-actin content that, as anticipated, causally influenced cell migration speed. Strikingly, we also found that cell speed can exert causal influence over organizational features, including cell shape and adhesion complex location, thus revealing causality in directions contradictory to previous expectations. Importantly, by comparing unperturbed and signalling-modulated cells, we provide proof-of-principle that causal interaction patterns are in fact plastic and context dependent, rather than stable and generalizable.

  11. Plasticity in the macromolecular-scale causal networks of cell migration.

    Directory of Open Access Journals (Sweden)

    John G Lock

    Full Text Available Heterogeneous and dynamic single cell migration behaviours arise from a complex multi-scale signalling network comprising both molecular components and macromolecular modules, among which cell-matrix adhesions and F-actin directly mediate migration. To date, the global wiring architecture characterizing this network remains poorly defined. It is also unclear whether such a wiring pattern may be stable and generalizable to different conditions, or plastic and context dependent. Here, synchronous imaging-based quantification of migration system organization, represented by 87 morphological and dynamic macromolecular module features, and migration system behaviour, i.e., migration speed, facilitated Granger causality analysis. We thereby leveraged natural cellular heterogeneity to begin mapping the directionally specific causal wiring between organizational and behavioural features of the cell migration system. This represents an important advance on commonly used correlative analyses that do not resolve causal directionality. We identified organizational features such as adhesion stability and adhesion F-actin content that, as anticipated, causally influenced cell migration speed. Strikingly, we also found that cell speed can exert causal influence over organizational features, including cell shape and adhesion complex location, thus revealing causality in directions contradictory to previous expectations. Importantly, by comparing unperturbed and signalling-modulated cells, we provide proof-of-principle that causal interaction patterns are in fact plastic and context dependent, rather than stable and generalizable.

  12. Directed self-assembly of nanoparticle array: A single electron device platform to make novel systems

    Science.gov (United States)

    Ong, Jason Kee Yang

    The biggest attraction of building nanometer structures is the emergence of novel properties and phenomena at these length scales. In the discipline of electronics particularly, nanoscale bridges the gap between the microscopic quantum world to the macroscopic classical world. The bridge can be tailored to effectively affect the material properties. One of the well-known phenomena that is altered at the nanoscale is the electron transport through a metal, i.e. the Ohm's law. As the size of the metal particle reduces to nanometer, Ohm's law breaks down due to trapping of a single electron charge, i.e. local charging, that prohibits the subsequent steam of electrons to pass through. This phenomenon is referred to as the Coulomb blockade, where the current is blocked below a threshold bias, VT. However, to observe a robust VT, the system has to be cooled to cryogenic temperatures. Here, fabrication and construction of a nano-system using directed self-assembled network of 1D necklace of 10 nm Au particles are described, which exhibits a robust single electron effect with a record high VT of 7.5 V at room temperature and a subsequent current, I rise as ( V/VT -- 1)ζ, where ζ is a critical constant, usually around 2. These physical parameters can be precisely tuned by tailoring the dimension and topology of the ensemble. The finding is important as nanoparticle based Single Electron Devices (SEDs) have become of great interest due to their orders of magnitude high sensitivity to gating. For over six decades of research on SEDs, it is clear that V T > 2 V at room temperature is required to make a robust device to eliminate the omnipresent "quantum noise" in these systems. Our system has not only shown a room temperature VT of well above 2 V but also its easy integrability with microelectronics circuits. Detailed scientific studies have been performed on the formation and structure of necklace array to understand the assembly process. Subsequent modification of the

  13. Due-date assignment for multi-server multi-stage assembly systems

    Science.gov (United States)

    Yaghoubi, Saeed

    2015-05-01

    In this paper, we attempt to present a constant due-date assignment policy in a multi-server multi-stage assembly system. This system is modelled as a queuing network, where new product orders are entered into the system according to a Poisson process. It is assumed that only one type of product is produced by the production system and multi-servers can be settled in each service station. Each operation of every work is operated at a devoted service station with only one of the servers located at a node of the network based on first come, first served (FCFS) discipline, while the processing times are independent random variables with exponential distributions. It is also assumed that the transport times between each pair of service stations are independent random variables with generalised Erlang distributions. Each product's end result has a penalty cost that is some linear function of its due date and its actual lead time. The due date is calculated by adding a constant to the time that the order enters into the system. Indeed, this constant value is decided at the beginning of the time horizon and is the constant lead time that a product might expect between the time of placing the order and the time of delivery. For computing the due date, we first convert the queuing network into a stochastic network with exponentially distributed arc lengths. Then, by constructing an appropriate finite-state continuous-time Markov model, a system of differential equations is created to find the manufacturing lead-time distribution for any particular product, analytically. Finally, the constant due date for delivery time is obtained by using a linear function of its due date and minimising the expected aggregate cost per product.

  14. Temperature-dependent macromolecular X-ray crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Weik, Martin, E-mail: martin.weik@ibs.fr; Colletier, Jacques-Philippe [CEA, IBS, Laboratoire de Biophysique Moléculaire, F-38054 Grenoble (France); CNRS, UMR5075, F-38027 Grenoble (France); Université Joseph Fourier, F-38000 Grenoble (France)

    2010-04-01

    The dynamical behaviour of crystalline macromolecules and their surrounding solvent as a function of cryo-temperature is reviewed. X-ray crystallography provides structural details of biological macromolecules. Whereas routine data are collected close to 100 K in order to mitigate radiation damage, more exotic temperature-controlled experiments in a broader temperature range from 15 K to room temperature can provide both dynamical and structural insights. Here, the dynamical behaviour of crystalline macromolecules and their surrounding solvent as a function of cryo-temperature is reviewed. Experimental strategies of kinetic crystallography are discussed that have allowed the generation and trapping of macromolecular intermediate states by combining reaction initiation in the crystalline state with appropriate temperature profiles. A particular focus is on recruiting X-ray-induced changes for reaction initiation, thus unveiling useful aspects of radiation damage, which otherwise has to be minimized in macromolecular crystallography.

  15. Macromolecular metamorphosis via stimulus-induced transformations of polymer architecture

    Science.gov (United States)

    Sun, Hao; Kabb, Christopher P.; Dai, Yuqiong; Hill, Megan R.; Ghiviriga, Ion; Bapat, Abhijeet P.; Sumerlin, Brent S.

    2017-08-01

    Macromolecular architecture plays a pivotal role in determining the properties of polymers. When designing polymers for specific applications, it is not only the size of a macromolecule that must be considered, but also its shape. In most cases, the topology of a polymer is a static feature that is inalterable once synthesized. Using reversible-covalent chemistry to prompt the disconnection of chemical bonds and the formation of new linkages in situ, we report polymers that undergo dramatic topological transformations via a process we term macromolecular metamorphosis. Utilizing this technique, a linear amphiphilic block copolymer or hyperbranched polymer undergoes 'metamorphosis' into comb, star and hydrophobic block copolymer architectures. This approach was extended to include a macroscopic gel which transitioned from a densely and covalently crosslinked network to one with larger distances between the covalent crosslinks when heated. These architectural transformations present an entirely new approach to 'smart' materials.

  16. Refinement of macromolecular structures against neutron data with SHELXL2013.

    Science.gov (United States)

    Gruene, Tim; Hahn, Hinrich W; Luebben, Anna V; Meilleur, Flora; Sheldrick, George M

    2014-02-01

    Some of the improvements in SHELX2013 make SHELXL convenient to use for refinement of macromolecular structures against neutron data without the support of X-ray data. The new NEUT instruction adjusts the behaviour of the SFAC instruction as well as the default bond lengths of the AFIX instructions. This work presents a protocol on how to use SHELXL for refinement of protein structures against neutron data. It includes restraints extending the Engh & Huber [Acta Cryst. (1991), A47, 392-400] restraints to H atoms and discusses several of the features of SHELXL that make the program particularly useful for the investigation of H atoms with neutron diffraction. SHELXL2013 is already adequate for the refinement of small molecules against neutron data, but there is still room for improvement, like the introduction of chain IDs for the refinement of macromolecular structures.

  17. Celebrando la cristalografía macromolecular: una perspectiva personal

    OpenAIRE

    Abad-Zapatero, Celerino

    2015-01-01

    The twentieth century has seen an enormous advance in the knowledge of the atomic structures that surround us. The discovery of the first crystal structures of simple inorganic salts by the Braggs in 1914, using the diffraction of X-rays by crystals, provided the critical elements to unveil the atomic structure of matter. Subsequent developments in the field leading to macromolecular crystallography are presented with a personal perspective, related to the cultural milieu of Spain in the late...

  18. Towards a compact and precise sample holder for macromolecular crystallography

    Science.gov (United States)

    Rossi, Christopher; Janocha, Robert; Sorez, Clement; Astruc, Anthony; McCarthy, Andrew; Belrhali, Hassan; Cipriani, Florent

    2017-01-01

    Most of the sample holders currently used in macromolecular crystallography offer limited storage density and poor initial crystal-positioning precision upon mounting on a goniometer. This has now become a limiting factor at high-throughput beamlines, where data collection can be performed in a matter of seconds. Furthermore, this lack of precision limits the potential benefits emerging from automated harvesting systems that could provide crystal-position information which would further enhance alignment at beamlines. This situation provided the motivation for the development of a compact and precise sample holder with corresponding pucks, handling tools and robotic transfer protocols. The development process included four main phases: design, prototype manufacture, testing with a robotic sample changer and validation under real conditions on a beamline. Two sample-holder designs are proposed: NewPin and miniSPINE. They share the same robot gripper and allow the storage of 36 sample holders in uni-puck footprint-style pucks, which represents 252 samples in a dry-shipping dewar commonly used in the field. The pucks are identified with human- and machine-readable codes, as well as with radio-frequency identification (RFID) tags. NewPin offers a crystal-repositioning precision of up to 10 µm but requires a specific goniometer socket. The storage density could reach 64 samples using a special puck designed for fully robotic handling. miniSPINE is less precise but uses a goniometer mount compatible with the current SPINE standard. miniSPINE is proposed for the first implementation of the new standard, since it is easier to integrate at beamlines. An upgraded version of the SPINE sample holder with a corresponding puck named SPINEplus is also proposed in order to offer a homogenous and interoperable system. The project involved several European synchrotrons and industrial companies in the fields of consumables and sample-changer robotics. Manual handling of mini

  19. Cryo-Electron Tomography for Structural Characterization of Macromolecular Complexes

    Science.gov (United States)

    Cope, Julia; Heumann, John; Hoenger, Andreas

    2011-01-01

    Cryo-electron tomography (cryo-ET) is an emerging 3-D reconstruction technology that combines the principles of tomographic 3-D reconstruction with the unmatched structural preservation of biological material embedded in vitreous ice. Cryo-ET is particularly suited to investigating cell-biological samples and large macromolecular structures that are too polymorphic to be reconstructed by classical averaging-based 3-D reconstruction procedures. This unit aims to make cryo-ET accessible to newcomers and discusses the specialized equipment required, as well as the relevant advantages and hurdles associated with sample preparation by vitrification and cryo-ET. Protocols describe specimen preparation, data recording and 3-D data reconstruction for cryo-ET, with a special focus on macromolecular complexes. A step-by-step procedure for specimen vitrification by plunge freezing is provided, followed by the general practicalities of tilt-series acquisition for cryo-ET, including advice on how to select an area appropriate for acquiring a tilt series. A brief introduction to the underlying computational reconstruction principles applied in tomography is described, along with instructions for reconstructing a tomogram from cryo-tilt series data. Finally, a method is detailed for extracting small subvolumes containing identical macromolecular structures from tomograms for alignment and averaging as a means to increase the signal-to-noise ratio and eliminate missing wedge effects inherent in tomographic reconstructions. PMID:21842467

  20. Macromolecular target prediction by self-organizing feature maps.

    Science.gov (United States)

    Schneider, Gisbert; Schneider, Petra

    2017-03-01

    Rational drug discovery would greatly benefit from a more nuanced appreciation of the activity of pharmacologically active compounds against a diverse panel of macromolecular targets. Already, computational target-prediction models assist medicinal chemists in library screening, de novo molecular design, optimization of active chemical agents, drug re-purposing, in the spotting of potential undesired off-target activities, and in the 'de-orphaning' of phenotypic screening hits. The self-organizing map (SOM) algorithm has been employed successfully for these and other purposes. Areas covered: The authors recapitulate contemporary artificial neural network methods for macromolecular target prediction, and present the basic SOM algorithm at a conceptual level. Specifically, they highlight consensus target-scoring by the employment of multiple SOMs, and discuss the opportunities and limitations of this technique. Expert opinion: Self-organizing feature maps represent a straightforward approach to ligand clustering and classification. Some of the appeal lies in their conceptual simplicity and broad applicability domain. Despite known algorithmic shortcomings, this computational target prediction concept has been proven to work in prospective settings with high success rates. It represents a prototypic technique for future advances in the in silico identification of the modes of action and macromolecular targets of bioactive molecules.

  1. What Macromolecular Crowding Can Do to a Protein

    Science.gov (United States)

    Kuznetsova, Irina M.; Turoverov, Konstantin K.; Uversky, Vladimir N.

    2014-01-01

    The intracellular environment represents an extremely crowded milieu, with a limited amount of free water and an almost complete lack of unoccupied space. Obviously, slightly salted aqueous solutions containing low concentrations of a biomolecule of interest are too simplistic to mimic the “real life” situation, where the biomolecule of interest scrambles and wades through the tightly packed crowd. In laboratory practice, such macromolecular crowding is typically mimicked by concentrated solutions of various polymers that serve as model “crowding agents”. Studies under these conditions revealed that macromolecular crowding might affect protein structure, folding, shape, conformational stability, binding of small molecules, enzymatic activity, protein-protein interactions, protein-nucleic acid interactions, and pathological aggregation. The goal of this review is to systematically analyze currently available experimental data on the variety of effects of macromolecular crowding on a protein molecule. The review covers more than 320 papers and therefore represents one of the most comprehensive compendia of the current knowledge in this exciting area. PMID:25514413

  2. Rigid Biopolymer Nanocrystal Systems for Controlling Multicomponent Nanoparticle Assembly and Orientation in Thin Film Solar Cells

    Energy Technology Data Exchange (ETDEWEB)

    Cha, Jennifer [Univ. of Colorado, Boulder, CO (United States)

    2016-10-31

    We have discovered techniques to synthesize well-defined DN conjugated nanostructures that are stable in a wide variety of conditions needed for DNA mediated assembly. Starting from this, we have shown that DNA can be used to control the assembly and integration of semiconductor nanocrystals into thin film devices that show photovoltaic effects.

  3. MxCuBE: a synchrotron beamline control environment customized for macromolecular crystallography experiments.

    Science.gov (United States)

    Gabadinho, José; Beteva, Antonia; Guijarro, Matias; Rey-Bakaikoa, Vicente; Spruce, Darren; Bowler, Matthew W; Brockhauser, Sandor; Flot, David; Gordon, Elspeth J; Hall, David R; Lavault, Bernard; McCarthy, Andrew A; McCarthy, Joanne; Mitchell, Edward; Monaco, Stéphanie; Mueller-Dieckmann, Christoph; Nurizzo, Didier; Ravelli, Raimond B G; Thibault, Xavier; Walsh, Martin A; Leonard, Gordon A; McSweeney, Sean M

    2010-09-01

    The design and features of a beamline control software system for macromolecular crystallography (MX) experiments developed at the European Synchrotron Radiation Facility (ESRF) are described. This system, MxCuBE, allows users to easily and simply interact with beamline hardware components and provides automated routines for common tasks in the operation of a synchrotron beamline dedicated to experiments in MX. Additional functionality is provided through intuitive interfaces that enable the assessment of the diffraction characteristics of samples, experiment planning, automatic data collection and the on-line collection and analysis of X-ray emission spectra. The software can be run in a tandem client-server mode that allows for remote control and relevant experimental parameters and results are automatically logged in a relational database, ISPyB. MxCuBE is modular, flexible and extensible and is currently deployed on eight macromolecular crystallography beamlines at the ESRF. Additionally, the software is installed at MAX-lab beamline I911-3 and at BESSY beamline BL14.1.

  4. C.R.I.S.T.A.L. Concurrent Repository & Information System for Tracking Assembly and production Lifecycles A data capture and production management tool for the assembly and construction of the CMS ECAL detector

    CERN Document Server

    Le Goff, J M; Barone, G; Bazan, A; Heath, H F; Kovács, Z; Le Flour, T; Leonardi, E; Lieunard, S; McClatchey, R; Organtini, G; Rousset, D; Vialle, J P

    2001-01-01

    The CMS experiment will comprise several very large high resolution detectors for physics. Each detector may be constructed of well over a million parts and will be produced and assembled during the next decade by specialised centres distributed world-wide. Each constituent part of each detector must be accurately measured and tested locally prior to its ultimate assembly and integration in the experimental area at CERN. The CRISTAL project (Concurrent Repository and Information System for Tracking Assembly and production Lifecycles) [1] aims to monitor and control the quality of the production and assembly process to aid in optimising the performance of the physics detectors and to reject unacceptable constituent parts as early as possible in the construction lifecycle. During assembly CRISTAL will capture all the information required for subsequent detector calibration. Distributed instances of Object databases linked via CORBA [2] and with WWW/Java-based query processing are the main technology aspects of ...

  5. Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways.

    Science.gov (United States)

    Seyler, Sean L; Kumar, Avishek; Thorpe, M F; Beckstein, Oliver

    2015-10-01

    Diverse classes of proteins function through large-scale conformational changes and various sophisticated computational algorithms have been proposed to enhance sampling of these macromolecular transition paths. Because such paths are curves in a high-dimensional space, it has been difficult to quantitatively compare multiple paths, a necessary prerequisite to, for instance, assess the quality of different algorithms. We introduce a method named Path Similarity Analysis (PSA) that enables us to quantify the similarity between two arbitrary paths and extract the atomic-scale determinants responsible for their differences. PSA utilizes the full information available in 3N-dimensional configuration space trajectories by employing the Hausdorff or Fréchet metrics (adopted from computational geometry) to quantify the degree of similarity between piecewise-linear curves. It thus completely avoids relying on projections into low dimensional spaces, as used in traditional approaches. To elucidate the principles of PSA, we quantified the effect of path roughness induced by thermal fluctuations using a toy model system. Using, as an example, the closed-to-open transitions of the enzyme adenylate kinase (AdK) in its substrate-free form, we compared a range of protein transition path-generating algorithms. Molecular dynamics-based dynamic importance sampling (DIMS) MD and targeted MD (TMD) and the purely geometric FRODA (Framework Rigidity Optimized Dynamics Algorithm) were tested along with seven other methods publicly available on servers, including several based on the popular elastic network model (ENM). PSA with clustering revealed that paths produced by a given method are more similar to each other than to those from another method and, for instance, that the ENM-based methods produced relatively similar paths. PSA applied to ensembles of DIMS MD and FRODA trajectories of the conformational transition of diphtheria toxin, a particularly challenging example, showed that

  6. Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways.

    Directory of Open Access Journals (Sweden)

    Sean L Seyler

    2015-10-01

    Full Text Available Diverse classes of proteins function through large-scale conformational changes and various sophisticated computational algorithms have been proposed to enhance sampling of these macromolecular transition paths. Because such paths are curves in a high-dimensional space, it has been difficult to quantitatively compare multiple paths, a necessary prerequisite to, for instance, assess the quality of different algorithms. We introduce a method named Path Similarity Analysis (PSA that enables us to quantify the similarity between two arbitrary paths and extract the atomic-scale determinants responsible for their differences. PSA utilizes the full information available in 3N-dimensional configuration space trajectories by employing the Hausdorff or Fréchet metrics (adopted from computational geometry to quantify the degree of similarity between piecewise-linear curves. It thus completely avoids relying on projections into low dimensional spaces, as used in traditional approaches. To elucidate the principles of PSA, we quantified the effect of path roughness induced by thermal fluctuations using a toy model system. Using, as an example, the closed-to-open transitions of the enzyme adenylate kinase (AdK in its substrate-free form, we compared a range of protein transition path-generating algorithms. Molecular dynamics-based dynamic importance sampling (DIMS MD and targeted MD (TMD and the purely geometric FRODA (Framework Rigidity Optimized Dynamics Algorithm were tested along with seven other methods publicly available on servers, including several based on the popular elastic network model (ENM. PSA with clustering revealed that paths produced by a given method are more similar to each other than to those from another method and, for instance, that the ENM-based methods produced relatively similar paths. PSA applied to ensembles of DIMS MD and FRODA trajectories of the conformational transition of diphtheria toxin, a particularly challenging example

  7. Dynamics simulations for engineering macromolecular interactions

    Science.gov (United States)

    Robinson-Mosher, Avi; Shinar, Tamar; Silver, Pamela A.; Way, Jeffrey

    2013-06-01

    The predictable engineering of well-behaved transcriptional circuits is a central goal of synthetic biology. The artificial attachment of promoters to transcription factor genes usually results in noisy or chaotic behaviors, and such systems are unlikely to be useful in practical applications. Natural transcriptional regulation relies extensively on protein-protein interactions to insure tightly controlled behavior, but such tight control has been elusive in engineered systems. To help engineer protein-protein interactions, we have developed a molecular dynamics simulation framework that simplifies features of proteins moving by constrained Brownian motion, with the goal of performing long simulations. The behavior of a simulated protein system is determined by summation of forces that include a Brownian force, a drag force, excluded volume constraints, relative position constraints, and binding constraints that relate to experimentally determined on-rates and off-rates for chosen protein elements in a system. Proteins are abstracted as spheres. Binding surfaces are defined radially within a protein. Peptide linkers are abstracted as small protein-like spheres with rigid connections. To address whether our framework could generate useful predictions, we simulated the behavior of an engineered fusion protein consisting of two 20 000 Da proteins attached by flexible glycine/serine-type linkers. The two protein elements remained closely associated, as if constrained by a random walk in three dimensions of the peptide linker, as opposed to showing a distribution of distances expected if movement were dominated by Brownian motion of the protein domains only. We also simulated the behavior of fluorescent proteins tethered by a linker of varying length, compared the predicted Förster resonance energy transfer with previous experimental observations, and obtained a good correspondence. Finally, we simulated the binding behavior of a fusion of two ligands that could

  8. Ultra-Precise Assembly of Micro-Electromechanical Systems (MEMS) Components

    Energy Technology Data Exchange (ETDEWEB)

    Feddema, J.T.; Simon, R.; Polosky, M.; Christenson, T.

    1999-04-01

    This report summarizes a three year effort to develop an automated microassembly workcell for the assembly of LIGA (Lithography Galvonoforming Abforming) parts. Over the last several years, Sandia has developed processes for producing surface machined silicon and LIGA parts for use in weapons surety devices. Some of these parts have outside dimensions as small as 100 micron, and most all have submicron tolerances. Parts this small and precise are extremely difficult to assembly by hand. Therefore, in this project, we investigated the technologies required to develop a robotic workcell to assembly these parts. In particular, we concentrated on micro-grippers, visual servoing, micro-assembly planning, and parallel assembly. Three different micro-grippers were tested: a pneumatic probe, a thermally actuated polysilicon tweezer, and a LIGA fabricated tweezer. Visual servoing was used to accuracy position two parts relative to one another. Fourier optics methods were used to generate synthetic microscope images from CAD drawings. These synthetic images are used off-line to test image processing routines under varying magnifications and depths of field. They also provide reference image features which are used to visually servo the part to the desired position. We also investigated a new aspect of fine motion planning for the micro-domain. As parts approach 1-10 {micro}m or less in outside dimensions, interactive forces such as van der Waals and electrostatic forces become major factors which greatly change the assembly sequence and path plans. We developed the mathematics required to determine the goal regions for pick up, holding, and release of a micro-sphere being handled by a rectangular tool. Finally, we implemented and tested the ability to assemble an array of LIGA parts attached to two 3 inch diameter wafers. In this way, hundreds of parts can be assembled in parallel rather than assembling each part individually.

  9. Some assembly required: evolutionary and systems perspectives on the mammalian reproductive system.

    Science.gov (United States)

    Mordhorst, Bethany R; Wilson, Miranda L; Conant, Gavin C

    2016-01-01

    In this review, we discuss the way that insights from evolutionary theory and systems biology shed light on form and function in mammalian reproductive systems. In the first part of the review, we contrast the rapid evolution seen in some reproductive genes with the generally conservative nature of development. We discuss directional selection and coevolution as potential drivers of rapid evolution in sperm and egg proteins. Such rapid change is very different from the highly conservative nature of later embryo development. However, it is not unique, as some regions of the sex chromosomes also show elevated rates of evolutionary change. To explain these contradictory trends, we argue that it is not reproductive functions per se that induce rapid evolution. Rather, it is the fact that biotic interactions, such as speciation events and sexual conflict, have no evolutionary endpoint and hence can drive continuous evolutionary changes. Returning to the question of sex chromosome evolution, we discuss the way that recent advances in evolutionary genomics and systems biology and, in particular, the development of a theory of gene balance provide a better understanding of the evolutionary patterns seen on these chromosomes. We end the review with a discussion of a surprising and incompletely understood phenomenon observed in early embryos: namely the Warburg effect, whereby glucose is fermented to lactate and alanine rather than respired to carbon dioxide. We argue that evolutionary insights, from both yeasts and tumor cells, help to explain the Warburg effect, and that new metabolic modeling approaches are useful in assessing the potential sources of the effect.

  10. Can visco-elastic phase separation, macromolecular crowding and colloidal physics explain nuclear organisation?

    Science.gov (United States)

    Iborra, Francisco J

    2007-04-12

    The cell nucleus is highly compartmentalized with well-defined domains, it is not well understood how this nuclear order is maintained. Many scientists are fascinated by the different set of structures observed in the nucleus to attribute functions to them. In order to distinguish functional compartments from non-functional aggregates, I believe is important to investigate the biophysical nature of nuclear organisation. The various nuclear compartments can be divided broadly as chromatin or protein and/or RNA based, and they have very different dynamic properties. The chromatin compartment displays a slow, constrained diffusional motion. On the other hand, the protein/RNA compartment is very dynamic. Physical systems with dynamical asymmetry go to viscoelastic phase separation. This phase separation phenomenon leads to the formation of a long-lived interaction network of slow components (chromatin) scattered within domains rich in fast components (protein/RNA). Moreover, the nucleus is packed with macromolecules in the order of 300 mg/ml. This high concentration of macromolecules produces volume exclusion effects that enhance attractive interactions between macromolecules, known as macromolecular crowding, which favours the formation of compartments. In this paper I hypothesise that nuclear compartmentalization can be explained by viscoelastic phase separation of the dynamically different nuclear components, in combination with macromolecular crowding and the properties of colloidal particles. I demonstrate that nuclear structure can satisfy the predictions of this hypothesis. I discuss the functional implications of this phenomenon.

  11. Long-wavelength macromolecular crystallography - First successful native SAD experiment close to the sulfur edge.

    Science.gov (United States)

    Aurelius, O; Duman, R; El Omari, K; Mykhaylyk, V; Wagner, A

    2017-11-15

    Phasing of novel macromolecular crystal structures has been challenging since the start of structural biology. Making use of anomalous diffraction of natively present elements, such as sulfur and phosphorus, for phasing has been possible for some systems, but hindered by the necessity to access longer X-ray wavelengths in order to make most use of the anomalous scattering contributions of these elements. Presented here are the results from a first successful experimental phasing study of a macromolecular crystal structure at a wavelength close to the sulfur K edge. This has been made possible by the in-vacuum setup and the long-wavelength optimised experimental setup at the I23 beamline at Diamond Light Source. In these early commissioning experiments only standard data collection and processing procedures have been applied, in particular no dedicated absorption correction has been used. Nevertheless the success of the experiment demonstrates that the capability to extract phase information can be even further improved once data collection protocols and data processing have been optimised.

  12. Construction, assembling and application of a trehalase-GOD enzyme electrode system.

    Science.gov (United States)

    Antonelli, M L; Arduini, F; Laganà, A; Moscone, D; Siliprandi, V

    2009-01-01

    Trehalose is a disaccharide important in foods, serving as a glucose source in many and also as an additive in the food preparation. Because of its peculiar physico-chemical properties it plays an important role as preservative in drying and deep-freezing treatments. A new biosensor for trehalose determination has been realized by means of a flow system, based on a reactor in which the trehalase enzyme catalyses its hydrolysis into two alpha,d-glucose molecules, and a GOD (glucose oxidase) amperometric biosensor is employed for the glucose determination. The optimum operative conditions have been laid out and a particular attention has been paid to the immobilization procedure of the two enzymes. The electrode used is of the SPE (screen-printed electrode) type and has been activated with the Prussian Blue (PB) and then assembled using GOD immobilized with Nafion. The reactor has been prepared with the trehalase enzyme chemically immobilized on an Immunodyne ABC membrane. As demonstration of its utility, the biosensor has been tested on a real sample of Boletus edulis mushroom.

  13. Nuclear reactor fuel assembly duct-tube-to-handling-socket attachment system

    Science.gov (United States)

    Christiansen, David W.; Smith, Bob G.

    1982-01-01

    A reusable system for removably attaching the upper end 10of a nuclear reactor duct tube to the lower end 30 of a nuclear reactor fuel assembly handling socket. A transition ring 20, fixed to the duct tube's upper end 10, has an interior-threaded section 22 with a first locking hole segment 24. An adaptor ring 40, fixed to the handling socket's lower end 30 has an outside-threaded section 42 with a second locking hole segment 44. The inside 22 and outside 42 threaded sections match and can be joined so that the first 24 and second 44 locking hole segments can be aligned to form a locking hole. A locking ring 50, with a locking pin 52, slides over the adaptor ring 40 so that the locking pin 52 fits in the locking hole. A swage lock 60 or a cantilever finger lock 70 is formed from the locking cup collar 26 to fit in a matching groove 54 or 56 in the locking ring 50 to prevent the locking ring's locking pin 52 from backing out of the locking hole.

  14. An impact test system design and its applications to dynamic buckling of a spacer grid assembly

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Sheng, E-mail: liusheng_05@126.com; Fan, Chenguang; Yang, Yiren

    2016-11-15

    This study is aimed at investigating the dynamic buckling load, dynamic stiffness, damping and buckling characteristics of the spacer grid assembly (SGA). A pendulum impact test system is designed to experiment the buckling of SGAs. Three criterions are discussed and compared to determine the buckling loads of SGAs: B-R criterion, energy criterion and extreme value criterion. Two approaches are applied to calculate the dynamic stiffness of SGAs: One method is natural period method based on the hypothesis of harmonic motion of the pendulum whose period is approximated because of the passivation and tailing of the impact force time history; and the other is energy method based on the conservation of mechanical energy. The equivalent viscous damping is defined as the resultant cause of dissipation and is obtained by the energy principle. The impact force time history loses its approximate symmetry after buckling occurs. The impact force and displacement reach their maxima almost at the same time at pre-buckling states but not post-buckling states. Vertical straps in SGA are found to be transversely shared by horizontal straps at the buckling position. The buckling of SGA results from the lack of strength of complete structure; and the strength of material has no effects on the buckling.

  15. Assembly of SIV virus-like particles containing envelope proteins using a baculovirus expression system.

    Science.gov (United States)

    Yamshchikov, G V; Ritter, G D; Vey, M; Compans, R W

    1995-12-01

    The requirements for SIV particle assembly and envelope incorporation were investigated using a baculovirus expression system. The Pr56gag precursor protein expressed under control of the polyhedrin promoter (pPolh) produced high levels of immature retrovirus-like particles (VLP) upon expression in Sf9 insect cells. To determine the optimal conditions for envelope protein (Env) incorporation into VLP, two recombinant baculoviruses expressing the SIV envelope protein under control of a very late pPolh or a hybrid late/very late capsid/polyhedrin (Pcap/polh) promoter and a recombinant expressing a truncated form of the SIV envelope protein (Envt) under the hybrid Pcap/polh promoter were compared. We have observed that utilization of the earlier hybrid promoter resulted in higher levels of Env expression on the cell surface and its incorporation into budding virus particles. We have also found that the Envt protein is transported to the cell surface of insect cells and incorporated into VLP more efficiently than full-length Env. In addition, we examined the effect of coexpression of the protease furin, which has been implicated in the proteolytic cleavage of the Env precursor gp160 in mammalian cells. Coexpression of furin in insect cells resulted in more efficient proteolytic cleavage into gp120 and gp41, and the cleaved proteins were incorporated into VLP.

  16. Molecular strategies of microbial iron assimilation: from high-affinity complexes to cofactor assembly systems.

    Science.gov (United States)

    Miethke, Marcus

    2013-01-01

    Microorganisms have to cope with restricted iron bioavailability in most environmental habitats as well as during host colonization. The continuous struggle for iron has brought forth a plethora of acquisition and assimilation strategies that share several functional and mechanistic principles. One common theme is the utilization of high-affinity chelators for extracellular iron mobilization, generally known as siderophore-dependent iron acquisition. This basic strategy is related with another central aspect of microbial iron acquisition, which is the release of the mobilized iron from extracellular sources to allow its transfer and incorporation into metabolically active proteins. A variety of mechanisms which are often coupled with high-affinity uptake have evolved to facilitate the removal of iron from siderophore ligands; however, they differ in many key aspects including substrate specificities and release efficiencies. The most sophisticated iron release pathways comprise processes of specific hydrolysis and reduction of ferric siderophores, especially in the case of high-affinity iron complexes with greatly negative redox potentials that often represent crucial factors for virulence development in bacterial and fungal pathogens. During the following steps of iron utilization, the acquired metal is transferred through intracellular trafficking pathways which may include diverse storage compartments in order to be directed to cofactor assembly systems and to final protein targeting. Several of these iron channeling routes have been described recently and provide first insights into the later steps of iron assimilation that characterize an essential part of the cellular iron homeostasis network.

  17. Study of self assembly system formed by malic acid and alkyloxy benzoic acids

    Energy Technology Data Exchange (ETDEWEB)

    Vijakumar, Vellalapalayam Nallagounder; Madhu Mohan, Mathukumalli Lakshmi Narayana [Bannari Amman Inst. of Technology, Sathyamangalam (IN). Liquid Crystal Research Lab. (LCRL)

    2010-12-15

    Self assembly systems formed by malic acid and alkyloxy benzoic acids are characterized. The ferroelectric ingredient malic acid formed double hydrogen bond with p-n-alkyloxy benzoic acids. Various hydrogen bonded complexes have been synthesized with malic acid and pentyl to dodecyloxy benzoic acid, respectively. Fourier transformation infrared (FTIR) studies confirm the hydrogen bond formation. Polarizing optical microscopic (POM) studies revealed the textural information while the transition and enthalpy values are calculated from differential scanning calorimetry (DSC) studies. A phase diagram has been constructed from the POMand DSC studies. Anew smectic ordering, smectic X*, has been identified which exhibits a finger print type texture. This phase has been characterized by POM, DSC, helix, and tilt angle studies. The transition from traditional cholesteric to smectic X{sup *} phase is observed to be first order. The tilt angle data in this phase has been fitted to a power law and the temperature variation of the tilt angle follows mean field theory predictions. The results of FTIR, POM, DSC, tilt angle, and helicoidal studies are discussed. (orig.)

  18. Advanced topographic laser altimeter system (ATLAS) receiver telescope assembly (RTA) and transmitter alignment and test

    Science.gov (United States)

    Hagopian, John; Bolcar, Matthew; Chambers, John; Crane, Allen; Eegholm, Bente; Evans, Tyler; Hetherington, Samuel; Mentzell, Eric; Thompson, Patrick L.; Ramos-Izquierdo, Luis; Vaughnn, David

    2016-09-01

    The sole instrument on NASA's ICESat-2 spacecraft shown in Figure 1 will be the Advanced Topographic Laser Altimeter System (ATLAS)1. The ATLAS is a Light Detection and Ranging (LIDAR) instrument; it measures the time of flight of the six transmitted laser beams to the Earth and back to determine altitude for geospatial mapping of global ice. The ATLAS laser beam is split into 6 main beams by a Diffractive Optical Element (DOE) that are reflected off of the earth and imaged by an 800 mm diameter Receiver Telescope Assembly (RTA). The RTA is composed of a 2-mirror telescope and Aft Optics Assembly (AOA) that collects and focuses the light from the 6 probe beams into 6 science fibers. Each fiber optic has a field of view on the earth that subtends 83 micro Radians. The light collected by each fiber is detected by a photomultiplier and timing related to a master clock to determine time of flight and therefore distance. The collection of the light from the 6 laser spots projected to the ground allows for dense cross track sampling to provide for slope measurements of ice fields. NASA LIDAR instruments typically utilize telescopes that are not diffraction limited since they function as a light collector rather than imaging function. The more challenging requirements of the ATLAS instrument require better performance of the telescope at the ¼ wave level to provide for improved sampling and signal to noise. NASA Goddard Space Flight Center (GSFC) contracted the build of the telescope to General Dynamics (GD). GD fabricated and tested the flight and flight spare telescope and then integrated the government supplied AOA for testing of the RTA before and after vibration qualification. The RTA was then delivered to GSFC for independent verification and testing over expected thermal vacuum conditions. The testing at GSFC included a measurement of the RTA wavefront error and encircled energy in several orientations to determine the expected zero gravity figure, encircled

  19. The PprA-PprB two-component system activates CupE, the first non-archetypal Pseudomonas aeruginosa chaperione-usher pathway system assembling fimbriae

    DEFF Research Database (Denmark)

    Giraud, Caroline; Bernard, Christophe S.; Calderon, Virginie

    2011-01-01

    The opportunistic pathogen Pseudomonas aeruginosa has redundant molecular systems that contribute to its pathogenicity. Those assembling fimbrial structures promote complex organized community lifestyle. We characterized a new 5.8 kb genetic locus, cupE, that includes the conserved usher- and cha......The opportunistic pathogen Pseudomonas aeruginosa has redundant molecular systems that contribute to its pathogenicity. Those assembling fimbrial structures promote complex organized community lifestyle. We characterized a new 5.8 kb genetic locus, cupE, that includes the conserved usher......AB two-component system (TCS) as a regulator of cupE expression, and further demonstrated the involvement of the PprAB TCS in direct CupE fimbrial assembly activation. Thus, this TCS represents a new regulatory element controlling the transition between planktonic and community lifestyles in P...

  20. Workshop on algorithms for macromolecular modeling. Final project report, June 1, 1994--May 31, 1995

    Energy Technology Data Exchange (ETDEWEB)

    Leimkuhler, B.; Hermans, J.; Skeel, R.D.

    1995-07-01

    A workshop was held on algorithms and parallel implementations for macromolecular dynamics, protein folding, and structural refinement. This document contains abstracts and brief reports from that workshop.

  1. Effect of minimizing amount of template by addition of macromolecular crowding agent on preparation of molecularly imprinted monolith.

    Science.gov (United States)

    Sun, Guang-Ying; Zhong, Dan-Dan; Li, Xiang-Jie; Luo, Yu-Qing; Ba, Hang; Liu, Zhao-Sheng; Aisa, Haji Akber

    2015-09-01

    One of the main challenges in the preparation of molecularly imprinted polymers (MIPs) is the substantial initial amount of template needed because of the requirement of high load capacities for most applications. A new strategy of macromolecular crowding was suggested to solve this problem by reducing the amount of template in the polymerization recipe. In a ternary porogenic system of polystyrene (PS) (crowding agent), tetrahydrofuran, and toluene, an imprinted monolithic column with high porosity and good permeability was synthesized using a mixture of ellagic acid (template), acrylamide, and ethylene glycol dimethacrylate. The effect of polymerization factors, including monomer-template molar ratio and the molecular weight and concentration of PS, on the imprinting effect of the resulting MIP monoliths was systematically investigated. At a high ratio of monomer-template (120:1), the greatest imprinting factor of 32.4 was obtained on the MIP monolith with the aid of macromolecular crowding agent. The PS-based imprinted monolith had imprinting even at the extremely high ratio of functional monomer to template of 1510:1. Furthermore, an off-line solid-phase extraction based on the ground MIP was conducted, and the purification recovery of ellagic acid from pomegranate-rind extract was up to 80 %. In conclusion, this approach based on macromolecular crowding is simple, and is especially valuable for those applications of MIP preparation for which a rare template is used.

  2. The contrasting effect of macromolecular crowding on amyloid fibril formation.

    Directory of Open Access Journals (Sweden)

    Qian Ma

    Full Text Available Amyloid fibrils associated with neurodegenerative diseases can be considered biologically relevant failures of cellular quality control mechanisms. It is known that in vivo human Tau protein, human prion protein, and human copper, zinc superoxide dismutase (SOD1 have the tendency to form fibril deposits in a variety of tissues and they are associated with different neurodegenerative diseases, while rabbit prion protein and hen egg white lysozyme do not readily form fibrils and are unlikely to cause neurodegenerative diseases. In this study, we have investigated the contrasting effect of macromolecular crowding on fibril formation of different proteins.As revealed by assays based on thioflavin T binding and turbidity, human Tau fragments, when phosphorylated by glycogen synthase kinase-3β, do not form filaments in the absence of a crowding agent but do form fibrils in the presence of a crowding agent, and the presence of a strong crowding agent dramatically promotes amyloid fibril formation of human prion protein and its two pathogenic mutants E196K and D178N. Such an enhancing effect of macromolecular crowding on fibril formation is also observed for a pathological human SOD1 mutant A4V. On the other hand, rabbit prion protein and hen lysozyme do not form amyloid fibrils when a crowding agent at 300 g/l is used but do form fibrils in the absence of a crowding agent. Furthermore, aggregation of these two proteins is remarkably inhibited by Ficoll 70 and dextran 70 at 200 g/l.We suggest that proteins associated with neurodegenerative diseases are more likely to form amyloid fibrils under crowded conditions than in dilute solutions. By contrast, some of the proteins that are not neurodegenerative disease-associated are unlikely to misfold in crowded physiological environments. A possible explanation for the contrasting effect of macromolecular crowding on these two sets of proteins (amyloidogenic proteins and non-amyloidogenic proteins has been

  3. SASSIE: A program to study intrinsically disordered biological molecules and macromolecular ensembles using experimental scattering restraints

    Science.gov (United States)

    Curtis, Joseph E.; Raghunandan, Sindhu; Nanda, Hirsh; Krueger, Susan

    2012-02-01

    A program to construct ensembles of biomolecular structures that are consistent with experimental scattering data are described. Specifically, we generate an ensemble of biomolecular structures by varying sets of backbone dihedral angles that are then filtered using experimentally determined restraints to rapidly determine structures that have scattering profiles that are consistent with scattering data. We discuss an application of these tools to predict a set of structures for the HIV-1 Gag protein, an intrinsically disordered protein, that are consistent with small-angle neutron scattering experimental data. We have assembled these algorithms into a program called SASSIE for structure generation, visualization, and analysis of intrinsically disordered proteins and other macromolecular ensembles using neutron and X-ray scattering restraints. Program summaryProgram title: SASSIE Catalogue identifier: AEKL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License v3 No. of lines in distributed program, including test data, etc.: 3 991 624 No. of bytes in distributed program, including test data, etc.: 826 Distribution format: tar.gz Programming language: Python, C/C++, Fortran Computer: PC/Mac Operating system: 32- and 64-bit Linux (Ubuntu 10.04, Centos 5.6) and Mac OS X (10.6.6) RAM: 1 GB Classification: 3 External routines: Python 2.6.5, numpy 1.4.0, swig 1.3.40, scipy 0.8.0, Gnuplot-py-1.8, Tcl 8.5, Tk 8.5, Mac installation requires aquaterm 1.0 (or X window system) and Xcode 3 development tools. Nature of problem: Open source software to generate structures of disordered biological molecules that subsequently allow for the comparison of computational and experimental results is limiting the use of scattering resources. Solution method: Starting with an all atom model of a protein, for example, users can input

  4. Thermodynamic signatures in macromolecular interactions involving conformational flexibility.

    Science.gov (United States)

    Menzel, Anja; Neumann, Piotr; Schwieger, Christian; Stubbs, Milton T

    2014-07-01

    The energetics of macromolecular interactions are complex, particularly where protein flexibility is involved. Exploiting serendipitous differences in the plasticity of a series of closely related trypsin variants, we analyzed the enthalpic and entropic contributions accompanying interaction with L45K-eglin C. Binding of the four variants show significant differences in released heat, although the affinities vary little, in accordance with the principle of enthalpy-entropy compensation. Binding of the most disordered variant is almost entirely enthalpically driven, with practically no entropy change. As structures of the complexes reveal negligible differences in protein-inhibitor contacts, we conclude that solvent effects contribute significantly to binding affinities.

  5. Phototrophic biofilm assembly in microbial-mat-derived unicyanobacterial consortia: model systems for the study of autotroph-heterotroph interactions

    Directory of Open Access Journals (Sweden)

    Jessica K Cole

    2014-04-01

    Full Text Available Microbial autotroph-heterotroph interactions influence biogeochemical cycles on a global scale, but the diversity and complexity of natural systems and their intractability to in situ manipulation make it challenging to elucidate the principles governing these interactions. The study of assembling phototrophic biofilm communities provides a robust means to identify such interactions and evaluate their contributions to the recruitment and maintenance of phylogenetic and functional diversity over time. To examine primary succession in phototrophic communities, we isolated two unicyanobacterial consortia from the microbial mat in Hot Lake, Washington, characterizing the membership and metabolic function of each consortium. We then analyzed the spatial structures and quantified the community compositions of their assembling biofilms. The consortia retained the same suite of heterotrophic species, identified as abundant members of the mat and assigned to Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes. Autotroph growth rates dominated early in assembly, yielding to increasing heterotroph growth rates late in succession. The two consortia exhibited similar assembly patterns, with increasing relative abundances of members from Bacteroidetes and Alphaproteobacteria concurrent with decreasing relative abundances of those from Gammaproteobacteria. Despite these similarities at higher taxonomic levels, the relative abundances of individual heterotrophic species were substantially different in the developing consortial biofilms. This suggests that, although similar niches are created by the cyanobacterial metabolisms, the resulting webs of autotroph-heterotroph and heterotroph-heterotroph interactions are specific to each primary producer. The relative simplicity and tractability of the Hot Lake unicyanobacterial consortia make them useful model systems for deciphering interspecies interactions and assembly principles relevant to natural

  6. ROSA-V large scale test facility (LSTF) system description for the third and fourth simulated fuel assemblies

    Energy Technology Data Exchange (ETDEWEB)

    Suzuki, Mitsuhiro; Nakamura, Hideo; Ohtsu, Iwao [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment] [and others

    2003-03-01

    The Large Scale Test Facility (LSTF) is a full-height and 1/48 volumetrically scaled test facility of the Japan Atomic Energy Research Institute (JAERI) for system integral experiments simulating the thermal-hydraulic responses at full-pressure conditions of a 1100 MWe-class pressurized water reactor (PWR) during small break loss-of-coolant accidents (SBLOCAs) and other transients. The LSTF can also simulate well a next-generation type PWR such as the AP600 reactor. In the fifth phase of the Rig-of-Safety Assessment (ROSA-V) Program, eighty nine experiments have been conducted at the LSTF with the third simulated fuel assembly until June 2001, and five experiments have been conducted with the newly-installed fourth simulated fuel assembly until December 2002. In the ROSA-V program, various system integral experiments have been conducted to certify effectiveness of both accident management (AM) measures in beyond design basis accidents (BDBAs) and improved safety systems in the next-generation reactors. In addition, various separate-effect tests have been conducted to verify and develop computer codes and analytical models to predict non-homogeneous and multi-dimensional phenomena such as heat transfer across the steam generator U-tubes under the presence of non-condensable gases in both current and next-generation reactors. This report presents detailed information of the LSTF system with the third and fourth simulated fuel assemblies for the aid of experiment planning and analyses of experiment results. (author)

  7. Improvements toward highly accurate diffraction experiments at the macromolecular micro-crystallography beamline BL-17A.

    Science.gov (United States)

    Yamada, Yusuke; Chavas, Leonard M G; Igarashi, Noriyuki; Hiraki, Masahiko; Wakatsuki, Soichi; Matsugaki, Naohiro

    2013-11-01

    BL-17A is a macromolecular crystallography beamline dedicated to diffraction experiments conducted using micro-crystals and structure determination studies using a lower energy X-ray beam. In these experiments, highly accurate diffraction intensity measurements are definitively important. Since this beamline was constructed, the beamline apparatus has been improved in several ways to enable the collection of accurate diffraction data. The stability of the beam intensities at the sample position was recently improved by modifying the monochromator. The diffractometer has also been improved. A new detector table was installed to prevent distortions in the diffractometer's base during the repositioning of the diffractometer detector. A new pinhole system and an on-axis viewing system were installed to improve the X-ray beam profile at the sample position and the centering of tiny crystal samples.

  8. TOPAAS, a Tomato and Potato Assembly Assistance System for Selection and Finishing of Bacterial Artificial Chromosomes1[W

    Science.gov (United States)

    Peters, Sander A.; van Haarst, Jan C.; Jesse, Taco P.; Woltinge, Dennis; Jansen, Kim; Hesselink, Thamara; van Staveren, Marjo J.; Abma-Henkens, Marleen H.C.; Klein-Lankhorst, René M.

    2006-01-01

    We have developed the software package Tomato and Potato Assembly Assistance System (TOPAAS), which automates the assembly and scaffolding of contig sequences for low-coverage sequencing projects. The order of contigs predicted by TOPAAS is based on read pair information; alignments between genomic, expressed sequence tags, and bacterial artificial chromosome (BAC) end sequences; and annotated genes. The contig scaffold is used by TOPAAS for automated design of nonredundant sequence gap-flanking PCR primers. We show that TOPAAS builds reliable scaffolds for tomato (Solanum lycopersicum) and potato (Solanum tuberosum) BAC contigs that were assembled from shotgun sequences covering the target at 6- to 8-fold coverage. More than 90% of the gaps are closed by sequence PCR, based on the predicted ordering information. TOPAAS also assists the selection of large genomic insert clones from BAC libraries for walking. For this, tomato BACs are screened by automated BLAST analysis and in parallel, high-density nonselective amplified fragment length polymorphism fingerprinting is used for constructing a high-resolution BAC physical map. BLAST and amplified fragment length polymorphism analysis are then used together to determine the precise overlap. Assembly onto the seed BAC consensus confirms the BACs are properly selected for having an extremely short overlap and largest extending insert. This method will be particularly applicable where related or syntenic genomes are sequenced, as shown here for the Solanaceae, and potentially useful for the monocots Brassicaceae and Leguminosea. PMID:16524981

  9. Assembling a prototype resonance electrical impedance spectroscopy system for breast tissue signal detection: preliminary assessment

    Science.gov (United States)

    Sumkin, Jules; Zheng, Bin; Gruss, Michelle; Drescher, John; Leader, Joseph; Good, Walter; Lu, Amy; Cohen, Cathy; Shah, Ratan; Zuley, Margarita; Gur, David

    2008-03-01

    Using electrical impedance spectroscopy (EIS) technology to detect breast abnormalities in general and cancer in particular has been attracting research interests for decades. Large clinical tests suggest that current EIS systems can achieve high specificity (>= 90%) at a relatively low sensitivity ranging from 15% to 35%. In this study, we explore a new resonance frequency based electrical impedance spectroscopy (REIS) technology to measure breast tissue EIS signals in vivo, which aims to be more sensitive to small tissue changes. Through collaboration between our imaging research group and a commercial company, a unique prototype REIS system has been assembled and preliminary signal acquisition has commenced. This REIS system has two detection probes mounted in the two ends of a Y-shape support device with probe separation of 60 mm. During REIS measurement, one probe touches the nipple and the other touches to an outer point of the breast. The electronic system continuously generates sweeps of multi-frequency electrical pulses ranging from 100 to 4100 kHz. The maximum electric voltage and the current applied to the probes are 1.5V and 30mA, respectively. Once a "record" command is entered, multi-frequency sweeps are recorded every 12 seconds until the program receives a "stop recording" command. In our imaging center, we have collected REIS measurements from 150 women under an IRB approved protocol. The database includes 58 biopsy cases, 78 screening negative cases, and other "recalled" cases (for additional imaging procedures). We measured eight signal features from the effective REIS sweep of each breast. We applied a multi-feature based artificial neural network (ANN) to classify between "biopsy" and normal "non-biopsy" breasts. The ANN performance is evaluated using a leave-one-out validation method and ROC analysis. We conducted two experiments. The first experiment attempted to classify 58 "biopsy" breasts and 58 "non-biopsy" breasts acquired on 58 women

  10. Surfaces wettability and morphology modulation in a fluorene derivative self-assembly system

    Science.gov (United States)

    Cao, Xinhua; Gao, Aiping; Zhao, Na; Yuan, Fangyuan; Liu, Chenxi; Li, Ruru

    2016-04-01

    A new organogelator based on fluorene derivative (gelator 1) was designed and synthesized. Organogels could be obtained via the self-assembly of the derivative in acetone, toluene, ethyl acetate, hexane, DMSO and petroleum ether. The self-assembly process was thoroughly characterized using field-emission scanning electron microscopy (FESEM), X-ray diffraction (XRD), UV-vis, FT-IR and the contact angle. Surfaces with different morphologies and wetting properties were formed via the self-assembly of gelator 1 in the six different solvents. Interestingly, a superhydrophobic surface with a contact angle of 150° was obtained from organogel 1 in DMSO and exhibited the lotus-effect. The sliding angle necessary for a water droplet to move on the glass was only 15°. Hydrogen bonding and van der Waals forces were attributed as the main driving forces for gel formation.

  11. Engineered Living Materials: Prospects and Challenges for Using Biological Systems to Direct the Assembly of Smart Materials.

    Science.gov (United States)

    Nguyen, Peter Q; Courchesne, Noémie-Manuelle Dorval; Duraj-Thatte, Anna; Praveschotinunt, Pichet; Joshi, Neel S

    2018-02-12

    Vast potential exists for the development of novel, engineered platforms that manipulate biology for the production of programmed advanced materials. Such systems would possess the autonomous, adaptive, and self-healing characteristics of living organisms, but would be engineered with the goal of assembling bulk materials with designer physicochemical or mechanical properties, across multiple length scales. Early efforts toward such engineered living materials (ELMs) are reviewed here, with an emphasis on engineered bacterial systems, living composite materials which integrate inorganic components, successful examples of large-scale implementation, and production methods. In addition, a conceptual exploration of the fundamental criteria of ELM technology and its future challenges is presented. Cradled within the rich intersection of synthetic biology and self-assembling materials, the development of ELM technologies allows the power of biology to be leveraged to grow complex structures and objects using a palette of bio-nanomaterials. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Systems and methods for creation of conducting networks of magnetic particles through dynamic self-assembly process

    Energy Technology Data Exchange (ETDEWEB)

    Snezhko, Oleksiy [Woodridge, IL; Aronson, Igor [Darien, IL; Kwok, Wai-Kwong [Downers Grove, IL

    2011-01-25

    Self-assembly of magnetic microparticles in AC magnetic fields. Excitation of the system by an AC magnetic field provides a variety of patterns that can be controlled by adjusting the frequency and the amplitude of the field. At low particle densities the low-frequency magnetic excitation favors cluster phase formation, while high frequency excitation favors chains and netlike structures. For denser configurations, an abrupt transition to the network phase was obtained.

  13. PRIGo: a new multi-axis goniometer for macromolecular crystallography.

    Science.gov (United States)

    Waltersperger, Sandro; Olieric, Vincent; Pradervand, Claude; Glettig, Wayne; Salathe, Marco; Fuchs, Martin R; Curtin, Adrian; Wang, Xiaoqiang; Ebner, Simon; Panepucci, Ezequiel; Weinert, Tobias; Schulze-Briese, Clemens; Wang, Meitian

    2015-07-01

    The Parallel Robotics Inspired Goniometer (PRIGo) is a novel compact and high-precision goniometer providing an alternative to (mini-)kappa, traditional three-circle goniometers and Eulerian cradles used for sample reorientation in macromolecular crystallography. Based on a combination of serial and parallel kinematics, PRIGo emulates an arc. It is mounted on an air-bearing stage for rotation around ω and consists of four linear positioners working synchronously to achieve x, y, z translations and χ rotation (0-90°), followed by a ϕ stage (0-360°) for rotation around the sample holder axis. Owing to the use of piezo linear positioners and active correction, PRIGo features spheres of confusion of <1 µm, <7 µm and <10 µm for ω, χ and ϕ, respectively, and is therefore very well suited for micro-crystallography. PRIGo enables optimal strategies for both native and experimental phasing crystallographic data collection. Herein, PRIGo hardware and software, its calibration, as well as applications in macromolecular crystallography are described.

  14. PRIGo: a new multi-axis goniometer for macromolecular crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Waltersperger, Sandro; Olieric, Vincent, E-mail: vincent.olieric@psi.ch; Pradervand, Claude [Paul Scherrer Institute, Villigen PSI (Switzerland); Glettig, Wayne [Centre Suisse d’Electronique et Microtechnique SA, Neuchâtel 2002 (Switzerland); Salathe, Marco; Fuchs, Martin R.; Curtin, Adrian; Wang, Xiaoqiang; Ebner, Simon; Panepucci, Ezequiel; Weinert, Tobias [Paul Scherrer Institute, Villigen PSI (Switzerland); Schulze-Briese, Clemens [Dectris Ltd, Baden 5400 (Switzerland); Wang, Meitian, E-mail: vincent.olieric@psi.ch [Paul Scherrer Institute, Villigen PSI (Switzerland)

    2015-05-09

    The design and performance of the new multi-axis goniometer PRIGo developed at the Swiss Light Source at Paul Scherrer Institute is described. The Parallel Robotics Inspired Goniometer (PRIGo) is a novel compact and high-precision goniometer providing an alternative to (mini-)kappa, traditional three-circle goniometers and Eulerian cradles used for sample reorientation in macromolecular crystallography. Based on a combination of serial and parallel kinematics, PRIGo emulates an arc. It is mounted on an air-bearing stage for rotation around ω and consists of four linear positioners working synchronously to achieve x, y, z translations and χ rotation (0–90°), followed by a ϕ stage (0–360°) for rotation around the sample holder axis. Owing to the use of piezo linear positioners and active correction, PRIGo features spheres of confusion of <1 µm, <7 µm and <10 µm for ω, χ and ϕ, respectively, and is therefore very well suited for micro-crystallography. PRIGo enables optimal strategies for both native and experimental phasing crystallographic data collection. Herein, PRIGo hardware and software, its calibration, as well as applications in macromolecular crystallography are described.

  15. Conformational studies of common protein templates in macromolecularly imprinted polymers.

    Science.gov (United States)

    Kryscio, David R; Fleming, Michael Q; Peppas, Nicholas A

    2012-08-01

    Unlike the molecular imprinting of small molecule templates, molecularly imprinted polymers specific to large templates (>1,500 Da), have achieved limited success to date. Conformational stability of these labile macromolecules is one of the main factors that prevent the direct extension of successful procedures from the small molecule regime. We continue our systematic investigation of the effect of common components in macromolecular MIPs on the conformation of protein templates. Circular dichroism was used to show that frequently employed monomers and crosslinkers induce significant changes in the secondary structures of lysozyme and bovine hemoglobin. The extent to which this change occurs, at ligand concentrations far below what are typically used reported work, is cause for concern and provides as rational explanation for the lack of success in this arena. This is because a change in the template structure prior to polymerization would lead to the binding sites formed during polymerization to be specific to this alternate conformation. Subsequent studies with the macromolecule in its native state and the crosslinked network would not be successful. Using this information as a guide, we offer suggestions as to where work in macromolecular imprinted polymers should focus going forward in order for these antibody mimics to reach their vast potential as a new class of biomedical diagnostic devices.

  16. Branched Macromolecular Architectures for Degradable, Multifunctional Phosphorus-Based Polymers.

    Science.gov (United States)

    Henke, Helena; Brüggemann, Oliver; Teasdale, Ian

    2017-02-01

    This feature article briefly highlights some of the recent advances in polymers in which phosphorus is an integral part of the backbone, with a focus on the preparation of functional, highly branched, soluble polymers. A comparison is made between the related families of materials polyphosphazenes, phosphazene/phosphorus-based dendrimers and polyphosphoesters. The work described herein shows this to be a rich and burgeoning field, rapidly catching up with organic chemistry in terms of the macromolecular synthetic control and variety of available macromolecular architectures, whilst offering unique property combinations not available with carbon backbones, such as tunable degradation rates, high multi-valency and facile post-polymerization functionalization. As an example of their use in advanced applications, we highlight some investigations into their use as water-soluble drug carriers, whereby in particular the degradability in combination with multivalent nature has made them useful materials, as underlined by some of the recent studies in this area. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Changes in the macromolecular structure of coals with pyrolysis temperature

    Energy Technology Data Exchange (ETDEWEB)

    Ndaji, F.E.; Butterfield, I.M.; Thomas, K.M. [University of Newcastle upon Tyne, Newcastle upon Tyne (United Kingdom). Northern Carbon Research Labs., Dept. of Chemistry

    1997-01-01

    The macromolecular structure of coal is characterised by its cross-link density. This paper describes a study of the effect of pyrolysis temperature on the macromolecular structure of coal using solvent swelling techniques. Heat treatment initially dissociates the intermolecular interactions in the coal and cleaves some cross-links, leading to increase in the solvent swelling of the coal, which indicates a decrease in the cross-link density. The solvent swelling reaches a maximum before cross-linking reactions predominate, causing a progressive increase in cross-link density and a decrease in solvent swelling. For lower-rank coals there appears to be an overlap (near the temperature of minimum cross-link density) of the dissociation of intermolecular interactions and thermal decomposition. Appreciable decrease in the apparent cross-link density of high-rank coals as indicated by increase in solvent swelling was observed only after thermal decomposition had commenced. Major decomposition involves cross-linking reactions leading to the formation of chars. However, the solvent swelling characteristics continue to change above the resolidification temperature, eventually ceasing at {approximately}600{degree}C. The results are discussed in relation to measurements of thermoplastic properties and devolatilization characteristics. 23 refs., 4 figs., 3 tabs.

  18. Mauve assembly metrics.

    Science.gov (United States)

    Darling, Aaron E; Tritt, Andrew; Eisen, Jonathan A; Facciotti, Marc T

    2011-10-01

    High-throughput DNA sequencing technologies have spurred the development of numerous novel methods for genome assembly. With few exceptions, these algorithms are heuristic and require one or more parameters to be manually set by the user. One approach to parameter tuning involves assembling data from an organism with an available high-quality reference genome, and measuring assembly accuracy using some metrics. We developed a system to measure assembly quality under several scoring metrics, and to compare assembly quality across a variety of assemblers, sequence data types, and parameter choices. When used in conjunction with training data such as a high-quality reference genome and sequence reads from the same organism, our program can be used to manually identify an optimal sequencing and assembly strategy for de novo sequencing of related organisms. GPL source code and a usage tutorial is at http://ngopt.googlecode.com aarondarling@ucdavis.edu Supplementary data is available at Bioinformatics online.

  19. Signal amplification by a self-assembled biosensor system designed on the principle of dockerin-cohesin interactions in a cellulosome complex.

    Science.gov (United States)

    Hyeon, Jeong Eun; Kang, Dae Hee; Han, Sung Ok

    2014-10-07

    To construct a self-assembled biosensor with signal amplification, a cellulosome system, comprising type I and type II dockerin-cohesin interactions with different specificities, from the anaerobic Clostridia bacterium was applied. The self-assembled biosensor was highly sensitive and achieved 128.1-fold increase in detection levels compared to the control.

  20. End-to-End Printed-Circuit Board Assembly Design Using Altium Designer and Solid Works Systems

    Directory of Open Access Journals (Sweden)

    A. M. Goncharenko

    2015-01-01

    Full Text Available The main goal of this white paper is to investigate the methods to accelerate the end-to-end simultaneous development of electronic PC assemblies in MCAD/ECAD systems. With raising the produced electronic equipment rates and quantities, there is a need to speed up the yield of new products. The article offers an alternate approach to the end-to-end simultaneous development in Altium Designer / Solid Works CAD/CAE systems, which enables a radically shortened time to design new devices and databases of components.The first part of the paper analyses the methods and models to solve the tasks of the endto-end simultaneous development of PC assemblies using the Circuit Works module for Solid Works. It examines the problems of traditional data exchange methods between Altium Designer and Solid Works arising from the limitations of the IDF 2.0 format used, as well as from the problems of 3D-models of components and because it is necessary to support two different databases.The second part gives guidelines and an example of the end-to-end simultaneous PC assembly development using the Altium Modeler module for Solid Works aimed at Altium Designer and presents a brief review of algorithms. The proposed method neither requires an additional database, nor uses an intermediate format such as IDF. The module translates the PCB model directly to Solid Works to generate the assembly model. The Altium Modeler is also capable to update its created assembly in Solid Works, which is very useful in case of modification of components and PCB itself. This approach is better tailored to the end-to-end development in terms of acceleration, enhancing facility of simultaneous work in different MCAD/ECAD systems, and eliminating errors arising from the need to support two CAD databases of the same functionality.In the conclusion the paper gives suggestions for using the modules for simultaneous development of electronic PC assemblies in Altium Designer and Solid Works.

  1. A computer-oriented system for assembling and displaying land management information

    Science.gov (United States)

    Elliot L. Amidon

    1964-01-01

    Maps contain information basic to land management planning. By transforming conventional map symbols into numbers which are punched into cards, the land manager can have a computer assemble and display information required for a specific job. He can let a computer select information from several maps, combine it with such nonmap data as treatment cost or benefit per...

  2. Species sorting during biofilm assembly by artificial substrates deployed in a cold seep system

    KAUST Repository

    Zhang, Wei Peng

    2014-10-17

    Studies focusing on biofilm assembly in deep-sea environments are rarely conducted. To examine the effects of substrate type on microbial community assembly, biofilms were developed on different substrates for different durations at two locations in the Red Sea: in a brine pool and in nearby bottom water (NBW) adjacent to the Thuwal cold seep II. The composition of the microbial communities in 51 biofilms and water samples were revealed by classification of pyrosequenced 16S rRNA gene amplicons. Together with the microscopic characteristics of the biofilms, the results indicate a stronger selection effect by the substrates on the microbial assembly in the brine pool compared with the NBW. Moreover, the selection effect by substrate type was stronger in the early stages compared with the later stages of the biofilm development. These results are consistent with the hypotheses proposed in the framework of species sorting theory, which states that the power of species sorting during microbial community assembly is dictated by habitat conditions, duration and the structure of the source community. Therefore, the results of this study shed light on the control strategy underlying biofilm-associated marine fouling and provide supporting evidence for ecological theories important for understanding the formation of deep-sea biofilms.

  3. Plant X-tender: An extension of the AssemblX system for the assembly and expression of multigene constructs in plants.

    Science.gov (United States)

    Lukan, Tjaša; Machens, Fabian; Coll, Anna; Baebler, Špela; Messerschmidt, Katrin; Gruden, Kristina

    2018-01-01

    Cloning multiple DNA fragments for delivery of several genes of interest into the plant genome is one of the main technological challenges in plant synthetic biology. Despite several modular assembly methods developed in recent years, the plant biotechnology community has not widely adopted them yet, probably due to the lack of appropriate vectors and software tools. Here we present Plant X-tender, an extension of the highly efficient, scar-free and sequence-independent multigene assembly strategy AssemblX, based on overlap-depended cloning methods and rare-cutting restriction enzymes. Plant X-tender consists of a set of plant expression vectors and the protocols for most efficient cloning into the novel vector set needed for plant expression and thus introduces advantages of AssemblX into plant synthetic biology. The novel vector set covers different backbones and selection markers to allow full design flexibility. We have included ccdB counterselection, thereby allowing the transfer of multigene constructs into the novel vector set in a straightforward and highly efficient way. Vectors are available as empty backbones and are fully flexible regarding the orientation of expression cassettes and addition of linkers between them, if required. We optimised the assembly and subcloning protocol by testing different scar-less assembly approaches: the noncommercial SLiCE and TAR methods and the commercial Gibson assembly and NEBuilder HiFi DNA assembly kits. Plant X-tender was applicable even in combination with low efficient homemade chemically competent or electrocompetent Escherichia coli. We have further validated the developed procedure for plant protein expression by cloning two cassettes into the newly developed vectors and subsequently transferred them to Nicotiana benthamiana in a transient expression setup. Thereby we show that multigene constructs can be delivered into plant cells in a streamlined and highly efficient way. Our results will support faster

  4. Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy.

    Science.gov (United States)

    Joseph, Agnel Praveen; Lagerstedt, Ingvar; Patwardhan, Ardan; Topf, Maya; Winn, Martyn

    2017-07-01

    Recent developments in 3-dimensional electron microcopy (3D-EM) techniques and a concomitant drive to look at complex molecular structures, have led to a rapid increase in the amount of volume data available for biomolecules. This creates a demand for better methods to analyse the data, including improved scores for comparison, classification and integration of data at different resolutions. To this end, we developed and evaluated a set of scoring functions that compare 3D-EM volumes. To test our scores we used a benchmark set of volume alignments derived from the Electron Microscopy Data Bank. We find that the performance of different scores vary with the map-type, resolution and the extent of overlap between volumes. Importantly, adding the overlap information to the local scoring functions can significantly improve their precision and accuracy in a range of resolutions. A combined score involving the local mutual information and overlap (LMI_OV) performs best overall, irrespective of the map category, resolution or the extent of overlap, and we recommend this score for general use. The local mutual information score itself is found to be more discriminatory than cross-correlation coefficient for intermediate-to-low resolution maps or when the map size and density distribution differ significantly. For comparing map surfaces, we implemented two filters to detect the surface points, including one based on the 'extent of surface exposure'. We show that scores that compare surfaces are useful at low resolutions and for maps with evident surface features. All the scores discussed are implemented in TEMPy (http://tempy.ismb.lon.ac.uk/). Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  5. Three-dimensional electron microscopy of macromolecular assemblies: visualization of biological molecules in their native state

    National Research Council Canada - National Science Library

    Frank, J

    2006-01-01

    ... Clusters 2.8 Support Grids 33 33 3 Principle of Image Formation in the Transmission Electron Microscope 34 3.1 Introduction 34 3.2 The Weak-Phase Object Approximation 35 3.3 The Contrast Transfer...

  6. Theory and applications of the generalized Born solvation model in macromolecular simulations.

    Science.gov (United States)

    Tsui, V; Case, D A

    Generalized Born (GB) models provide an attractive way to include some thermodynamic aspects of aqueous solvation into simulations that do not explicitly model the solvent molecules. Here we discuss our recent experience with this model, presenting in detail the way it is implemented and parallelized in the AMBER molecular modeling code. We compare results using the GB model (or GB plus a surface-area based "hydrophobic" term) to explicit solvent simulations for a 10 base-pair DNA oligomer, and for the 108-residue protein thioredoxin. A slight modification of our earlier suggested parameters makes the GB results more like those found in explicit solvent, primarily by slightly increasing the strength of NH [bond] O and NH [bond] N internal hydrogen bonds. Timing and energy stability results are reported, with an eye toward using these model for simulations of larger macromolecular systems and longer time scales. Copyright 2001 John Wiley & Sons, Inc. Biopolymers (Nucleic Acid Sci) 56: 275-291, 2001

  7. Prevention of significant deterioration permit application for the Fueled Clad Fabrication System, the Radioisotope Power Systems Facility, and the Fuel Assembly Area

    Energy Technology Data Exchange (ETDEWEB)

    1989-08-01

    This New Source Review'' has been submitted by the US Department of Energy-Richland Operations Office (PO Box 550, Richland, Washington 99352), pursuant to WAC 173-403-050 and in compliance with the Department of Ecology Guide to Processing A Prevention Of Significant Deterioration (PSD) Permit'' for three new sources of radionuclide emissions at the Hanford Site in Washington State. The three new sources, the Fueled Clad Fabrication System (FCFS), the Radioisotope Power Systems Facility (RPSF), and the Fuel Assembly Area (FAA), will be located in one facility, the Fuels and Materials Examination Facility (FMEF) of the 400 Area. The FMEF was originally designed to provide for post-irradiation examination and fabrication of breeder reactor fuels. These FMEF missions were cancelled before the introduction of any fuel materials or any irradiated material. The current plans are to use the facility to fabricate power supplies for use in space applications and to produce Fast Flux Test Facility (FFTF) fuel and target assemblies. The FCFS and the RPSF will produce materials and assemblies for application in space. The FAA project will produce FFTF fuel and target assemblies. The FCFS and the RPSF will share the same building, stack, and, in certain cases, the same floor space. Given this relationship, these systems will be dealt with separately to the extent possible. The FAA is a comparatively independent operation though it will share the FMEF complex.

  8. A biomimetic colorimetric logic gate system based on multi-functional peptide-mediated gold nanoparticle assembly.

    Science.gov (United States)

    Li, Yong; Li, Wang; He, Kai-Yu; Li, Pei; Huang, Yan; Nie, Zhou; Yao, Shou-Zhuo

    2016-04-28

    In natural biological systems, proteins exploit various functional peptide motifs to exert target response and activity switch, providing a functional and logic basis for complex cellular activities. Building biomimetic peptide-based bio-logic systems is highly intriguing but remains relatively unexplored due to limited logic recognition elements and complex signal outputs. In this proof-of-principle work, we attempted to address these problems by utilizing multi-functional peptide probes and the peptide-mediated nanoparticle assembly system. Here, the rationally designed peptide probes function as the dual-target responsive element specifically responsive to metal ions and enzymes as well as the mediator regulating the assembly of gold nanoparticles (AuNPs). Taking advantage of Zn2+ ions and chymotrypsin as the model inputs of metal ions and enzymes, respectively, we constructed the peptide logic system computed by the multi-functional peptide probes and outputted by the readable colour change of AuNPs. In this way, the representative binary basic logic gates (AND, OR, INHIBIT, NAND, IMPLICATION) have been achieved by delicately coding the peptide sequence, demonstrating the versatility of our logic system. Additionally, we demonstrated that the three-input combinational logic gate (INHIBIT-OR) could also be successfully integrated and applied as a multi-tasking biosensor for colorimetric detection of dual targets. This nanoparticle-based peptide logic system presents a valid strategy to illustrate peptide information processing and provides a practical platform for executing peptide computing or peptide-related multiplexing sensing, implying that the controllable nanomaterial assembly is a promising and potent methodology for the advancement of biomimetic bio-logic computation.

  9. Morphogenesis and Optoelectronic Properties of Supramolecular Assemblies of Chiral Perylene Diimides in a Binary Solvent System.

    Science.gov (United States)

    Shang, Xiaobo; Song, Inho; Ohtsu, Hiroyoshi; Tong, Jiaqi; Zhang, Haoke; Oh, Joon Hak

    2017-07-14

    Chiral supramolecular structures are attracting great attention due to their specific properties and high potential in chiral sensing and separation. Herein, supramolecular assembling behaviors of chiral perylene diimides have been systematically investigated in a mixed solution of tetrahydrofuran and water. They exhibit remarkably different morphologies and chiral aggregation behaviors depending on the mixing ratio of the solvents, i.e., the fraction of water. The morphogenesis and optoelectronic properties of chiral supramolecular structures have been thoroughly studied using a range of experimental and theoretical methods to investigate the morphological effects of chiral supramolecular assemblies on the electrical performances and photogenerated charge-carrier behaviors. In addition, chiral perylene diimides have been discriminated by combining vibrational circular dichroism with theoretical calculations, for the first time. The chiral supramolecular nanostructures developed herein strongly absorb visible spectral region and exhibit high photoresponsivity and detectivity, opening up new opportunities for practical applications in optoelectronics.

  10. A strategy for tuning achiral main-chain polymers into helical assemblies and chiral memory systems.

    Science.gov (United States)

    Yang, Dong; Zhao, Yin; Lv, Kai; Wang, Xiufeng; Zhang, Wei; Zhang, Li; Liu, Minghua

    2016-01-28

    A general strategy to tune the achiral main chain polymers into helical nanoassemblies was proposed based on the co-gelation approach. As an example, two achiral main chain polymers, PCz8 and PSi8, were selected, and their co-assembly with an amphiphilic l- or d-glutamide gelator was investigated. Although the polymers could not form gels individually, they could form co-gels with the gelator and the resultant gels exhibited macroscopic supramolecular chirality, which could be confirmed by CD spectra and SEM observations. Moreover, the supramolecular chirality can be memorized even after the gelator molecules were removed. Remarkably, either the gelator-containing or gelator-free chiral polymer assemblies showed circularly polarized luminescence (CPL), which is usually inherent to intrinsic chiral polymers. It was suggested that during the co-gelation, the chirality of the gelator was transferred to and memorized by the achiral polymers. The approach seems to be general and we provided the first example to tune the achiral polymers into helical assemblies through the co-gelation.

  11. Bistability in a self-assembling system confined by elastic walls: Exact results in a one-dimensional lattice model

    Energy Technology Data Exchange (ETDEWEB)

    Pȩkalski, J.; Ciach, A. [Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warszawa (Poland); Almarza, N. G. [Instituto de Química Física Rocasolano, CSIC, Serrano 119, E-28006 Madrid (Spain)

    2015-01-07

    The impact of confinement on self-assembly of particles interacting with short-range attraction and long-range repulsion potential is studied for thermodynamic states corresponding to local ordering of clusters or layers in the bulk. Exact and asymptotic expressions for the local density and for the effective potential between the confining surfaces are obtained for a one-dimensional lattice model introduced by J. Pȩkalski et al. [J. Chem. Phys. 138, 144903 (2013)]. The simple asymptotic formulas are shown to be in good quantitative agreement with exact results for slits containing at least 5 layers. We observe that the incommensurability of the system size and the average distance between the clusters or layers in the bulk leads to structural deformations that are different for different values of the chemical potential μ. The change of the type of defects is reflected in the dependence of density on μ that has a shape characteristic for phase transitions. Our results may help to avoid misinterpretation of the change of the type of defects as a phase transition in simulations of inhomogeneous systems. Finally, we show that a system confined by soft elastic walls may exhibit bistability such that two system sizes that differ approximately by the average distance between the clusters or layers are almost equally probable. This may happen when the equilibrium separation between the soft boundaries of an empty slit corresponds to the largest stress in the confined self-assembling system.

  12. Cryo-electron Microscopy Analysis of Structurally Heterogeneous Macromolecular Complexes.

    Science.gov (United States)

    Jonić, Slavica

    2016-01-01

    Cryo-electron microscopy (cryo-EM) has for a long time been a technique of choice for determining structure of large and flexible macromolecular complexes that were difficult to study by other experimental techniques such as X-ray crystallography or nuclear magnetic resonance. However, a fast development of instruments and software for cryo-EM in the last decade has allowed that a large range of complexes can be studied by cryo-EM, and that their structures can be obtained at near-atomic resolution, including the structures of small complexes (e.g., membrane proteins) whose size was earlier an obstacle to cryo-EM. Image analysis to identify multiple coexisting structures in the same specimen (multiconformation reconstruction) is now routinely done both to solve structures at near-atomic resolution and to study conformational dynamics. Methods for multiconformation reconstruction and latest examples of their applications are the focus of this review.

  13. NATO Advanced Study Institute on Evolving Methods for Macromolecular Gystallography

    CERN Document Server

    Read, Randy J

    2007-01-01

    X-ray crystallography is the pre-eminent technique for visualizing the structures of macromolecules at atomic resolution. These structures are central to understanding the detailed mechanisms of biological processes, and to discovering novel therapeutics using a structure-based approach. As yet, structures are known for only a small fraction of the proteins encoded by human and pathogenic genomes. To counter the myriad modern threats of disease, there is an urgent need to determine the structures of the thousands of proteins whose structure and function remain unknown. This volume draws on the expertise of leaders in the field of macromolecular crystallography to illuminate the dramatic developments that are accelerating progress in structural biology. Their contributions span the range of techniques from crystallization through data collection, structure solution and analysis, and show how modern high-throughput methods are contributing to a deeper understanding of medical problems.

  14. Spontaneous and specific activation of chemical bonds in macromolecular fluids.

    Science.gov (United States)

    Park, Insun; Shirvanyants, David; Nese, Alper; Matyjaszewski, Krzysztof; Rubinstein, Michael; Sheiko, Sergei S

    2010-09-08

    Mechanical activation of chemical bonds typically involves the application of external forces, which implies a broad distribution of bond tensions. We demonstrate that controlling the flow profile of a macromolecular fluid generates and delineates mechanical force concentration, enabling a hierarchical activation of chemical bonds on different length scales from the macroscopic to the molecular. Bond tension is spontaneously generated within brushlike macromolecules as they spread on a solid substrate. The molecular architecture creates an uneven distribution of tension in the covalent bonds, leading to spatially controlled bond scission. By controlling the flow rate and the gradient of the film pressure, one can sever the flowing macromolecules with high precision. Specific chemical bonds are activated within distinct macromolecules located in a defined area of a thin film. Furthermore, the flow-controlled loading rate enables quantitative analysis of the bond activation parameters.

  15. Macromolecular and dendrimer-based magnetic resonance contrast agents

    Energy Technology Data Exchange (ETDEWEB)

    Bumb, Ambika; Brechbiel, Martin W. (Radiation Oncology Branch, National Cancer Inst., National Inst. of Health, Bethesda, MD (United States)), e-mail: pchoyke@mail.nih.gov; Choyke, Peter (Molecular Imaging Program, National Cancer Inst., National Inst. of Health, Bethesda, MD (United States))

    2010-09-15

    Magnetic resonance imaging (MRI) is a powerful imaging modality that can provide an assessment of function or molecular expression in tandem with anatomic detail. Over the last 20-25 years, a number of gadolinium-based MR contrast agents have been developed to enhance signal by altering proton relaxation properties. This review explores a range of these agents from small molecule chelates, such as Gd-DTPA and Gd-DOTA, to macromolecular structures composed of albumin, polylysine, polysaccharides (dextran, inulin, starch), poly(ethylene glycol), copolymers of cystamine and cystine with GD-DTPA, and various dendritic structures based on polyamidoamine and polylysine (Gadomers). The synthesis, structure, biodistribution, and targeting of dendrimer-based MR contrast agents are also discussed

  16. Detecting stoichiometry of macromolecular complexes in live cells using FRET

    Science.gov (United States)

    Ben-Johny, Manu; Yue, Daniel N.; Yue, David T.

    2016-01-01

    The stoichiometry of macromolecular interactions is fundamental to cellular signalling yet challenging to detect from living cells. Fluorescence resonance energy transfer (FRET) is a powerful phenomenon for characterizing close-range interactions whereby a donor fluorophore transfers energy to a closely juxtaposed acceptor. Recognizing that FRET measured from the acceptor's perspective reports a related but distinct quantity versus the donor, we utilize the ratiometric comparison of the two to obtain the stoichiometry of a complex. Applying this principle to the long-standing controversy of calmodulin binding to ion channels, we find a surprising Ca2+-induced switch in calmodulin stoichiometry with Ca2+ channels—one calmodulin binds at basal cytosolic Ca2+ levels while two calmodulins interact following Ca2+ elevation. This feature is curiously absent for the related Na channels, also potently regulated by calmodulin. Overall, our assay adds to a burgeoning toolkit to pursue quantitative biochemistry of dynamic signalling complexes in living cells. PMID:27922011

  17. Designing a synchrotron micro-focusing beamline for macromolecular crystallography.

    Science.gov (United States)

    Grochulski, Paweł; Cygler, Mirosław; Yates, Brian

    After a successful 10 years of operation, the Canadian Macromolecular Crystallography Facility 08ID-1 beamline will undergo an upgrade to establish micro-beam capability. This paper is mostly focussed on optics and computer simulations for ray tracing of the beamline. After completion, the focussed beam at the sample will have a much smaller size of 50 × 5 µm2 (H x V), allowing measurement of X-ray diffraction patterns from much smaller crystals than possible presently. The beamline will be equipped with a fast sample changer and an ultra-low noise photon counting detector, allowing shutter-less operation of the beamline. Additionally, it will be possible to perform in-situ room-temperature experiments.

  18. 129 Xe NMR Relaxation-Based Macromolecular Sensing

    Energy Technology Data Exchange (ETDEWEB)

    Gomes, Muller D. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Dao, Phuong [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Jeong, Keunhong [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Slack, Clancy C. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Vassiliou, Christophoros C. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Finbloom, Joel A. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Francis, Matthew B. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Wemmer, David E. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences Division; Pines, Alexander [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Univ. of California, Berkeley, CA (United States). Dept. of Chemistry

    2016-07-29

    A 129Xe NMR relaxation-based sensing approach is reported on that exploits changes in the bulk xenon relaxation rate induced by slowed tumbling of a cryptophane-based sensor upon target binding. The amplification afforded by detection of the bulk dissolved xenon allows sensitive detection of targets. The sensor comprises a xenon-binding cryptophane cage, a target interaction element, and a metal chelating agent. Xenon associated with the target-bound cryptophane cage is rapidly relaxed and then detected after exchange with the bulk. Here we show that large macromolecular targets increase the rotational correlation time of xenon, increasing its relaxation rate. Upon binding of a biotin-containing sensor to avidin at 1.5 μM concentration, the free xenon T2 is reduced by a factor of 4.

  19. In-vacuum long-wavelength macromolecular crystallography.

    Science.gov (United States)

    Wagner, Armin; Duman, Ramona; Henderson, Keith; Mykhaylyk, Vitaliy

    2016-03-01

    Structure solution based on the weak anomalous signal from native (protein and DNA) crystals is increasingly being attempted as part of synchrotron experiments. Maximizing the measurable anomalous signal by collecting diffraction data at longer wavelengths presents a series of technical challenges caused by the increased absorption of X-rays and larger diffraction angles. A new beamline at Diamond Light Source has been built specifically for collecting data at wavelengths beyond the capability of other synchrotron macromolecular crystallography beamlines. Here, the theoretical considerations in support of the long-wavelength beamline are outlined and the in-vacuum design of the endstation is discussed, as well as other hardware features aimed at enhancing the accuracy of the diffraction data. The first commissioning results, representing the first in-vacuum protein structure solution, demonstrate the promising potential of the beamline.

  20. The Impact of the Availability of Resources, the Allocation of Buffers and Number of Workers on the Effectiveness of an Assembly Manufacturing System

    National Research Council Canada - National Science Library

    Sławomir Kłos; Peter Trebuna

    2017-01-01

    .... The manufacturing system includes both machining and assembly operations. Simulation experiments were conducted the availability of the different manufacturing resources, the various allocations of buffer capacities and the number of employees...

  1. Design of Introspective Circuits for Analysis of Cell-Level Dis-orientation in Self-Assembled Cellular Systems

    Directory of Open Access Journals (Sweden)

    Nicholas Jesse Macias

    2016-02-01

    Full Text Available This paper discusses a novel approach to managing complexity in a large self-assembled system, by employing the self-assembling components themselves to address the complexity. Challenges are discussed, including the question of how to deal with elements that are assembled in different orientations from each other, and a solution based on the idea of introspective circuits is described. A methodology for determining a single cell’s orientation from an adjacent cell is given. An algorithm is then described for using such re-oriented edge cells to determine orientation of more-interior cells, thus allowing re-orientation of an entire 2D region of cells. Test procedures are described, and results are presented to show better-than-linear time performance (O(sqrt(n. The significance of this work is discussed, not only in terms of managing arrays of dis-oriented cells, but more importantly as an example of the usefulness of local, distributed self-configuration to create and use introspective circuitry. Finally, future work is discussed, including extension to 3D collections of cells.

  2. Dynamic simulation of concentrated macromolecular solutions with screened long-range hydrodynamic interactions: algorithm and limitations.

    Science.gov (United States)

    Ando, Tadashi; Chow, Edmond; Skolnick, Jeffrey

    2013-09-28

    Hydrodynamic interactions exert a critical effect on the dynamics of macromolecules. As the concentration of macromolecules increases, by analogy to the behavior of semidilute polymer solutions or the flow in porous media, one might expect hydrodynamic screening to occur. Hydrodynamic screening would have implications both for the understanding of macromolecular dynamics as well as practical implications for the simulation of concentrated macromolecular solutions, e.g., in cells. Stokesian dynamics (SD) is one of the most accurate methods for simulating the motions of N particles suspended in a viscous fluid at low Reynolds number, in that it considers both far-field and near-field hydrodynamic interactions. This algorithm traditionally involves an O(N(3)) operation to compute Brownian forces at each time step, although asymptotically faster but more complex SD methods are now available. Motivated by the idea of hydrodynamic screening, the far-field part of the hydrodynamic matrix in SD may be approximated by a diagonal matrix, which is equivalent to assuming that long range hydrodynamic interactions are completely screened. This approximation allows sparse matrix methods to be used, which can reduce the apparent computational scaling to O(N). Previously there were several simulation studies using this approximation for monodisperse suspensions. Here, we employ newly designed preconditioned iterative methods for both the computation of Brownian forces and the solution of linear systems, and consider the validity of this approximation in polydisperse suspensions. We evaluate the accuracy of the diagonal approximation method using an intracellular-like suspension. The diffusivities of particles obtained with this approximation are close to those with the original method. However, this approximation underestimates intermolecular correlated motions, which is a trade-off between accuracy and computing efficiency. The new method makes it possible to perform large

  3. Facilities for macromolecular crystallography at the Helmholtz-Zentrum Berlin

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, Uwe, E-mail: umue@helmholtz-berlin.de; Darowski, Nora [Institute for Soft Matter and Functional Materials, Macromolecular Crystallography, Albert-Einstein-Strasse 15, D-12489 Berlin (Germany); Fuchs, Martin R. [Swiss Light Source at Paul Scherrer Institut, CH-5232 Villigen PSI (Switzerland); Förster, Ronald [Freie Universität Berlin, Fachbereich Biologie, Chemie, Pharmazie, Institut für Chemie und Biochemie, AG Strukturbiochemie, Takustrasse 6, D-14195 Berlin (Germany); Hellmig, Michael; Paithankar, Karthik S. [Institute for Soft Matter and Functional Materials, Macromolecular Crystallography, Albert-Einstein-Strasse 15, D-12489 Berlin (Germany); Pühringer, Sandra [Freie Universität Berlin, Fachbereich Biologie, Chemie, Pharmazie, Institut für Chemie und Biochemie, AG Strukturbiochemie, Takustrasse 6, D-14195 Berlin (Germany); Steffien, Michael [Institute for Soft Matter and Functional Materials, Macromolecular Crystallography, Albert-Einstein-Strasse 15, D-12489 Berlin (Germany); Zocher, Georg [Universität Tübingen, Interfakultäres Institut für Biochemie, Hoppe-Seyler-Strasse 4, D-72076 Tübingen (Germany); Weiss, Manfred S. [Institute for Soft Matter and Functional Materials, Macromolecular Crystallography, Albert-Einstein-Strasse 15, D-12489 Berlin (Germany)

    2012-05-01

    The three macromolecular crystallography beamlines BL14.1, BL14.2 and BL14.3 at the BESSY II storage ring at the Helmholtz-Zentrum Berlin are described. Three macromolecular crystallography (MX) beamlines at the Helmholtz-Zentrum Berlin (HZB) are available for the regional, national and international structural biology user community. The state-of-the-art synchrotron beamlines for MX BL14.1, BL14.2 and BL14.3 are located within the low-β section of the BESSY II electron storage ring. All beamlines are fed from a superconducting 7 T wavelength-shifter insertion device. BL14.1 and BL14.2 are energy tunable in the range 5–16 keV, while BL14.3 is a fixed-energy side station operated at 13.8 keV. All three beamlines are equipped with CCD detectors. BL14.1 and BL14.2 are in regular user operation providing about 200 beam days per year and about 600 user shifts to approximately 50 research groups across Europe. BL14.3 has initially been used as a test facility and was brought into regular user mode operation during the year 2010. BL14.1 has recently been upgraded with a microdiffractometer including a mini-κ goniometer and an automated sample changer. Additional user facilities include office space adjacent to the beamlines, a sample preparation laboratory, a biology laboratory (safety level 1) and high-end computing resources. In this article the instrumentation of the beamlines is described, and a summary of the experimental possibilities of the beamlines and the provided ancillary equipment for the user community is given.

  4. Macromolecular structure analysis and effective liquefaction pretreatment. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Suuberg, E.M.; Yun, Y.; Lilly, W.D.; Leung, K.; Gates, T.; Otake, Y.; Deevi, S.C.

    1994-07-01

    This project was concerned with characterizing the changes in coal macromolecular structure, that are of significance for liquefaction pretreatments of coal. The macromolecular structure of the insoluble portion of coal is difficult to characterize. Techniques that do so indirectly (based upon, for example, NMR and FTIR characterizations of atomic linkages) are not particularly sensitive for this purpose. Techniques that characterize the elastic structure (such as solvent swelling) are much more sensitive to subtle changes in the network structure. It is for this reason that we focused upon these techniques. The overall objective involved identifying pretreatments that reduce the crosslinking (physical or chemical) of the network structure, and thus lead to materials that can be handled to a greater extent by traditional liquid-phase processing techniques. These techniques tend to be inherently more efficient at producing desirable products. This report is divided into seven chapters. Chapter II summarizes the main experimental approaches used throughout the project, and summarizes the main findings on the Argonne Premium coal samples. Chapter III considers synergistic effects of solvent pairs. It is divided into two subsections. The first is concerned with mixtures of CS{sub 2} with electron donor solvents. The second subsection is concerned with aromatic hydrocarbon - alcohol or hydrocarbon - alcohol mixtures, as might be of interest for preliquefaction delivery of catalysts into bituminous coals. Chapter IV deals with questions of how oxidation might influence the results that are obtained. Chapter V briefly details what conclusions may be drawn concerning the elastic behavior of coals, and the effects of thermal treatments on this behavior. Chapter VI is concerned with theories to describe the action of solvents that are capable of dissociating non-covalent crosslinks. Finally, Chapter VII discusses the practical implications of the study.

  5. Self-Assembly by Instruction: Designing Nanoscale Systems Using DNA-Based Approaches (474th Brookhaven Lecture)

    Energy Technology Data Exchange (ETDEWEB)

    Gang, Oleg [Center for Functional Nanomaterials

    2012-01-18

    In the field of nanoscience, if you can control how nanoparticles self-assemble in particular structures — joining each other, for example, as molecules can form, atom-by-atom — you can design new materials that have unique properties that industry needs. Nature already uses the DNA genetic code to instruct the building of specific proteins and whole organisms in both plants and people. Taking a cue from nature, scientists at BNL devised a way of using strands of synthetic DNA attached to the surface of nanoparticles to instruct them to self-assemble into specific nanoscale structures, clusters, and three-dimensional organizations. Novel materials designed and fabricated this way promise use in photovoltaics, energy storage, catalysis, cell-targeted systems for more effective medical treatments, and biomolecular sensing for environmental monitoring and medical applications. To find out more about the rapid evolution of this nanoassembly method and its applications, join Physicist Oleg Gang of the Center for Functional Nanomaterials (CFN) as he gives the 474th Brookhaven Lecture, titled “Self-Assembly by Instruction: Designing Nanoscale Systems Using DNA-Based Approaches." Gang, who has led this work at the CFN, will explain the rapid evolution of this nanoassembly method, and discuss its present and future applications in highly specific biosensors, optically active nano-materials, and new ways to fabricate complex architectures in a rational manner via self-assembly. Gang and his colleagues used the CFN and the National Synchrotron Light Source (NSLS) facilities to perform their groundbreaking research. At the CFN, the scientists used electron microscopes and optical methods to visualize the clusters that they fabricated. At the NSLS, they applied x-rays to study a particles-assembly process in solution, DNA’s natural environment. Gang earned a Ph.D. in soft matter physics from Bar-Ilan University in 2000, and he was a Rothschild Fellow at Harvard

  6. Reconstitution of a minimal machinery capable of assembling periplasmic type IV pili.

    Science.gov (United States)

    Goosens, Vivianne J; Busch, Andreas; Georgiadou, Michaella; Castagnini, Marta; Forest, Katrina T; Waksman, Gabriel; Pelicic, Vladimir

    2017-06-20

    Type IV pili (Tfp), which are key virulence factors in many bacterial pathogens, define a large group of multipurpose filamentous nanomachines widespread in Bacteria and Archaea. Tfp biogenesis is a complex multistep process, which relies on macromolecular assemblies composed of 15 conserved proteins in model gram-negative species. To improve our limited understanding of the molecular mechanisms of filament assembly, we have used a synthetic biology approach to reconstitute, in a nonnative heterologous host, a minimal machinery capable of building Tfp. Here we show that eight synthetic genes are sufficient to promote filament assembly and that the corresponding proteins form a macromolecular complex at the cytoplasmic membrane, which we have purified and characterized biochemically. Our results contribute to a better mechanistic understanding of the assembly of remarkable dynamic filaments nearly ubiquitous in prokaryotes.

  7. X-Ray Assembler Data

    Data.gov (United States)

    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...

  8. Elucidating energy and electron transfer dynamics within molecular assemblies for solar energy conversion

    Science.gov (United States)

    Morseth, Zachary Aaron

    The use of sunlight to make chemical fuels (i.e. solar fuels) is an attractive approach in the quest to develop sustainable energy sources. Using nature as a guide, assemblies for artificial photosynthesis will need to perform multiple functions. They will need to be able to harvest light across a broad region of the solar spectrum, transport excited-state energy to charge-separation sites, and then transport and store redox equivalents for use in the catalytic reactions that produce chemical fuels. This multifunctional behavior will require the assimilation of multiple components into a single macromolecular system. A wide variety of different architectures including porphyrin arrays, peptides, dendrimers, and polymers have been explored, with each design posing unique challenges. Polymer assemblies are attractive due to their relative ease of production and facile synthetic modification. However, their disordered nature gives rise to stochastic dynamics not present in more ordered assemblies. The rational design of assemblies requires a detailed understanding of the energy and electron transfer events that follow light absorption, which can occur on timescales ranging from femtoseconds to hundreds of microseconds, necessitating the use of sophisticated techniques. We have used a combination of time-resolved absorption and emission spectroscopies with observation times that span nine orders of magnitude to follow the excited-state evolution within single-site and polymer-based molecular assemblies. We complement experimental observations with electronic structure calculations, molecular dynamics simulations, and kinetic modeling to develop a microscopic view of these dynamics. This thesis provides an overview of work on single-site molecular assemblies and polymers decorated with pendant chromophores, both in solution and on surfaces. This work was made possible through extensive collaboration with Dr. Kirk Schanze's and Dr. John Reynolds' research groups who

  9. Sequence assembly

    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 plays an important role in processing the information generated by these methods. Here, we provide a comprehensive overview of the current publicly available sequence assembly programs. We describe the basic principles of computational assembly along with the main concerns, such as repetitive sequences...... 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....

  10. Hydrogen-bonded rosettes comprising π-conjugated systems as building blocks for functional one-dimensional assemblies.

    Science.gov (United States)

    Adhikari, Bimalendu; Lin, Xu; Yamauchi, Mitsuaki; Ouchi, Hayato; Aratsu, Keisuke; Yagai, Shiki

    2017-08-29

    Hydrogen-bonded supermacrocycles (rosettes) are attractive disk-shaped noncovalent synthons for extended functional columnar nanoassemblies. They can serve not only as noncovalent monomer units for supramolecular polymers and discrete oligomers in a dilute solution but also as constituent entities for soft matters such as gels and lyotropic/thermotropic liquid crystals. However, what are the merits of using supramolecular rosettes instead of using expanded π-conjugated covalent molecules? This review covers the self-assembly of photochemically and electrochemically active π-conjugated molecules through the formation of supramolecular rosettes via directional complementary multiple hydrogen-bonding interactions. These rosettes comprising π-conjugated covalent functional units stack into columnar nanoassemblies with unique structures and properties. By overviewing the design principle, characterization, and properties and functionalities of various examples, we illustrate the merits of utilizing rosette motifs. Basically, one can easily access a well-defined expanded π-surface composed of multi-chromophoric systems, which can ultimately afford stable extended nanoassemblies even in a dilute solution due to the higher association constants of supermacrocyclized π-systems. Importantly, these columnar nanoassemblies exhibit unique features in self-assembly processes, chiroptical, photophysical and electrochemical properties, nanoscale morphologies, and bulk properties. Moreover, the stimuli responsiveness of individual building blocks can be amplified to a greater extent by exploiting rosette intermediates to organize them into one-dimensional columnar structures. In the latter parts of the review, we also highlight the application of rosettes in supramolecular polymer systems, photovoltaic devices, and others.

  11. High-Resolution Spore Coat Architecture and Assembly of Bacillus Spores

    Energy Technology Data Exchange (ETDEWEB)

    Malkin, A J; Elhadj, S; Plomp, M

    2011-03-14

    Elucidating the molecular architecture of bacterial and cellular surfaces and its structural dynamics is essential to understanding mechanisms of pathogenesis, immune response, physicochemical interactions, environmental resistance, and provide the means for identifying spore formulation and processing attributes. I will discuss the application of in vitro atomic force microscopy (AFM) for studies of high-resolution coat architecture and assembly of several Bacillus spore species. We have demonstrated that bacterial spore coat structures are phylogenetically and growth medium determined. We have proposed that strikingly different species-dependent coat structures of bacterial spore species are a consequence of sporulation media-dependent nucleation and crystallization mechanisms that regulate the assembly of the outer spore coat. Spore coat layers were found to exhibit screw dislocations and two-dimensional nuclei typically observed on inorganic and macromolecular crystals. This presents the first case of non-mineral crystal growth patterns being revealed for a biological organism, which provides an unexpected example of nature exploiting fundamental materials science mechanisms for the morphogenetic control of biological ultrastructures. We have discovered and validated, distinctive formulation-specific high-resolution structural spore coat and dimensional signatures of B. anthracis spores (Sterne strain) grown in different formulation condition. We further demonstrated that measurement of the dimensional characteristics of B. anthracis spores provides formulation classification and sample matching with high sensitivity and specificity. I will present data on the development of an AFM-based immunolabeling technique for the proteomic mapping of macromolecular structures on the B. anthracis surfaces. These studies demonstrate that AFM can probe microbial surface architecture, environmental dynamics and the life cycle of bacterial and cellular systems at near

  12. Methods for disassembling, replacing and assembling parts of a steam cooling system for a gas turbine

    Science.gov (United States)

    Wilson, Ian D.; Wesorick, Ronald R.

    2002-01-01

    The steam cooling circuit for a gas turbine includes a bore tube assembly supplying steam to circumferentially spaced radial tubes coupled to supply elbows for transitioning the radial steam flow in an axial direction along steam supply tubes adjacent the rim of the rotor. The supply tubes supply steam to circumferentially spaced manifold segments located on the aft side of the 1-2 spacer for supplying steam to the buckets of the first and second stages. Spent return steam from these buckets flows to a plurality of circumferentially spaced return manifold segments disposed on the forward face of the 1-2 spacer. Crossover tubes couple the steam supply from the steam supply manifold segments through the 1-2 spacer to the buckets of the first stage. Crossover tubes through the 1-2 spacer also return steam from the buckets of the second stage to the return manifold segments. Axially extending return tubes convey spent cooling steam from the return manifold segments to radial tubes via return elbows. The bore tube assembly, radial tubes, elbows, manifold segments and crossover tubes are removable from the turbine rotor and replaceable.

  13. Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012)

    Science.gov (United States)

    Foffi, G.; Pastore, A.; Piazza, F.; Temussi, P. A.

    2013-08-01

    held in Ascona from 10 to 14 June 2012. In the unique scenario of the Maggiore lake and absorbed in the magic atmosphere of the Centro Stefano Franscini (CSF) at Monte Verità, we enjoyed three-and-a-half days of intense and inspiring activity, where not only many of the most prominent scientists working on macromolecular crowding, but also experts in closely related fields such as colloids and soft matter presented their work. The meeting was intended and has been organized to bring theoreticians and experimentalists together in the attempt to promote an active dialogue. Moreover, we wanted different disciplines to be represented, notably physics and chemistry, besides biology, as cross-fertilization is proving an increasingly fundamental source of inspiration and advancement. This issue of Physical Biology (PB) features a selection of the oral contributions presented at the conference, expanded in the form of research or review articles. PB, one of the scientific journals of the Institute of Physics (IOP), is one of the most dynamic and lively forums active at the interface between biology on one side, and physics and mathematics on the other. As its mission is stated by IOP, PB 'focuses on research in which physics-based approaches lead to new insights into biological systems at all scales of space and time, and all levels of complexity'. For these reasons, and also in view of its high reputation and broad readership, PB appears to be the ideal place for disseminating the thriving pieces of research presented at the conference. We are extremely grateful to PB and its kind and efficient editorial staff who helped make this issue a great scientific follow-up to the conference. The opening lecture of the conference, the first of four day-opening keynote lectures, was given by Allen P Minton from NIH (USA), possibly the most influential among the pioneers in the field. He provided a lucid and well-thought-out overview of the concept of macromolecular crowding through an

  14. Self-assembled nanostructures

    CERN Document Server

    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.

  15. Self-assembled polyelectrolyte complexes films as efficient compression coating layers for controlled-releasing tablets.

    Science.gov (United States)

    Li, Wenyan; Huo, Mengmeng; Sen Chaudhuri, Arka; Yang, Chen; Cao, Dazhong; Wu, Zhenghong; Qi, Xiaole

    2017-05-01

    Currently, polysaccharide-based hydrogels are widely studied macromolecular networks to modify drug dissolution from controlled-releasing matrix tablets. Among them, polyelectrolyte complexes (PEC) films consisted of chitosan (CS) and sodium alginate (SA) could be obtained via spontaneously assembling under physiological gastrointestinal environment. Here, we utilized these self-assembled PEC films as an efficient coating materials to develop controlled-released matrix tablets through compression coating process, with paracetamol (APAP) as model drug. The constitutive and morphology characteristic studies on these PEC films illustrated that the mixture of CS and SA with the weight ratio of 1:1 would be an promising outer layer for compression-coating tablets. In addition, the in vitro drug releasing behavior experiments demonstrated that the optimized compression coating tablets displayed satisfied zero-order drug releasing profits. Furthermore, the in vivo pharmacokinetic studies of these APAP loaded compression-coated tablets in New Zealand rabbits gave that the T max (12.32 ± 1.05 h) was significantly prolonged (p tablets (Jinfuning ® ) after oral administration. These studies suggest that the compression-coated tablets with self-assembled PEC film as coating outer layer may be a promising strategy for peroral controlled release delivery system of water soluble drugs.

  16. Conceptual Design of Target Assembly System for Boron Neutron Capture Therapy

    Energy Technology Data Exchange (ETDEWEB)

    Kye, Y. U.; Shin, S. G. [POSTECH, Pohang (Korea, Republic of); Namkung, W.; Cho, M. H. [Pohang Accelerator Laboratory, Pohang (Korea, Republic of); Bae, Y. S. [National Fusion Research Institute, Daejeon (Korea, Republic of)

    2016-05-15

    There are many type of accelerator based BNCT. Cyclotron based proton beam is high energy. But it has weakness about low current, severe target damage, and radioactivity problem. This research would be treat by LINAC based proton beam because LINAC based proton beam has high current and low energy. These point are possible to reduce treatment time. Therefore, patients don't have to irradiate at normal cell by neutron beam. Monte Carlo and thermal hydraulics simulation were conducted as neutron flux after moderator assembly, temperature distribution of beryllium target. General consensus is that an epithermal neutron fluence of about 1 x 10{sup 13} /cm{sup 2} is required for successful Neutron Capture Therapy (NCT). If epithermal neutron flux is 1 x 10{sup 10} /cm{sup 2}· sec, the neutron irradiation time would be necessary about 3 hours for therapy.

  17. Modeling of RFID-Enabled Real-Time Manufacturing Execution System in Mixed-Model Assembly Lines

    Directory of Open Access Journals (Sweden)

    Zhixin Yang

    2015-01-01

    Full Text Available To quickly respond to the diverse product demands, mixed-model assembly lines are well adopted in discrete manufacturing industries. Besides the complexity in material distribution, mixed-model assembly involves a variety of components, different process plans and fast production changes, which greatly increase the difficulty for agile production management. Aiming at breaking through the bottlenecks in existing production management, a novel RFID-enabled manufacturing execution system (MES, which is featured with real-time and wireless information interaction capability, is proposed to identify various manufacturing objects including WIPs, tools, and operators, etc., and to trace their movements throughout the production processes. However, being subject to the constraints in terms of safety stock, machine assignment, setup, and scheduling requirements, the optimization of RFID-enabled MES model for production planning and scheduling issues is a NP-hard problem. A new heuristical generalized Lagrangian decomposition approach has been proposed for model optimization, which decomposes the model into three subproblems: computation of optimal configuration of RFID senor networks, optimization of production planning subjected to machine setup cost and safety stock constraints, and optimization of scheduling for minimized overtime. RFID signal processing methods that could solve unreliable, redundant, and missing tag events are also described in detail. The model validity is discussed through algorithm analysis and verified through numerical simulation. The proposed design scheme has important reference value for the applications of RFID in multiple manufacturing fields, and also lays a vital research foundation to leverage digital and networked manufacturing system towards intelligence.

  18. Laser Ultrasonic System for Surface Crack Visualization in Dissimilar Welds of Control Rod Drive Mechanism Assembly of Nuclear Power Plant

    Directory of Open Access Journals (Sweden)

    Yun-Shil Choi

    2014-01-01

    Full Text Available In this paper, we propose a J-groove dissimilar weld crack visualization system based on ultrasonic propagation imaging (UPI technology. A full-scale control rod drive mechanism (CRDM assembly specimen was fabricated to verify the proposed system. An ultrasonic sensor was contacted at one point of the inner surface of the reactor vessel head part of the CRDM assembly. Q-switched laser beams were scanned to generate ultrasonic waves around the weld bead. The localization and sizing of the crack were possible by ultrasonic wave propagation imaging. Furthermore, ultrasonic spectral imaging unveiled frequency components of damage-induced waves, while wavelet-transformed ultrasonic propagation imaging enhanced damage visibility by generating a wave propagation video focused on the frequency component of the damage-induced waves. Dual-directional anomalous wave propagation imaging with adjacent wave subtraction was also developed to enhance the crack visibility regardless of crack orientation and wave propagation direction. In conclusion, the full-scale specimen test demonstrated that the multiple damage visualization tools are very effective in the visualization of J-groove dissimilar weld cracks.

  19. Side-chain-controlled self-assembly of polystyrene-polypeptide miktoarm star copolymers

    KAUST Repository

    Junnila, Susanna

    2012-03-27

    We show how the self-assembly of miktoarm star copolymers can be controlled by modifying the side chains of their polypeptide arms, using A 2B and A 2B 2 type polymer/polypeptide hybrids (macromolecular chimeras). Initially synthesized PS 2PBLL and PS 2PBLL 2 (PS, polystyrene; PBLL, poly(ε-tert-butyloxycarbonyl-l-lysine) ) miktoarms were first deprotected to PS 2PLLHCl and PS 2PLLHCl 2 miktoarms (PLLHCl, poly(l-lysine hydrochloride)) and then complexed ionically with sodium dodecyl sulfonate (DS) to give the supramolecular complexes PS 2PLL(DS) and PS 2(PLL(DS)) 2. The solid-state self-assemblies of these six miktoarm systems were studied by transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), and small- and wide-angle X-ray scattering (SAXS, WAXS). The side chains of the polypeptide arms were observed to have a large effect on the solubility, polypeptide conformation, and self-assembly of the miktoarms. Three main categories were observed: (i) lamellar self-assemblies at the block copolymer length scale with packed layers of α-helices in PS 2PBLL and PS 2PBLL 2; (ii) charge-clustered polypeptide micelles with less-defined conformations in a nonordered lattice within a PS matrix in PS 2PLLHCl and PS 2PLLHCl 2; (iii) lamellar polypeptide-surfactant self-assemblies with β-sheet conformation in PS 2PLL(DS) and PS 2(PLL(DS)) 2 which dominate over the formation of block copolymer scale structures. Differences between the 3- and 4-arm systems illustrate how packing frustration between the coil-like PS arms and rigid polypeptide conformations can be relieved by the right number of arms, leading to differences in the extent of order. © 2012 American Chemical Society.

  20. Macromolecular crowding for tailoring tissue-derived fibrillated matrices.

    Science.gov (United States)

    Magno, Valentina; Friedrichs, Jens; Weber, Heather M; Prewitz, Marina C; Tsurkan, Mikhail V; Werner, Carsten

    2017-06-01

    Tissue-derived fibrillated matrices can be instrumental for the in vitro reconstitution of multiphasic extracellular microenvironments. However, despite of several advantages, the obtained scaffolds so far offer a rather narrow range of materials characteristics only. In this work, we demonstrate how macromolecular crowding (MMC) - the supplementation of matrix reconstitution media with synthetic or natural macromolecules in ways to create excluded volume effects (EVE) - can be employed for tailoring important structural and biophysical characteristics of kidney-derived fibrillated matrices. Porcine kidneys were decellularized, ground and the obtained extracellular matrix (ECM) preparations were reconstituted under varied MMC conditions. We show that MMC strongly influences the fibrillogenesis kinetics and impacts the architecture and the elastic modulus of the reconstituted matrices, with diameters and relative alignment of fibrils increasing at elevated concentrations of the crowding agent Ficoll400, a nonionic synthetic polymer of sucrose. Furthermore, we demonstrate how MMC modulates the distribution of key ECM molecules within the reconstituted matrix scaffolds. As a proof of concept, we compared different variants of kidney-derived fibrillated matrices in cell culture experiments referring to specific requirements of kidney tissue engineering approaches. The results revealed that MMC-tailored matrices support the morphogenesis of human umbilical vein endothelial cells (HUVECs) into capillary networks and of murine kidney stem cells (KSCs) into highly branched aggregates. The established methodology is concluded to provide generally applicable new options for tailoring tissue-specific multiphasic matrices in vitro. Tissue-derived fibrillated matrices can be instrumental for the in vitro reconstitution of multiphasic extracellular microenvironments. However, despite of several advantages, the obtained scaffolds so far offer a rather narrow range of materials

  1. Self-Assembled Hydrogel Nanoparticles for Drug Delivery Applications

    Directory of Open Access Journals (Sweden)

    Miguel Gama

    2010-02-01

    Full Text Available Hydrogel nanoparticles—also referred to as polymeric nanogels or macromolecular micelles—are emerging as promising drug carriers for therapeutic applications. These nanostructures hold versatility and properties suitable for the delivery of bioactive molecules, namely of biopharmaceuticals. This article reviews the latest developments in the use of self-assembled polymeric nanogels for drug delivery applications, including small molecular weight drugs, proteins, peptides, oligosaccharides, vaccines and nucleic acids. The materials and techniques used in the development of self-assembling nanogels are also described.

  2. Multilayer Thin Films Sequential Assembly of Nanocomposite Materials

    CERN Document Server

    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

  3. Defining the Architecture of the Core Machinery for the Assembly of Fe-S Clusters in Human Mitochondria.

    Science.gov (United States)

    Gakh, Oleksandr; Ranatunga, Wasantha; Galeano, Belinda K; Smith, Douglas S; Thompson, James R; Isaya, Grazia

    2017-01-01

    Although Fe-S clusters may assemble spontaneously from elemental iron and sulfur in protein-free systems, the potential toxicity of free Fe(2+), Fe(3+), and S(2-) ions in aerobic environments underscores the requirement for specialized proteins to oversee the safe assembly of Fe-S clusters in living cells. Prokaryotes first developed multiprotein systems for Fe-S cluster assembly, from which mitochondria later derived their own system and became the main Fe-S cluster suppliers for eukaryotic cells. Early studies in yeast and human mitochondria indicated that Fe-S cluster assembly in eukaryotes is centered around highly conserved Fe-S proteins (human ISCU) that serve as scaffolds upon which new Fe-S clusters are assembled from (i) elemental sulfur, provided by a pyridoxal phosphate-dependent cysteine desulfurase (human NFS1) and its stabilizing-binding partner (human ISD11), and (ii) elemental iron, provided by an iron-binding protein of the frataxin family (human FXN). Further studies revealed that all of these proteins could form stable complexes that could reach molecular masses of megadaltons. However, the protein-protein interaction surfaces, catalytic mechanisms, and overall architecture of these macromolecular machines remained undefined for quite some time. The delay was due to difficulties inherent in reconstituting these very large multiprotein complexes in vitro or isolating them from cells in sufficient quantities to enable biochemical and structural studies. Here, we describe approaches we developed to reconstitute the human Fe-S cluster assembly machinery in Escherichia coli and to define its remarkable architecture. © 2017 Elsevier Inc. All rights reserved.

  4. Metagenomic systems biology and metabolic modeling of the human microbiome: from species composition to community assembly rules.

    Science.gov (United States)

    Levy, Roie; Borenstein, Elhanan

    2014-01-01

    The human microbiome is a key contributor to health and development. Yet little is known about the ecological forces that are at play in defining the composition of such host-associated communities. Metagenomics-based studies have uncovered clear patterns of community structure but are often incapable of distinguishing alternative structuring paradigms. In a recent study, we integrated metagenomic analysis with a systems biology approach, using a reverse ecology framework to model numerous human microbiota species and to infer metabolic interactions between species. Comparing predicted interactions with species composition data revealed that the assembly of the human microbiome is dominated at the community level by habitat filtering. Furthermore, we demonstrated that this habitat filtering cannot be accounted for by known host phenotypes or by the metabolic versatility of the various species. Here we provide a summary of our findings and offer a brief perspective on related studies and on future approaches utilizing this metagenomic systems biology framework.

  5. Hypoxic tumor environments exhibit disrupted collagen I fibers and low macromolecular transport.

    Directory of Open Access Journals (Sweden)

    Samata M Kakkad

    Full Text Available Hypoxic tumor microenvironments result in an aggressive phenotype and resistance to therapy that lead to tumor progression, recurrence, and metastasis. While poor vascularization and the resultant inadequate drug delivery are known to contribute to drug resistance, the effect of hypoxia on molecular transport through the interstitium, and the role of the extracellular matrix (ECM in mediating this transport are unexplored. The dense mesh of fibers present in the ECM can especially influence the movement of macromolecules. Collagen 1 (Col1 fibers form a key component of the ECM in breast cancers. Here we characterized the influence of hypoxia on macromolecular transport in tumors, and the role of Col1 fibers in mediating this transport using an MDA-MB-231 breast cancer xenograft model engineered to express red fluorescent protein under hypoxia. Magnetic resonance imaging of macromolecular transport was combined with second harmonic generation microscopy of Col1 fibers. Hypoxic tumor regions displayed significantly decreased Col1 fiber density and volume, as well as significantly lower macromolecular draining and pooling rates, than normoxic regions. Regions adjacent to severely hypoxic areas revealed higher deposition of Col1 fibers and increased macromolecular transport. These data suggest that Col1 fibers may facilitate macromolecular transport in tumors, and their reduction in hypoxic regions may reduce this transport. Decreased macromolecular transport in hypoxic regions may also contribute to poor drug delivery and tumor recurrence in hypoxic regions. High Col1 fiber density observed around hypoxic regions may facilitate the escape of aggressive cancer cells from hypoxic regions.

  6. Hypoxic tumor environments exhibit disrupted collagen I fibers and low macromolecular transport.

    Science.gov (United States)

    Kakkad, Samata M; Penet, Marie-France; Akhbardeh, Alireza; Pathak, Arvind P; Solaiyappan, Meiyappan; Raman, Venu; Leibfritz, Dieter; Glunde, Kristine; Bhujwalla, Zaver M

    2013-01-01

    Hypoxic tumor microenvironments result in an aggressive phenotype and resistance to therapy that lead to tumor progression, recurrence, and metastasis. While poor vascularization and the resultant inadequate drug delivery are known to contribute to drug resistance, the effect of hypoxia on molecular transport through the interstitium, and the role of the extracellular matrix (ECM) in mediating this transport are unexplored. The dense mesh of fibers present in the ECM can especially influence the movement of macromolecules. Collagen 1 (Col1) fibers form a key component of the ECM in breast cancers. Here we characterized the influence of hypoxia on macromolecular transport in tumors, and the role of Col1 fibers in mediating this transport using an MDA-MB-231 breast cancer xenograft model engineered to express red fluorescent protein under hypoxia. Magnetic resonance imaging of macromolecular transport was combined with second harmonic generation microscopy of Col1 fibers. Hypoxic tumor regions displayed significantly decreased Col1 fiber density and volume, as well as significantly lower macromolecular draining and pooling rates, than normoxic regions. Regions adjacent to severely hypoxic areas revealed higher deposition of Col1 fibers and increased macromolecular transport. These data suggest that Col1 fibers may facilitate macromolecular transport in tumors, and their reduction in hypoxic regions may reduce this transport. Decreased macromolecular transport in hypoxic regions may also contribute to poor drug delivery and tumor recurrence in hypoxic regions. High Col1 fiber density observed around hypoxic regions may facilitate the escape of aggressive cancer cells from hypoxic regions.

  7. Synchrotron radiation macromolecular crystallography: science and spin-offs

    Directory of Open Access Journals (Sweden)

    John R. Helliwell

    2015-03-01

    Full Text Available A current overview of synchrotron radiation (SR in macromolecular crystallography (MX instrumentation, methods and applications is presented. Automation has been and remains a central development in the last decade, as have the rise of remote access and of industrial service provision. Results include a high number of Protein Data Bank depositions, with an increasing emphasis on the successful use of microcrystals. One future emphasis involves pushing the frontiers of using higher and lower photon energies. With the advent of X-ray free-electron lasers, closely linked to SR developments, the use of ever smaller samples such as nanocrystals, nanoclusters and single molecules is anticipated, as well as the opening up of femtosecond time-resolved diffraction structural studies. At SR sources, a very high-throughput assessment for the best crystal samples and the ability to tackle just a few micron and sub-micron crystals will become widespread. With higher speeds and larger detectors, diffraction data volumes are becoming long-term storage and archiving issues; the implications for today and the future are discussed. Together with the rise of the storage ring to its current pre-eminence in MX data provision, the growing tendency of central facility sites to offer other centralized facilities complementary to crystallography, such as cryo-electron microscopy and NMR, is a welcome development.

  8. Synchrotron radiation macromolecular crystallography: science and spin-offs.

    Science.gov (United States)

    Helliwell, John R; Mitchell, Edward P

    2015-03-01

    A current overview of synchrotron radiation (SR) in macromolecular crystallography (MX) instrumentation, methods and applications is presented. Automation has been and remains a central development in the last decade, as have the rise of remote access and of industrial service provision. Results include a high number of Protein Data Bank depositions, with an increasing emphasis on the successful use of microcrystals. One future emphasis involves pushing the frontiers of using higher and lower photon energies. With the advent of X-ray free-electron lasers, closely linked to SR developments, the use of ever smaller samples such as nanocrystals, nanoclusters and single molecules is anticipated, as well as the opening up of femtosecond time-resolved diffraction structural studies. At SR sources, a very high-throughput assessment for the best crystal samples and the ability to tackle just a few micron and sub-micron crystals will become widespread. With higher speeds and larger detectors, diffraction data volumes are becoming long-term storage and archiving issues; the implications for today and the future are discussed. Together with the rise of the storage ring to its current pre-eminence in MX data provision, the growing tendency of central facility sites to offer other centralized facilities complementary to crystallography, such as cryo-electron microscopy and NMR, is a welcome development.

  9. Macromolecular crystallography with a large format CMOS detector

    Energy Technology Data Exchange (ETDEWEB)

    Nix, Jay C., E-mail: jcnix@lbl.gov [Molecular Biology Consortium 12003 S. Pulaski Rd. #166 Alsip, IL 60803 U.S.A (United States)

    2016-07-27

    Recent advances in CMOS technology have allowed the production of large surface area detectors suitable for macromolecular crystallography experiments [1]. The Molecular Biology Consortium (MBC) Beamline 4.2.2 at the Advanced Light Source in Berkeley, CA, has installed a 2952 x 2820 mm RDI CMOS-8M detector with funds from NIH grant S10OD012073. The detector has a 20nsec dead pixel time and performs well with shutterless data collection strategies. The sensor obtains sharp point response and minimal optical distortion by use of a thin fiber-optic plate between the phosphor and sensor module. Shutterless data collections produce high-quality redundant datasets that can be obtained in minutes. The fine-sliced data are suitable for processing in standard crystallographic software packages (XDS, HKL2000, D*TREK, MOSFLM). Faster collection times relative to the previous CCD detector have resulted in a record number of datasets collected in a calendar year and de novo phasing experiments have resulted in publications in both Science and Nature [2,3]. The faster collections are due to a combination of the decreased overhead requirements of shutterless collections combined with exposure times that have decreased by over a factor of 2 for images with comparable signal to noise of the NOIR-1 detector. The overall increased productivity has allowed the development of new beamline capabilities and data collection strategies.

  10. Early Diagnosis of Orthopedic Implant Failure Using Macromolecular Imaging Agents

    Science.gov (United States)

    Ren, Ke; Dusad, Anand; Zhang, Yijia; Purdue, P. Edward; Fehringer, Edward V.; Garvin, Kevin L.; Goldring, Steven R.; Wang, Dong

    2014-01-01

    Purpose To develop and evaluate diagnostic tools for early detection of wear particle-induced orthopaedic implant loosening. Methods N-(2-hydroxypropyl)methacrylamide (HPMA) copolymer was tagged with an near infrared dye and used to detect the inflammation induced by polymethylmethacrylate (PMMA) particles in a murine peri-implant osteolysis model. It was established by inserting implant into distal femur and with routine PMMA particles challenging. The osteolysis was evaluated by micro-CT and histological analysis at different time points. Results Significant peri-implant osteolysis was found three-month post PMMA particle challenge by micro-CT and histological analysis. At one-month time point, when there was no significant peri-implant bone loss, HPMA copolymer-near infrared dye conjugate was found to specifically target to the femur with PMMA particles deposition, but not the contralateral control femur with PBS infusion. Conclusion The results from this study demonstrated the feasibility of utilizing the macromolecular diagnostic agent to report particle-induced peri-implant inflammation prior to the development of detectable osteolysis. Recognition of this early pathological event would provide the window of opportunity for prevention of peri-implant osteolysis and subsequent orthopaedic implant failure. PMID:24590878

  11. Role of Ocrl1 and Inpp5E in primary cilia assembly and maintenance: a phosphatidylinositol phosphatase relay system?

    Directory of Open Access Journals (Sweden)

    Madhivanan K

    2016-02-01

    Full Text Available Kayalvizhi Madhivanan,* Swetha Ramadesikan,* R Claudio Aguilar Department of Biological Sciences, Purdue University, West Lafayette, IN, USA *These authors contributed equally to this work Abstract: The primary cilium (PC is a plasma membrane-derived structure of great importance for cell and organismal physiology. Indeed, abnormalities in assembly or function of the PC trigger the onset of a group of genetic diseases collectively known as ciliopathies. In recent years, it has become evident that the integrity and function of the PC depends substantially on signaling elements such as phosphoinositides (PI and their regulators. Because phospholipids such as PI(4,5P2 constitute recruitment platforms for cytoskeleton, signaling, and trafficking machinery, control over their levels is critical for PC function. Although information about phosphoinositol phosphate (PIP kinases in the PC is scarce, a growing body of evidence supports a role for PIP phosphatases in cilia assembly/maintenance. Indeed, deficiencies in two 5′ PIP phosphatases, Inpp5E and Ocrl1, are clearly linked to ciliopathies like Joubert/MORM syndromes, or ciliopathy-associated diseases like Lowe syndrome. Here, we review the unique roles of these proteins and their specific site of action for ensuring ciliary integrity. Further, we discuss the possibility that a phosphatase relay system able to pass PI control from a preciliary to an intraciliary compartment is in place to ensure PC integrity/function. Keywords: primary cilia, Ocrl1, Inpp5E, Pip2, Pip3

  12. DESIGN, FABRICATION, ASSEMBLY AND BENCH TESTING OF A TEXACO INFRARED RATIO PYROMETER SYSTEM FOR THE MEASUREMENT OF REACTION CHAMBER TEMPERATURE

    Energy Technology Data Exchange (ETDEWEB)

    Tom Leininger

    2001-03-31

    Reliable measurement of gasifier reaction chamber temperature is important for the proper operation of slagging, entrained-flow gasification processes. Historically, thermocouples have been used as the main measurement technique, with the temperature inferred from syngas methane concentration being used as a backup measurement. While these have been sufficient for plant operation in many cases, both techniques suffer from limitations. The response time of methane measurements is too slow to detect rapid upset conditions, and thermocouples are subject to long-term drift, as well as slag attack, which eventually leads to failure of the thermocouple. Texaco's Montebello Technology Center (MTC) has developed an infrared ratio pyrometer system for measuring gasifier reaction chamber temperature. This system has a faster response time than both methane and thermocouples, and has been demonstrated to provide reliable temperature measurements for longer periods of time when compared to thermocouples installed in the same MTC gasifier. In addition, the system can be applied to commercial gasifiers without any significant scale-up issues. The major equipment items, the purge system, and the safety shutdown system in a commercial plant are essentially identical to the prototypes at MTC. The desired result of this DOE program is ''a bench-scale prototype, either assembled or with critical components (laboratory) tested in a convincing manner.'' The prototype of the pyrometer system (including gasifier optical access port) that was designed, assembled and tested for this program, has had previous prototypes that have been built and successfully tested under actual coal and coke gasification conditions in three pilot units at MTC. It was the intent of the work performed under the auspices of this program to review and update the existing design, and to fabricate and bench test an updated system that can be field tested in one or more commercial gasifiers

  13. The self-assembly and dynamics of weakly multivalent, peptide-based, host-guest systems

    NARCIS (Netherlands)

    Satav, Tushar Narendra

    2015-01-01

    Multivalency is the key principle dictating receptor-ligand interactions in biological systems. To understand these interactions in detail a model system taken out of biological complexity is required. Most of the model systems reported so far have been focused on employing strong intrinsic

  14. A Method for Designing Assembly Tolerance Networks of Mechanical Assemblies

    Directory of Open Access Journals (Sweden)

    Yi Zhang

    2012-01-01

    Full Text Available When designing mechanical assemblies, assembly tolerance design is an important issue which must be seriously considered by designers. Assembly tolerances reflect functional requirements of assembling, which can be used to control assembling qualities and production costs. This paper proposes a new method for designing assembly tolerance networks of mechanical assemblies. The method establishes the assembly structure tree model of an assembly based on its product structure tree model. On this basis, assembly information model and assembly relation model are set up based on polychromatic sets (PS theory. According to the two models, the systems of location relation equations and interference relation equations are established. Then, using methods of topologically related surfaces (TTRS theory and variational geometric constraints (VGC theory, three VGC reasoning matrices are constructed. According to corresponding relations between VGCs and assembly tolerance types, the reasoning matrices of tolerance types are also established by using contour matrices of PS. Finally, an exemplary product is used to construct its assembly tolerance networks and meanwhile to verify the feasibility and effectiveness of the proposed method.

  15. A novel intracorporeal assembling robotic system for single-port laparoscopic surgery.

    Science.gov (United States)

    Petroni, Gianluigi; Niccolini, Marta; Menciassi, Arianna; Dario, Paolo; Cuschieri, Alfred

    2013-02-01

    Single-port laparoscopic surgery (SPLS) is a novel surgical approach consisting of a single umbilical incision through which multiple instruments are inserted, thus avoiding additional incisions necessary in traditional multi-port laparoscopic surgery. SPLS imposes a number of ergonomic restrictions on the surgeon. As a partial solution, several dedicated instruments, including hand-held manipulators with 6 degrees of freedom (DOF), have been introduced to overcome these manipulative restrictions. Robotics has the potential to overcome all of the ergonomic restrictions imposed by the SPLS approach. A novel, teleoperated, robotic platform has been developed. SPRINT (Single-Port lapaRoscopy bImaNual roboT) is a multiarm robot enabling bimanual interventions. The robotic arms are introduced into the abdomen through a cylindrical introducer. The surgeon is able to control the robot in a master-slave configuration through a dedicated console, allowing translation of the surgeon's hand movements to the end-effectors. Laboratory tests have been performed with the prototype by experienced surgeons for pick and place and suturing exercises. These confirmed the fast-learning curve with the use of the SPRINT robot. In the pick and place exercise, the mean successful peg transfer rate decreased from 97 s at the start to 50 s required for the transfer of the seventh peg. Thereafter, the slope of the curve decreased to 31 s after 17 transfers. The percentage error rate declined from an initial value 50 % to 25 % after 15 pegs had been transferred. In the intracorporeal suture test, needle passage and knot tying were completed by four surgeons in 314 s or less. A new surgical robot for SPLS has been developed, and its usability and efficacy have been demonstrated. The SPRINT may pave the way for the next generation of surgical robots, the arms of which are assembled inside the insufflated peritoneal cavity, providing full dexterity and manipulative ability with the SPLS approach.

  16. Controlling Interfacial Adhesion of Self-Assembled Polypeptide Fibrils for Novel Nanoelectromechanical System (NEMS Applications

    Directory of Open Access Journals (Sweden)

    Christopher Kossow

    2011-01-01

    Full Text Available The relative adhesion of two genetically engineered polypeptides termed as H6-(YEHKx21-H6 and C6-(YEHKX21-H6 has been investigated following growth and self-assembly on highly oriented pyrolytic graphite (HOPG, SiO2, Ni, and Au substrates to study covalent surface attachment via histidine (H and cysteine (C groups incorporated in the polypeptides. Both polypeptides formed predominantly bilayer fibrils upon deposition, in agreement with previous studies. The relative adhesion of polypeptide fibrils to the substrate, as well as intra-fibril cohesion, was examined via a forced-scanning method employing contact mode atomic force microscopy (AFM. H6-(YEHKx21-H6 polypeptide fibrils were observed to detach from Ni, Au, SiO2, and HOPG substrates at normal tip forces of 106 ± 10 nN, 21 ± 3 nN, 22 ± 3 nN, and 3 ± 1 nN, respectively. C6-(YEHKx21-H6 polypeptide fibrils were seen to detach from Au substrates at a normal spring force of 90 ± 10 nN. It is concluded that the H6-(YEHKx21-H6 and C6-(YEHKx21-H6 polypeptide fibrils are covalently attached to, respectively, Ni and Au substrates, which has important implications for the use of these materials for NEMS fabrication. The structural stability of deposited polypeptide fibrils was also evaluated by using normal tip forces less than those required for fibril detachment. H6-(YEHKx21-H6 polypeptide fibrils on Ni substrates were the most structurally stable compared to C6-(YEHKx21-H6 polypeptide fibrils on Au substrates. Controlled delayering of bilayer fibrils was also detected for sub-detachment normal forces.

  17. Pervasive Investigations of Critical Speed over Weight and Deflection Factors of Shaft Assembly in CNC Ball Screw System

    Directory of Open Access Journals (Sweden)

    Kuldeep Verma

    2016-01-01

    Full Text Available The demand for higher productivity requires machine tools to work on the adequate critical speed to have faster and more accurate ball screw system. Ball screw affects severely over the higher rotation speed of the shaft in computer numeric control (CNC machining centers. This paper deals with an approach to calculate the initial critical speed of the shaft. Critical speed requires significant attention due to its major use in the manufacturing sectors. The impacts of weight on the critical speed of shaft assembly have been analyzed from theoretical as well as analytical investigations. Additionally, we evaluated the impact of weight on the deflection of the shafts along with failure analysis of shafts with respect to critical speed. Further, we computed the results for critical speed based factor to enhance the accuracy of CNC machining centers. Finally, the analytical estimations have been carried out to prove the validity of our proposal.

  18. Preclinical imaging and translational animal models of cancer for accelerated clinical implementation of nanotechnologies and macromolecular agents.

    Science.gov (United States)

    De Souza, Raquel; Spence, Tara; Huang, Huang; Allen, Christine

    2015-12-10

    The majority of animal models of cancer have performed poorly in terms of predicting clinical performance of new therapeutics, which are most often first evaluated in patients with advanced, metastatic disease. The development and use of metastatic models of cancer may enhance clinical translatability of preclinical studies focused on the development of nanotechnology-based drug delivery systems and macromolecular therapeutics, potentially accelerating their clinical implementation. It is recognized that the development and use of such models are not without challenge. Preclinical imaging tools offer a solution by allowing temporal and spatial characterization of metastatic lesions. This paper provides a review of imaging methods applicable for evaluation of novel therapeutics in clinically relevant models of advanced cancer. An overview of currently utilized models of oncology in small animals is followed by image-based development and characterization of visceral metastatic cancer models. Examples of imaging tools employed for metastatic lesion detection, evaluation of anti-tumor and anti-metastatic potential and biodistribution of novel therapies, as well as the co-development and/or use of imageable surrogates of response, are also discussed. While the focus is on development of macromolecular and nanotechnology-based therapeutics, examples with small molecules are included in some cases to illustrate concepts and approaches that can be applied in the assessment of nanotechnologies or macromolecules. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. Nucleic acid encoding a self-assembling split-fluorescent protein system

    Energy Technology Data Exchange (ETDEWEB)

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2015-07-14

    The invention provides a protein labeling and detection system based on self-complementing fragments of fluorescent and chromophoric proteins. The system of the invention is exemplified with various combinations of self-complementing fragments derived from Aequorea victoria Green Fluorescent Protein (GFP), which are used to detect and quantify protein solubility in multiple assay formats, both in vitro and in vivo.

  20. Nucleic acid encoding a self-assembling split-fluorescent protein system

    Science.gov (United States)

    Waldo, Geoffrey S [Santa Fe, NM; Cabantous, Stephanie [Los Alamos, NM

    2011-06-07

    The invention provides a protein labeling and detection system based on self-complementing fragments of fluorescent and chromophoric proteins. The system of the invention is exemplified with various combinations of self-complementing fragments derived from Aequorea victoria Green Fluorescent Protein (GFP), which are used to detect and quantify protein solubility in multiple assay formats, both in vitro and in vivo.

  1. Nucleic acid encoding a self-assembling split-fluorescent protein system

    Science.gov (United States)

    Waldo, Geoffrey S; Cabantous, Stephanie

    2014-04-01

    The invention provides a protein labeling and detection system based on self-complementing fragments of fluorescent and chromophoric proteins. The system of the invention is exemplified with various combinations of self-complementing fragments derived from Aequorea victoria Green Fluorescent Protein (GFP), which are used to detect and quantify protein solubility in multiple assay formats, both in vitro and in vivo.

  2. The use of workflows in the design and implementation of complex experiments in macromolecular crystallography.

    Science.gov (United States)

    Brockhauser, Sandor; Svensson, Olof; Bowler, Matthew W; Nanao, Max; Gordon, Elspeth; Leal, Ricardo M F; Popov, Alexander; Gerring, Matthew; McCarthy, Andrew A; Gotz, Andy

    2012-08-01

    The automation of beam delivery, sample handling and data analysis, together with increasing photon flux, diminishing focal spot size and the appearance of fast-readout detectors on synchrotron beamlines, have changed the way that many macromolecular crystallography experiments are planned and executed. Screening for the best diffracting crystal, or even the best diffracting part of a selected crystal, has been enabled by the development of microfocus beams, precise goniometers and fast-readout detectors that all require rapid feedback from the initial processing of images in order to be effective. All of these advances require the coupling of data feedback to the experimental control system and depend on immediate online data-analysis results during the experiment. To facilitate this, a Data Analysis WorkBench (DAWB) for the flexible creation of complex automated protocols has been developed. Here, example workflows designed and implemented using DAWB are presented for enhanced multi-step crystal characterizations, experiments involving crystal reorientation with kappa goniometers, crystal-burning experiments for empirically determining the radiation sensitivity of a crystal system and the application of mesh scans to find the best location of a crystal to obtain the highest diffraction quality. Beamline users interact with the prepared workflows through a specific brick within the beamline-control GUI MXCuBE.

  3. Influence of temperature and macromolecular mobility on sorption of TCE on humic acid coated mineral surfaces.

    Science.gov (United States)

    Bell, Katherine Young; LeBoeuf, Eugene J

    2013-01-01

    This study demonstrates differences in sorptive capacity of volatile organic compound (VOC) trichloroethylene (TCE) onto natural organic matter (NOM) coated and uncoated mineral surfaces above and below the NOM glass transition temperature. TCE sorption isotherms for dry NOM-mineral systems below the NOM glass transition temperature (T(g)) demonstrated sorption behavior characteristic of micropore filling, with sorption capacities reduced relative to uncoated mineral matrices. Such differences were not entirely associated with differences in surface areas of the coated and uncoated mineral matrices, but were likely associated with either a blockage of pore space available to the VOC or a kinetic limitation that does not allow the VOC access to the internal porosity of the model soil within the time periods of the experiment. TCE sorption in dry NOM-mineral matrices above the T(g), however, was described in terms of sorption within a more fluid, macromolecular dissolution medium that does not hinder access to mineral surfaces. Such observations have potential important implications for modeling the fate and transport of VOCs in soils and sediment systems. Copyright © 2012 Elsevier Ltd. All rights reserved.

  4. Assembly and comparison of available solar hot water system reliability databases and information.

    Energy Technology Data Exchange (ETDEWEB)

    Menicucci, David F. (Building Specialists, Inc., Albuquerque, NM)

    2009-05-01

    Solar hot water (SHW) systems have been installed commercially for over 30 years, yet few quantitative details are known about their reliability. This report describes a comprehensive analysis of all of the known major previous research and data regarding the reliability of SHW systems and components. Some important conclusions emerged. First, based on a detailed inspection of ten-year-old systems in Florida, about half of active systems can be expected to fail within a ten-year period. Second, valves were identified as the probable cause of a majority of active SHW failures. Third, passive integral and thermosiphon SHW systems have much lower failure rates than active ones, probably due to their simple design that employs few mechanical parts. Fourth, it is probable that the existing data about reliability do not reveal the full extent of fielded system failures because most of the data were based on trouble calls. Often an SHW system owner is not aware of a failure because the backup system silently continues to produce hot water. Thus, a repair event may not be generated in a timely manner, if at all. This final report for the project provides all of the pertinent details about this study, including the source of the data, the techniques to assure their quality before analysis, the organization of the data into perhaps the most comprehensive reliability database in existence, a detailed statistical analysis, and a list of recommendations for additional critical work. Important recommendations include the inclusion of an alarm on SHW systems to identify a failed system, the need for a scientifically designed study to collect high-quality reliability data that will lead to design improvements and lower costs, and accelerated testing of components that are identified as highly problematic.

  5. Macromolecular query language (MMQL): prototype data model and implementation.

    Science.gov (United States)

    Shindyalov, I N; Chang, W; Pu, C; Bourne, P E

    1994-11-01

    Macromolecular query language (MMQL) is an extensible interpretive language in which to pose questions concerning the experimental or derived features of the 3-D structure of biological macromolecules. MMQL portends to be intuitive with a simple syntax, so that from a user's perspective complex queries are easily written. A number of basic queries and a more complex query--determination of structures containing a five-strand Greek key motif--are presented to illustrate the strengths and weaknesses of the language. The predominant features of MMQL are a filter and pattern grammar which are combined to express a wide range of interesting biological queries. Filters permit the selection of object attributes, for example, compound name and resolution, whereas the patterns currently implemented query primary sequence, close contacts, hydrogen bonding, secondary structure, conformation and amino acid properties (volume, polarity, isoelectric point, hydrophobicity and different forms of exposure). MMQL queries are processed by MMQLlib; a C++ class library, to which new query methods and pattern types are easily added. The prototype implementation described uses PDBlib, another C(++)-based class library from representing the features of biological macromolecules at the level of detail parsable from a PDB file. Since PDBlib can represent data stored in relational and object-oriented databases, as well as PDB files, once these data are loaded they too can be queried by MMQL. Performance metrics are given for queries of PDB files for which all derived data are calculated at run time and compared to a preliminary version of OOPDB, a prototype object-oriented database with a schema based on a persistent version of PDBlib which offers more efficient data access and the potential to maintain derived information. MMQLlib, PDBlib and associated software are available via anonymous ftp from cuhhca.hhmi.columbia.edu.

  6. Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).

    Science.gov (United States)

    Foffi, G; Pastore, A; Piazza, F; Temussi, P A

    2013-08-02

    conference held in Ascona from 10 to 14 June 2012. In the unique scenario of the Maggiore lake and absorbed in the magic atmosphere of the Centro Stefano Franscini (CSF) at Monte Verità, we enjoyed three-and-a-half days of intense and inspiring activity, where not only many of the most prominent scientists working on macromolecular crowding, but also experts in closely related fields such as colloids and soft matter presented their work. The meeting was intended and has been organized to bring theoreticians and experimentalists together in the attempt to promote an active dialogue. Moreover, we wanted different disciplines to be represented, notably physics and chemistry, besides biology, as cross-fertilization is proving an increasingly fundamental source of inspiration and advancement. This issue of Physical Biology (PB) features a selection of the oral contributions presented at the conference, expanded in the form of research or review articles. PB, one of the scientific journals of the Institute of Physics (IOP), is one of the most dynamic and lively forums active at the interface between biology on one side, and physics and mathematics on the other. As its mission is stated by IOP, PB 'focuses on research in which physics-based approaches lead to new insights into biological systems at all scales of space and time, and all levels of complexity'. For these reasons, and also in view of its high reputation and broad readership, PB appears to be the ideal place for disseminating the thriving pieces of research presented at the conference. We are extremely grateful to PB and its kind and efficient editorial staff who helped make this issue a great scientific follow-up to the conference. The opening lecture of the conference, the first of four day-opening keynote lectures, was given by Allen P Minton from NIH (USA), possibly the most influential among the pioneers in the field. He provided a lucid and well-thought-out overview of the concept of macromolecular crowding

  7. Evolution of International Space Station GN&C System Across ISS Assembly Stages

    Science.gov (United States)

    Lee, Roscoe; Frank, K. D. (Technical Monitor)

    1999-01-01

    The Guidance Navigation and Control (GN&C) system for the International Space Station is initially implemented by the Functional Cargo Block (FGB) which was built by the Khrunichev Space Center under direct contract to Boeing. This element (Stage 1A/R) was launched on 20 November 1998 and is currently operating on-orbit. The components and capabilities of the FGB Motion Control System (MCS) are described. The next ISS element, which has GN&C functionality will be the Service Module (SM) built by Rocket Space Corporation-Energia. This module is scheduled for launch (Stage 1R) in early 2000. Following activation of the SM GN&C system, the FGB MCS is deactivated and no longer used. The components and capabilities of the SM GN&C system are described. When a Progress vehicle is attached to the ISS it can be used for reboost operations, based on commands provided by the Mission Control Center-Moscow. When a data connection is implemented between the SM and the Progress, the SM can command the Progress thrusters for attitude control and reboosts. On Stage 5A, the U.S. GN&C system will become activated when the U.S. Laboratory is de loyed and installed (launch schedule is currently TBD). The U.S. GN&C system provides non-propulsive control capabilities to support micro-gravity operations and minimize the use of propellant for attitude control, and an independent capability for determining the ISS state vector, attitude, attitude rate. and time.. The components and capabilities of the U.S. GN&C system are described and the interactions between the U.S. and Russian Segment GN&C systems are also described.

  8. A simple quantitative model of macromolecular crowding effects on protein folding: Application to the murine prion protein(121-231)

    Science.gov (United States)

    Bergasa-Caceres, Fernando; Rabitz, Herschel A.

    2013-06-01

    A model of protein folding kinetics is applied to study the effects of macromolecular crowding on protein folding rate and stability. Macromolecular crowding is found to promote a decrease of the entropic cost of folding of proteins that produces an increase of both the stability and the folding rate. The acceleration of the folding rate due to macromolecular crowding is shown to be a topology-dependent effect. The model is applied to the folding dynamics of the murine prion protein (121-231). The differential effect of macromolecular crowding as a function of protein topology suffices to make non-native configurations relatively more accessible.

  9. An All-Organic Composite System for Resistive Change Memory via the Self-Assembly of Plastic-Crystalline Molecules.

    Science.gov (United States)

    Cha, An-Na; Lee, Sang-A; Bae, Sukang; Lee, Sang Hyun; Lee, Dong Su; Wang, Gunuk; Kim, Tae-Wook

    2017-01-25

    An all-organic composite system was introduced as an active component for organic resistive memory applications. The active layer was prepared by mixing a highly polar plastic-crystalline organic molecule (succinonitrile, SN) into an insulating polymer (poly(methyl methacrylate), PMMA). As increasing concentrations of SN from 0 to 3.0 wt % were added to solutions of different concentrations of PMMA, we observed distinguishable microscopic surface structures on blended films of SN and PMMA at certain concentrations after the spin-casting process. The structures were organic dormant volcanos composed of micron-scale PMMA craters and disk type SN lava. Atomic force microscopy (AFM), cross-sectional transmission electron microscopy (TEM), scanning electron microscopy (SEM), and energy dispersive X-ray spectrometer (EDX) analysis showed that these structures were located in the middle of the film. Self-assembly of the plastic-crystalline molecules resulted in the phase separation of the SN:PMMA mixture during solvent evaporation. The organic craters remained at the surface after the spin-casting process, indicative of the formation of an all-organic composite film. Because one organic crater contains one SN disk, our system has a coplanar monolayer disk composite system, indicative of the simplest composite type of organic memory system. Current-voltage (I-V) characteristics of the composite films with organic craters revealed that our all-organic composite system showed unipolar type resistive switching behavior. From logarithmic I-V characteristics, we found that the current flow was governed by space charge limited current (SCLC). From these results, we believe that a plastic-crystalline molecule-polymer composite system is one of the most reliable ways to develop organic composite systems as potential candidates for the active components of organic resistive memory applications.

  10. Investigation of Supramolecular Coordination Self-Assembly and Polymerization Confined on Metal Surfaces Using Scanning Tunneling Microscopy

    Science.gov (United States)

    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

  11. 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.

  12. Development of large-area CCD-based x-ray detector for macromolecular crystallography

    Science.gov (United States)

    Pokric, M.; Allinson, Nigel M.; Jorden, Anthony R.; Cox, Matthew P.; Marshall, Andrew R.; Long, P. G.; Moon, Kevin; Jerram, Paul; Pool, Peter J.; Nave, Colin; Derbyshire, Gareth E.; Helliwell, John R.

    1999-10-01

    The design and development of an area CCD-based X-ray detector system, using the first CCD imagers specially designed for macromolecular crystallography, is presented. The system is intended to produce the highest quality data for physically small crystals at synchrotron sources through the use of large CCDs--that is approaching wafer scale. This work is part of a large research and development program for advanced X-ray sensor technology, funded by industry and the Particle Physics and Astronomy Research Council in the UK. The detector has been optimized by increasing its efficiency at low X-ray energies for conventional laboratory sources, and offers fast readout and high dynamic range needed for efficient measurements at synchrotron sources. The detector consists of CCDs optically coupled to a X-ray sensitive phosphor via skewed fiber-optic studs. The individual three- sides buttable CCD consists of 2048 X 1536 27 micrometers square pixels (55.3 X 41.5 mm). The pixel size has been optimized to match diffraction spot profiling needs and the high dynamic range required for such applications. The multiple amplifier outputs possess switched responsivity to maximize the trade-off between signal handling capabilities and linearity. The readout noise is 5 electrons rms at a 1 MHz pixel rate at the high responsivity setting. A prototype detector system comprising two close-butted cooled CCDs is being developed. This system employs a high-efficiency scintillator with very low point spread function, skewed optical-fiber studs (instead of the more usual demagnifying tapers) to maximize the system's detective quantum efficiency and minimize optical distortions. Full system specifications and a novel crystallographic data processing are presented.

  13. Detection of Macromolecular Fractions in HCN Polymers Using Electrophoretic and Ultrafiltration Techniques.

    Science.gov (United States)

    Marín-Yaseli, Margarita R; Cid, Cristina; Yagüe, Ana I; Ruiz-Bermejo, Marta

    2017-02-01

    Elucidating the origin of life involves synthetic as well as analytical challenges. Herein, for the first time, we describe the use of gel electrophoresis and ultrafiltration to fractionate HCN polymers. Since the first prebiotic synthesis of adenine by Oró, HCN polymers have gained much interest in studies on the origins of life due to the identification of biomonomers and related compounds within them. Here, we demonstrate that macromolecular fractions with electrophoretic mobility can also be detected within HCN polymers. The migration of polymers under the influence of an electric field depends not only on their sizes (one-dimensional electrophoresis) but also their different isoelectric points (two-dimensional electrophoresis, 2-DE). The same behaviour was observed for several macromolecular fractions detected in HCN polymers. Macromolecular fractions with apparent molecular weights as high as 250 kDa were detected by tricine-SDS gel electrophoresis. Cationic macromolecular fractions with apparent molecular weights as high as 140 kDa were also detected by 2-DE. The HCN polymers synthesized were fractionated by ultrafiltration. As a result, the molecular weight distributions of the macromolecular fractions detected in the HCN polymers directly depended on the synthetic conditions used to produce these polymers. The implications of these results for prebiotic chemistry will be discussed. © 2017 Wiley-VHCA AG, Zurich, Switzerland.

  14. Fifteen years of the Protein Crystallography Station: the coming of age of macromolecular neutron crystallography

    Directory of Open Access Journals (Sweden)

    Julian C.-H. Chen

    2017-01-01

    Full Text Available The Protein Crystallography Station (PCS, located at the Los Alamos Neutron Scattering Center (LANSCE, was the first macromolecular crystallography beamline to be built at a spallation neutron source. Following testing and commissioning, the PCS user program was funded by the Biology and Environmental Research program of the Department of Energy Office of Science (DOE-OBER for 13 years (2002–2014. The PCS remained the only dedicated macromolecular neutron crystallography station in North America until the construction and commissioning of the MaNDi and IMAGINE instruments at Oak Ridge National Laboratory, which started in 2012. The instrument produced a number of research and technical outcomes that have contributed to the field, clearly demonstrating the power of neutron crystallography in helping scientists to understand enzyme reaction mechanisms, hydrogen bonding and visualization of H-atom positions, which are critical to nearly all chemical reactions. During this period, neutron crystallography became a technique that increasingly gained traction, and became more integrated into macromolecular crystallography through software developments led by investigators at the PCS. This review highlights the contributions of the PCS to macromolecular neutron crystallography, and gives an overview of the history of neutron crystallography and the development of macromolecular neutron crystallography from the 1960s to the 1990s and onwards through the 2000s.

  15. The cooling control system for focal plane assembly of astronomical satellite camera based on TEC

    Science.gov (United States)

    He, Yuqing; Du, Yunfei; Gao, Wei; Li, Baopeng; Fan, Xuewu; Yang, Wengang

    2017-02-01

    The dark current noise existing in the CCD of the astronomical observation camera has a serious influence on its working performance, reducing the working temperature of CCD can suppress the influence of dark current effectively. By analyzing the relationship between the CCD chip and the dark current noise, the optimum working temperature of the red band CCD focal plane is identified as -75°. According to the refrigeration temperature, a cooling control system for focal plane based on a thermoelectric cooler (TEC) was designed. It is required that the system can achieve high precision temperature control for the target. In the cooling control system, the 80C32 microcontroller was used as its systematic core processor. The advanced PID control algorithm is adopted to control the temperature of the top end of TEC. The bottom end of the TEC setting a constant value according to the target temperature used to assist the upper TEC to control the temperature. The experimental results show that the cooling system satisfies the requirements of the focal plane for the astronomical observation camera, it can reach the working temperature of -75° and the accuracy of ±2°.

  16. The state of Ghana's local government system: the case of Assembly ...

    African Journals Online (AJOL)

    International development organisations have, for a long time, presented Ghana as having a highly functional intergovernment system or decentralisation. While this projection is far from the country's grounded reality, Ghana continues to benefit from the 'misrepresentation' as one of the preferred destinations in the ...

  17. The Impact of the Availability of Resources, the Allocation of Buffers and Number of Workers on the Effectiveness of an Assembly Manufacturing System

    Directory of Open Access Journals (Sweden)

    Kłos Sławomir

    2017-09-01

    Full Text Available This paper proposes the application of computer simulation methods in order to analyse the availability of resources, buffers and the impact of the allocation of workers on the throughput and work-in-progress of a manufacturing system. The simulation model of the production system is based on an existing example of a manufacturing company in the automotive industry. The manufacturing system includes both machining and assembly operations. Simulation experiments were conducted vis-à-vis the availability of the different manufacturing resources, the various allocations of buffer capacities and the number of employees. The production system consists of three manufacturing cells – each cell including two CNC machines – and two assembly stations. The parts produced by the manufacturing cells are stored in buffers and transferred to the assembly stations. Workers are allocated to the manufacturing cells and assembly stations, but the number of workers may be less than number of workplaces and are thus termed ‘multi-workstations’. Using computer simulation methods, the impact of the availability of resources, the number of employees and of the allocation of buffer capacity on the throughput and work-in-progress of the manufacturing system is analysed. The results of the research are used to improve the effectiveness of manufacturing systems using a decision support system and the proper control of resources. Literature analysis shows that the study of the impact of buffer capacities, availability of resources and the number of employees on assembly manufacturing system performance have not been carried out so far.

  18. About Small Streams and Shiny Rocks: Macromolecular Crystal Growth in Microfluidics

    Science.gov (United States)

    vanderWoerd, Mark; Ferree, Darren; Spearing, Scott; Monaco, Lisa; Molho, Josh; Spaid, Michael; Brasseur, Mike; Curreri, Peter A. (Technical Monitor)

    2002-01-01

    We are developing a novel technique with which we have grown diffraction quality protein crystals in very small volumes, utilizing chip-based, microfluidic ("LabChip") technology. With this technology volumes smaller than achievable with any laboratory pipette can be dispensed with high accuracy. We have performed a feasibility study in which we crystallized several proteins with the aid of a LabChip device. The protein crystals are of excellent quality as shown by X-ray diffraction. The advantages of this new technology include improved accuracy of dispensing for small volumes, complete mixing of solution constituents without bubble formation, highly repeatable recipe and growth condition replication, and easy automation of the method. We have designed a first LabChip device specifically for protein crystallization in batch mode and can reliably dispense and mix from a range of solution constituents. We are currently testing this design. Upon completion additional crystallization techniques, such as vapor diffusion and liquid-liquid diffusion will be accommodated. Macromolecular crystallization using microfluidic technology is envisioned as a fully automated system, which will use the 'tele-science' concept of remote operation and will be developed into a research facility aboard the International Space Station.

  19. The Effect of Attractive Interactions and Macromolecular Crowding on Crystallins Association.

    Directory of Open Access Journals (Sweden)

    Jiachen Wei

    Full Text Available In living systems proteins are typically found in crowded environments where their effective interactions strongly depend on the surrounding medium. Yet, their association and dissociation needs to be robustly controlled in order to enable biological function. Uncontrolled protein aggregation often causes disease. For instance, cataract is caused by the clustering of lens proteins, i.e., crystallins, resulting in enhanced light scattering and impaired vision or blindness. To investigate the molecular origins of cataract formation and to design efficient treatments, a better understanding of crystallin association in macromolecular crowded environment is needed. Here we present a theoretical study of simple coarse grained colloidal models to characterize the general features of how the association equilibrium of proteins depends on the magnitude of intermolecular attraction. By comparing the analytic results to the available experimental data on the osmotic pressure in crystallin solutions, we identify the effective parameters regimes applicable to crystallins. Moreover, the combination of two models allows us to predict that the number of binding sites on crystallin is small, i.e. one to three per protein, which is different from previous estimates. We further observe that the crowding factor is sensitive to the size asymmetry between the reactants and crowding agents, the shape of the protein clusters, and to small variations of intermolecular attraction. Our work may provide general guidelines on how to steer the protein interactions in order to control their association.

  20. Exhaust system for use with a turbine and method of assembling same

    Energy Technology Data Exchange (ETDEWEB)

    Dalsania, Prakash Bavanjibhai; Sadhu, Antanu

    2015-08-18

    An exhaust system for use with a steam turbine is provided. An exhaust hood includes an input and an output, the input receiving fluid from the steam turbine. The exhaust hood includes a first side wall that extends between the input and the output. The first side wall includes an aperture. An ejector is coupled to the exhaust hood. The ejector includes inlets and an outlet. At least one of the inlets receives fluid from the exhaust hood via the aperture.

  1. On Constraints in Assembly Planning

    Energy Technology Data Exchange (ETDEWEB)

    Calton, T.L.; Jones, R.E.; Wilson, R.H.

    1998-12-17

    Constraints on assembly plans vary depending on product, assembly facility, assembly volume, and many other factors. Assembly costs and other measures to optimize vary just as widely. To be effective, computer-aided assembly planning systems must allow users to express the plan selection criteria that appIy to their products and production environments. We begin this article by surveying the types of user criteria, both constraints and quality measures, that have been accepted by assembly planning systems to date. The survey is organized along several dimensions, including strategic vs. tactical criteria; manufacturing requirements VS. requirements of the automated planning process itself and the information needed to assess compliance with each criterion. The latter strongly influences the efficiency of planning. We then focus on constraints. We describe a framework to support a wide variety of user constraints for intuitive and efficient assembly planning. Our framework expresses all constraints on a sequencing level, specifying orders and conditions on part mating operations in a number of ways. Constraints are implemented as simple procedures that either accept or reject assembly operations proposed by the planner. For efficiency, some constraints are supplemented with special-purpose modifications to the planner's algorithms. Fast replanning enables an interactive plan-view-constrain-replan cycle that aids in constraint discovery and documentation. We describe an implementation of the framework in a computer-aided assembly planning system and experiments applying the system to a number of complex assemblies, including one with 472 parts.

  2. Design and verification of focal plane assembly thermal control system of one space-based astronomy telescope

    Science.gov (United States)

    Yang, Wen-gang; Fan, Xue-wu; Wang, Chen-jie; Wang, Ying-hao; Feng, Liang-jie; Du, Yun-fei; Ren, Guo-rui; Wang, Wei; Li, Chuang; Gao, Wei

    2015-10-01

    One space-based astronomy telescope will observe astronomy objects whose brightness should be lower than 23th magnitude. To ensure the telescope performance, very low system noise requirements need extreme low CCD operating temperature (lower than -65°C). Because the satellite will be launched in a low earth orbit, inevitable space external heat fluxes will result in a high radiator sink temperature (higher than -65°C). Only passive measures can't meet the focal plane cooling specification and active cooling technologies must be utilized. Based on detailed analysis on thermal environment of the telescope and thermal characteristics of focal plane assembly (FPA), active cooling system which is based on thermo-electric cooler (TEC) and heat rejection system (HRS) which is based on flexible heat pipe and radiator have been designed. Power consumption of TECs is dependent on the heat pumped requirements and its hot side temperature. Heat rejection capability of HRS is mainly dependent on the radiator size and temperature. To compromise TEC power consumption and the radiator size requirement, thermal design of FPA must be optimized. Parasitic heat loads on the detector is minimized to reduce the heat pumped demands of TECs and its power consumption. Thermal resistance of heat rejection system is minimized to reject the heat dissipation of TECs from the hot side to the radiator efficiently. The size and surface coating of radiator are optimized to compromise heat reject ion requirements and system constraints. Based on above work, transient thermal analysis of FPA is performed. FPA prototype model has been developed and thermal vacuum/balance test has been accomplished. From the test, temperature of key parts and working parameters of TECs in extreme cases have been acquired. Test results show that CCD can be controlled below -65°C and all parts worked well during the test. All of these verified the thermal design of FPA and some lessons will be presented in this

  3. Purely entropic self-assembly of the bicontinuous Ia3d gyroid phase in equilibrium hard-pear systems.

    Science.gov (United States)

    Schönhöfer, Philipp W A; Ellison, Laurence J; Marechal, Matthieu; Cleaver, Douglas J; Schröder-Turk, Gerd E

    2017-08-06

    We investigate a model of hard pear-shaped particles which forms the bicontinuous Ia[Formula: see text]d structure by entropic self-assembly, extending the previous observations of Barmes et al. (2003 Phys. Rev. E68, 021708. (doi:10.1103/PhysRevE.68.021708)) and Ellison et al. (2006 Phys. Rev. Lett.97, 237801. (doi:10.1103/PhysRevLett.97.237801)). We specifically provide the complete phase diagram of this system, with global density and particle shape as the two variable parameters, incorporating the gyroid phase as well as disordered isotropic, smectic and nematic phases. The phase diagram is obtained by two methods, one being a compression-decompression study and the other being a continuous change of the particle shape parameter at constant density. Additionally, we probe the mechanism by which interdigitating sheets of pears in these systems create surfaces with negative Gauss curvature, which is needed to form the gyroid minimal surface. This is achieved by the use of Voronoi tessellation, whereby both the shape and volume of Voronoi cells can be assessed in regard to the local Gauss curvature of the gyroid minimal surface. Through this, we show that the mechanisms prevalent in this entropy-driven system differ from those found in systems which form gyroid structures in nature (lipid bilayers) and from synthesized materials (di-block copolymers) and where the formation of the gyroid is enthalpically driven. We further argue that the gyroid phase formed in these systems is a realization of a modulated splay-bend phase in which the conventional nematic has been predicted to be destabilized at the mesoscale due to molecular-scale coupling of polar and orientational degrees of freedom.

  4. 75 FR 3253 - Lamb Assembly and Test, LLC, Subsidiary of Mag Industrial Automation Systems, Machesney Park, IL...

    Science.gov (United States)

    2010-01-20

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF LABOR Employment and Training Administration Lamb Assembly and Test, LLC, Subsidiary of Mag Industrial Automation... assembly automation equipment to companies which have been recently certified eligible for TAA. The...

  5. Microtubule Self- Assembly

    Science.gov (United States)

    Jho, Yongseok; Choi, M. C.; Farago, O.; Kim, Mahnwon; Pincus, P. A.

    2008-03-01

    Microtubules are important structural elements for neurons. Microtubles are cylindrical pipes that are self-assembled from tubulin dimers, These structures are intimately related to the neuron transport system. Abnormal microtubule disintegration contributes to neuro-disease. For several decades, experimentalists investigated the structure of the microtubules using TEM and Cryo-EM. However, the detailed structure at a molecular level remain incompletely understood. . In this presentation, we report numerically studies of the self-assembly process using a toy model for tubulin dimers. We investigate the nature of the interactions which are essential to stabilize such the cylindrical assembly of protofilaments. We use Monte Carlo simulations to suggest the pathways for assembly and disassembly of the microtubules.

  6. Molecular self-assembly advances and applications

    CERN Document Server

    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

  7. 48 CFR 239.7409 - Special assembly.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 3 2010-10-01 2010-10-01 false Special assembly. 239.7409... Services 239.7409 Special assembly. (a) Special assembly is the designing, manufacturing, arranging... general use equipment. (b) Special assembly rates and charges shall be based on estimated costs. The...

  8. Ultra-Portable Smartphone Controlled Integrated Digital Microfluidic System in a 3D-Printed Modular Assembly

    Directory of Open Access Journals (Sweden)

    Mohamed Yafia

    2015-09-01

    Full Text Available Portable sensors and biomedical devices are influenced by the recent advances in microfluidics technologies, compact fabrication techniques, improved detection limits and enhanced analysis capabilities. This paper reports the development of an integrated ultraportable, low-cost, and modular digital microfluidic (DMF system and its successful integration with a smartphone used as a high-level controller and post processing station. Low power and cost effective electronic circuits are designed to generate the high voltages required for DMF operations in both open and closed configurations (from 100 to 800 V. The smartphone in turn commands a microcontroller that manipulate the voltage signals required for droplet actuation in the DMF chip and communicates wirelessly with the microcontroller via Bluetooth module. Moreover, the smartphone acts as a detection and image analysis station with an attached microscopic lens. The holder assembly is fabricated using three-dimensional (3D printing technology to facilitate rapid prototyping. The holder features a modular design that enables convenient attachment/detachment of a variety of DMF chips to/from an electrical busbar. The electrical circuits, controller and communication system are designed to minimize the power consumption in order to run the device on small lithium ion batteries. Successful controlled DMF operations and a basic colorimetric assay using the smartphone are demonstrated.

  9. High Performance Fuel Cell and Electrolyzer Membrane Electrode Assemblies (MEAs) for Space Energy Storage Systems

    Science.gov (United States)

    Valdez, Thomas I.; Billings, Keith J.; Kisor, Adam; Bennett, William R.; Jakupca, Ian J.; Burke, Kenneth; Hoberecht, Mark A.

    2012-01-01

    Regenerative fuel cells provide a pathway to energy storage system development that are game changers for NASA missions. The fuel cell/ electrolysis MEA performance requirements 0.92 V/ 1.44 V at 200 mA/cm2 can be met. Fuel Cell MEAs have been incorporated into advanced NFT stacks. Electrolyzer stack development in progress. Fuel Cell MEA performance is a strong function of membrane selection, membrane selection will be driven by durability requirements. Electrolyzer MEA performance is catalysts driven, catalyst selection will be driven by durability requirements. Round Trip Efficiency, based on a cell performance, is approximately 65%.

  10. Dynamic Nanoparticles Assemblies

    Science.gov (United States)

    WANG, LIBING; XU, LIGUANG; KUANG, HUA; XU, CHUANLAI; KOTOV, NICHOLAS A.

    2012-01-01

    CONSPECTUS Importance Although nanoparticle (NP) assemblies are at the beginning of their development, their unique geometrical shapes and media-responsive optical, electronic and magnetic properties have attracted significant interest. Nanoscale assembly bridges multiple sizes of materials: individual nanoparticles, discrete molecule-like or virus-like nanoscale agglomerates, microscale devices, and macroscale materials. The capacity to self-assemble can greatly facilitate the integration of nanotechnology with other technologies and, in particular, with microscale fabrication. In this Account, we describe developments in the emerging field of dynamic NP assemblies, which are spontaneously formed superstructures containing more than two inorganic nanoscale particles that display ability to change their geometrical, physical, chemical, and other attributes. In many ways, dynamic assemblies can represent a bottleneck in the ‘bottom-up’ fabrication of NP-based devices because they can produce a much greater variety of assemblies, but they also provide a convenient tool for variation of geometries and dimensions of nanoparticle assemblies. Classification Superstructures of NPs (and those held together by similar intrinsic forces) are classified into two groups: Class 1 where media and external fields can alter shape, conformation, and order of stable superstructures with a nearly constant number same. The future development of successful dynamic assemblies requires understanding the equilibrium in dynamic NP systems. The dynamic nature of Class 1 assemblies is associated with the equilibrium between different conformations of a superstructure and is comparable to the isomerization in classical chemistry. Class 2 assemblies involve the formation and/or breakage of linkages between the NPs, which is analogous to the classical chemical equilibrium for the formation of a molecule from atoms. Finer classification of NP assemblies in accord with established conventions

  11. Dynamic nanoparticle assemblies.

    Science.gov (United States)

    Wang, Libing; Xu, Liguang; Kuang, Hua; Xu, Chuanlai; Kotov, Nicholas A

    2012-11-20

    Although nanoparticle (NP) assemblies are at the beginning of their development, their unique geometrical shapes and media-responsive optical, electronic, and magnetic properties have attracted significant interest. Nanoscale assembly bridges multiple levels of hierarchy of materials: individual nanoparticles, discrete molecule-like or virus-like nanoscale agglomerates, microscale devices, and macroscale materials. The capacity to self-assemble can greatly facilitate the integration of nanotechnology with other technologies and, in particular, with microscale fabrication. In this Account, we describe developments in the emerging field of dynamic NP assemblies, which are spontaneously form superstructures containing more than two inorganic nanoscale particles that display the ability to change their geometrical, physical, chemical, and other attributes. In many ways, dynamic assemblies can represent a bottleneck in the "bottom-up" fabrication of NP-based devices because they can produce a much greater variety of assemblies, but they also provide a convenient tool for variation of geometries and dimensions of nanoparticle assemblies. Superstructures of NPs (and those held together by similar intrinsic forces)are classified into two groups: Class 1 where media and external fields can alter shape, conformation, and order of stable super structures with a nearly constant number of NPs or Class 2 where the total number of NPs changes, while the organizational motif in the final superstructure remains the same. The future development of successful dynamic assemblies requires understanding the equilibrium in dynamic NP systems. The dynamic nature of Class 1 assemblies is associated with the equilibrium between different conformations of a superstructure and is comparable to the isomerization in classical chemistry. Class 2 assemblies involve the formation or breakage of linkages between the NPs, which is analogous to the classical chemical equilibrium for the formation of

  12. Elucidating Complicated Assembling Systems in Biology Using Size-and-Shape Analysis of Sedimentation Velocity Data.

    Science.gov (United States)

    Chaton, Catherine T; Herr, Andrew B

    2015-01-01

    Sedimentation velocity analytical ultracentrifugation (SV-AUC) has seen a resurgence in popularity as a technique for characterizing macromolecules and complexes in solution. SV-AUC is a particularly powerful tool for studying protein conformation, complex stoichiometry, and interacting systems in general. Deconvoluting velocity data to determine a sedimentation coefficient distribution c(s) allows for the study of either individual proteins or multicomponent mixtures. The standard c(s) approach estimates molar masses of the sedimenting species based on determination of the frictional ratio (f/f0) from boundary shapes. The frictional ratio in this case is a weight-averaged parameter, which can lead to distortion of mass estimates and loss of information when attempting to analyze mixtures of macromolecules with different shapes. A two-dimensional extension of the c(s) analysis approach provides size-and-shape distributions that describe the data in terms of a sedimentation coefficient and frictional ratio grid. This allows for better resolution of species with very distinct shapes that may co-sediment and provides better molar mass determinations for multicomponent mixtures. An example case is illustrated using globular and nonglobular proteins of different masses with nearly identical sedimentation coefficients that could only be resolved using the size-and-shape distribution. Other applications of this analytical approach to complex biological systems are presented, focusing on proteins involved in the innate immune response to cytosolic microbial DNA. © 2015 Elsevier Inc. All rights reserved.

  13. Status of Functional Qualification System for Nuclear Valve Assembly in KIMM

    Energy Technology Data Exchange (ETDEWEB)

    Kim, J. H.; Park, T. J.; Kim, Y. J. [Korea Institute of Machinery and Materials, Daejeon (Korea, Republic of)

    2016-05-15

    In this paper, the status of the test facility, the basic concept of the ASME QME-1 test, and the future work are presented. The measured performance parameter, such as pressure, temperature, flow rate, thrust, stroke, and time, is used for the maintenance method and the evaluation of the aging and fatigue in the operating valve. In these days, the survival of the safety related valve in severe accident is important issue. In Korea Institute of Machinery and Materials (KIMM), the functional facility and related Quality Assure (QA) system are made. In addition, the qualification research was made for the functional test of the valve as ASME QME-1. The methodology is based on the ASME QME-1 1997. But the future work for the ASME QME-1 2007 was performed. In real situation, the engineering work is needed for the functional test of the nuclear valve in QA system. So the research work for the qualification is needed. The functional qualification of the valve in the nuclear power plant is performed in KIMM The development of the research and facility required in the functional qualification is in progress. Now the functional qualification is possible domestically, that was impossible in previous time due to the lack of qualification technology and facility.

  14. The use of a mini-κ goniometer head in macromolecular crystallography diffraction experiments.

    Science.gov (United States)

    Brockhauser, Sandor; Ravelli, Raimond B G; McCarthy, Andrew A

    2013-07-01

    Most macromolecular crystallography (MX) diffraction experiments at synchrotrons use a single-axis goniometer. This markedly contrasts with small-molecule crystallography, in which the majority of the diffraction data are collected using multi-axis goniometers. A novel miniaturized κ-goniometer head, the MK3, has been developed to allow macromolecular crystals to be aligned. It is available on the majority of the structural biology beamlines at the ESRF, as well as elsewhere. In addition, the Strategy for the Alignment of Crystals (STAC) software package has been developed to facilitate the use of the MK3 and other similar devices. Use of the MK3 and STAC is streamlined by their incorporation into online analysis tools such as EDNA. The current use of STAC and MK3 on the MX beamlines at the ESRF is discussed. It is shown that the alignment of macromolecular crystals can result in improved diffraction data quality compared with data obtained from randomly aligned crystals.

  15. Use of Site-Specifically Tethered Chemical Nucleases to Study Macromolecular Reactions

    Directory of Open Access Journals (Sweden)

    Mukherjee Srabani

    2003-01-01

    Full Text Available During a complex macromolecular reaction multiple changes in molecular conformation and interactions with ligands may occur. X-ray crystallography may provide only a limited set of snapshots of these changes. Solution methods can augment such structural information to provide a more complete picture of a macromolecular reaction. We analyzed the changes in protein conformation and protein:nucleic acid interactions which occur during transcription initiation by using a chemical nuclease tethered to cysteines introduced site-specifically into the RNA polymerase of bacteriophage T7 (T7 RNAP. Changes in cleavage patterns as the polymerase steps through transcription reveal a series of structural transitions which mediate transcription initiation. Cleavage by tethered chemical nucleases is seen to be a powerful method for revealing the conformational dynamics of macromolecular reactions, and has certain advantages over cross-linking or energy transfer approaches.

  16. Design, Analyses, and Fabrication Procedure of Amtec Cell, Test Assembly, and Radioisotope Power System for Outer-Planet Missions

    Science.gov (United States)

    Schock, A.; Noravian, H.; Or, C.; Kumar, V.

    2002-04-01

    interim cell design, which is being implemented by AMPS, Inc., for a DOE-sponsored technology development program. It then describes the extension of that analytical procedure to a variety of OSC-designed radioisotope-heated generators employing the recommended cell design, with particular attention to the thermal insulation between the outside of the 16 cells and the inside of the generator housing. The studies found that the performance of the generator is optimized by employing a hybrid insulation system, in which the space between the cells is filled with fibrous Min-K insulation, and the generator walls are lined with tapered (i.e., graded-length) multifoil insulation. The paper then examines the performance of the OSC generator designs for various fuel loadings, output voltages, and mission phases, and assesses their ability to meet the stipulated temperature constraints and power demands of the Europa Orbiter and Pluto Express missions under consideration by NASA. Finally, it presents an OSC-recommended design and fabrication procedure of an electrically heated four-cell test assembly with hybrid insulation to simulate the prototypic 16-cell generator. That test assembly will be analyzed by OSC, built by AMPS, and tested by the Air Force Phillips Laboratory (AFPL), to check the validity of the analytical predictions. The reason for basing the recommended test assembly on the interim rather than the ultimate refractory metal cell design is to avoid the delays required to develop the new technology for the latter.

  17. Accounting for large amplitude protein deformation during in silico macromolecular docking.

    Science.gov (United States)

    Bastard, Karine; Saladin, Adrien; Prévost, Chantal

    2011-02-22

    Rapid progress of theoretical methods and computer calculation resources has turned in silico methods into a conceivable tool to predict the 3D structure of macromolecular assemblages, starting from the structure of their separate elements. Still, some classes of complexes represent a real challenge for macromolecular docking methods. In these complexes, protein parts like loops or domains undergo large amplitude deformations upon association, thus remodeling the surface accessible to the partner protein or DNA. We discuss the problems linked with managing such rearrangements in docking methods and we review strategies that are presently being explored, as well as their limitations and success.

  18. Accounting for Large Amplitude Protein Deformation during in Silico Macromolecular Docking

    Directory of Open Access Journals (Sweden)

    Chantal Prévost

    2011-02-01

    Full Text Available Rapid progress of theoretical methods and computer calculation resources has turned in silico methods into a conceivable tool to predict the 3D structure of macromolecular assemblages, starting from the structure of their separate elements. Still, some classes of complexes represent a real challenge for macromolecular docking methods. In these complexes, protein parts like loops or domains undergo large amplitude deformations upon association, thus remodeling the surface accessible to the partner protein or DNA.We discuss the problems linked with managing such rearrangements in docking methods and we review strategies that are presently being explored, as well as their limitations and success.

  19. An acoustic on-chip goniometer for room temperature macromolecular crystallography.

    Science.gov (United States)

    Burton, C G; Axford, D; Edwards, A M J; Gildea, R J; Morris, R H; Newton, M I; Orville, A M; Prince, M; Topham, P D; Docker, P T

    2017-11-10

    This paper describes the design, development and successful use of an on-chip goniometer for room-temperature macromolecular crystallography via acoustically induced rotations. We present for the first time a low cost, rate-tunable, acoustic actuator for gradual in-fluid sample reorientation about varying axes and its utilisation for protein structure determination on a synchrotron beamline. The device enables the efficient collection of diffraction data via a rotation method from a sample within a surface confined droplet. This method facilitates efficient macromolecular structural data acquisition in fluid environments for dynamical studies.

  20. Components of the CMS magnet system at the detector's assembly site.

    CERN Multimedia

    Maximilien Brice

    2002-01-01

    Photos 01, 05: Outer cylinder of the CMS vacuum tank. The vacuum tank consists of inner and outer stainless-steel cylinders and houses the superconducting coil. As can be seen, the cylinder is attached to the innermost ring of the barrel yoke. Photos 02, 04: CMS end-cap yoke. The magnetic flux generated by the superconducting coil in the CMS detector is returned via an iron yoke comprising three end-cap discs at each end (end-cap yoke) and five concentric cylinders (barrel yoke).Photo 03: Inner cylinder of the CMS vacuum tank. The vacuum tank consists of inner and outer stainless-steel cylinders and houses the superconducting coil. The inner cylinder contains all the barrel sub-detectors, which it supports via a system of horizontal rails. The cylinder is pictured here in the vertical position on a yellow platform mounted on the ferris-wheel support structure. This will allow it to be pivoted and inserted into the outer cylinder already attached to the innermost ring of the barrel yoke.

  1. Clay Generic Disposal System Model - Sensitivity Analysis for 32 PWR Assembly Canisters (+2 associated model files).

    Energy Technology Data Exchange (ETDEWEB)

    Morris, Edgar [Argonne National Lab. (ANL), Argonne, IL (United States)

    2014-10-01

    The Used Fuel Disposition Campaign (UFDC), as part of the DOE Office of Nuclear Energy’s (DOE-NE) Fuel Cycle Technology program (FCT) is investigating the disposal of high level radioactive waste (HLW) and spent nuclear fuela (SNF) in a variety of geologic media. The feasibility of disposing SNF and HLW in clay media has been investigated and has been shown to be promising [Ref. 1]. In addition the disposal of these wastes in clay media is being investigated in Belgium, France, and Switzerland. Thus, Argillaceous media is one of the environments being considered by UFDC. As identified by researchers at Sandia National Laboratory, potentially suitable formations that may exist in the U.S. include mudstone, clay, shale, and argillite formations [Ref. 1]. These formations encompass a broad range of material properties. In this report, reference to clay media is intended to cover the full range of material properties. This report presents the status of the development of a simulation model for evaluating the performance of generic clay media. The clay Generic Disposal System Model (GDSM) repository performance simulation tool has been developed with the flexibility to evaluate not only different properties, but different waste streams/forms and different repository designs and engineered barrier configurations/ materials that could be used to dispose of these wastes.

  2. Copy number variability in Parkinson's disease: assembling the puzzle through a systems biology approach.

    Science.gov (United States)

    La Cognata, Valentina; Morello, Giovanna; D'Agata, Velia; Cavallaro, Sebastiano

    2017-01-01

    Parkinson's disease (PD), the second most common progressive neurodegenerative disorder of aging, was long believed to be a non-genetic sporadic origin syndrome. The proof that several genetic loci are responsible for rare Mendelian forms has represented a revolutionary breakthrough, enabling to reveal molecular mechanisms underlying this debilitating still incurable condition. While single nucleotide polymorphisms (SNPs) and small indels constitute the most commonly investigated DNA variations accounting for only a limited number of PD cases, larger genomic molecular rearrangements have emerged as significant PD-causing mutations, including submicroscopic Copy Number Variations (CNVs). CNVs constitute a prevalent source of genomic variations and substantially participate in each individual's genomic makeup and phenotypic outcome. However, the majority of genetic studies have focused their attention on single candidate-gene mutations or on common variants reaching a significant statistical level of acceptance. This gene-centric approach is insufficient to uncover the genetic background of polygenic multifactorial disorders like PD, and potentially masks rare individual CNVs that all together might contribute to disease development or progression. In this review, we will discuss literature and bioinformatic data describing the involvement of CNVs on PD pathobiology. We will analyze the most frequent copy number changes in familiar PD genes and provide a "systems biology" overview of rare individual rearrangements that could functionally act on commonly deregulated molecular pathways. Assessing the global genome-wide burden of CNVs in PD patients may reveal new disease-related molecular mechanisms, and open the window to a new possible genetic scenario in the unsolved PD puzzle.

  3. 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.

  4. A Dual-Thermoresponsive Gemini-Type Supra-amphiphilic Macromolecular [3]Pseudorotaxane Based on Pillar[10]arene/Paraquat Cooperative Complexation.

    Science.gov (United States)

    Chi, Xiaodong; Yu, Guocan; Shao, Li; Chen, Jianzhuang; Huang, Feihe

    2016-03-09

    Herein, first we report the preparation of a thermoresponsive [3]pseudorotaxane from cooperative complexation between a water-soluble pillar[10]arene and a paraquat derivative in water. Then we successfully construct the first pillararene-based gemini-type supra-amphiphilic [3]pseudorotaxane from the water-soluble pillar[10]arene and a paraquat-containing poly(N-isopropylacrylamide) based on this new molecular recognition motif in water. This macromolecular [3]pseudorotaxane shows unique dual-thermoresponsiveness. Furthermore, it can self-assemble into polymeric vesicles at 37 °C in water. These vesicles can be further used in the controlled release of small molecules induced by cooling to 25 °C or heating to 60 °C.

  5. In₂S₃/carbon nanofibers/Au ternary synergetic system: hierarchical assembly and enhanced visible-light photocatalytic activity.

    Science.gov (United States)

    Zhang, Xin; Shao, Changlu; Li, Xinghua; Lu, Na; Wang, Kexin; Miao, Fujun; Liu, Yichun

    2015-01-01

    In this paper, carbon nanofibers (CNFs) were successfully synthesized by electrospinning technique. Next, Au nanoparticles (NPs) were assembled on the electrospun CNFs through in situ reduction method. By using the obtained Au NPs modified CNFs (CNFs/Au) as hard template, the In2S3/CNFs/Au composites were synthesized through hydrothermal technique. The results showed that the super long one-dimensional (1D) CNFs (about 306 nm in average diameter) were well connected to form a nanofibrous network; and, the Au NPs with 18 nm in average diameter and In2S3 nanosheets with 5-10nm in thickness were uniformly grown onto the surface of CNFs. Photocatalytic studies revealed that the In2S3/CNFs/Au composites exhibited highest visible-light photocatalytic activities for the degradation of Rhodamine B (RB) compared with pure In2S3 and In2S3/CNFs. The enhanced photocatalytic activity might arise from the high separation efficiency of photogenerated electron-hole pairs based on the positive synergetic effect between In2S3, CNFs and Au components in this ternary photocatalytic system. Meanwhile, the In2S3/CNFs/Au composites with hierarchical structure possess a strong adsorption ability towards organic dyes, which also contributed to the enhancement of photocatalytic activity. Moreover, the In2S3/CNFs/Au composites could be recycled easily by sedimentation due to their nanofibrous network structure. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. A Light-Responsive Self-Assembly Formed by a Cationic Azobenzene Derivative and SDS as a Drug Delivery System.

    Science.gov (United States)

    Geng, Shengyong; Wang, Yuzhu; Wang, Liping; Kouyama, Tsutomu; Gotoh, Toshiaki; Wada, Satoshi; Wang, Jin-Ye

    2017-01-04

    The structure of a self-assembly formed from a cationic azobenzene derivative, 4-cholesterocarbonyl-4'-(N,N,N-triethylamine butyloxyl bromide) azobenzene (CAB) and surfactant sodium dodecyl sulfate (SDS) in aqueous solution was studied by cryo-TEM and synchrotron radiation small-angle X-ray scattering (SAXS). Both unilamellar and multilamellar vesicles could be observed. CAB in vesicles were capable to undergo reversible trans-to-cis isomerization upon UV or visible light irradiation. The structural change upon UV light irradiation could be catched by SAXS, which demonstrated that the interlamellar spacing of the cis-multilamellar vesicles increased by 0.2-0.3 nm. Based on this microstructural change, the release of rhodamine B (RhB) and doxorubicin (DOX) could be triggered by UV irradiation. When incubated NIH 3T3 cells and Bel 7402 cells with DOX-loaded CAB/SDS vesicles, UV irradiation induced DOX release decreased the viability of both cell lines significantly compared with the non-irradiated cells. The in vitro experiment indicated that CAB/SDS vesicles had high efficiency to deliver loaded molecules into cells. The in vivo experiment showed that CAB/SDS vesicles not only have high drug delivery efficiency into rat retinas, but also could maintain high drug concentration for a longer time. CAB/SDS catanionic vesicles may find potential applications as a smart drug delivery system for controlled release by light.

  7. A Light-Responsive Self-Assembly Formed by a Cationic Azobenzene Derivative and SDS as a Drug Delivery System

    Science.gov (United States)

    Geng, Shengyong; Wang, Yuzhu; Wang, Liping; Kouyama, Tsutomu; Gotoh, Toshiaki; Wada, Satoshi; Wang, Jin-Ye

    2017-01-01

    The structure of a self-assembly formed from a cationic azobenzene derivative, 4-cholesterocarbonyl-4‧-(N,N,N-triethylamine butyloxyl bromide) azobenzene (CAB) and surfactant sodium dodecyl sulfate (SDS) in aqueous solution was studied by cryo-TEM and synchrotron radiation small-angle X-ray scattering (SAXS). Both unilamellar and multilamellar vesicles could be observed. CAB in vesicles were capable to undergo reversible trans-to-cis isomerization upon UV or visible light irradiation. The structural change upon UV light irradiation could be catched by SAXS, which demonstrated that the interlamellar spacing of the cis-multilamellar vesicles increased by 0.2-0.3 nm. Based on this microstructural change, the release of rhodamine B (RhB) and doxorubicin (DOX) could be triggered by UV irradiation. When incubated NIH 3T3 cells and Bel 7402 cells with DOX-loaded CAB/SDS vesicles, UV irradiation induced DOX release decreased the viability of both cell lines significantly compared with the non-irradiated cells. The in vitro experiment indicated that CAB/SDS vesicles had high efficiency to deliver loaded molecules into cells. The in vivo experiment showed that CAB/SDS vesicles not only have high drug delivery efficiency into rat retinas, but also could maintain high drug concentration for a longer time. CAB/SDS catanionic vesicles may find potential applications as a smart drug delivery system for controlled release by light.

  8. Self-assembled nanostructures of fully hydrated monoelaidin-elaidic acid and monoelaidin-oleic acid systems.

    Science.gov (United States)

    Yaghmur, Anan; Sartori, Barbara; Rappolt, Michael

    2012-07-03

    In recent years, there has been a surge of interest in exploring the effect of trans-fatty acids (TFAs) on biological membrane properties. The research studies are motivated by an increasing body of evidence suggesting that the consumption of TFAs increases the risk of developing negative health effects such as coronary heart disease and cancer. The ultimate goal of studying the lipid-fatty acid interactions at the molecular level is to predict the biological role of fatty acids in cells. In this regard, it is interesting to elucidate the effect of loading TFAs and their counterpart cis-fatty acids (CFAs) on the physical properties of lipid model membranes. Here, the present study focuses on discussing the following: (1) the effect of mixing monoelaidin (ME, TFA-containing lipid) with its counterpart monoolein (MO, CFA-containing lipid) on modulating the fully hydrated self-assembled structure, and (2) the influence of solubilizing oleic acid (OA) and its trans counterpart elaidic acid (EA) on the fully hydrated ME system. The ME model membrane was selected due to its sensitivity to variations in lipid composition and temperature. Synchrotron small-angle X-ray scattering (SAXS) was applied for studying the temperature-dependent structural behavior of the fully hydrated ME/MO-based system prepared with an equal ME/MO weight ratio and also for characterizing the fully hydrated OA- and EA-loaded ME systems. Wide-angle X-ray (WAXS) experiments were also performed for characterizing the formed crystalline lamellar phases at ambient temperatures. The results demonstrate the significant influence of the partial replacement of ME by MO on the phase behavior. The addition of MO induces the lamellar-nonlamellar phase transitions at ambient temperatures and promotes the formation of the inverted type hexagonal (H(2)) phase above 72 °C. The fully hydrated ME/EA and ME/OA systems with their rich polymorphism exhibit an interesting temperature-dependent complex behavior. The

  9. Topological defects in liquid crystals as templates for molecular self-assembly

    Science.gov (United States)

    Wang, Xiaoguang; Miller, Daniel S.; Bukusoglu, Emre; de Pablo, Juan J.; Abbott, Nicholas L.

    2016-01-01

    Topological defects in liquid crystals (LCs) have been widely used to organize colloidal dispersions and template polymerization, leading to a range of assemblies, elastomers and gels. However, little is understood about molecular-level assembly processes within defects. Here, we report that nanoscopic environments defined by LC topological defects can selectively trigger processes of molecular self-assembly. By using fluorescence microscopy, cryogenic transmission electron microscopy and super-resolution optical microscopy, we observed signatures of molecular self-assembly of amphiphilic molecules in topological defects, including cooperativity, reversibility and controlled growth. We also show that nanoscopic o-rings synthesized from Saturn-ring disclinations and other molecular assemblies templated by defects can be preserved by using photocrosslinkable amphiphiles. Our results reveal that, in analogy to other classes of macromolecular templates such as polymer-surfactant complexes, topological defects in LCs are a versatile class of three-dimensional, dynamic and reconfigurable templates that can direct processes of molecular self-assembly.

  10. Issues in the Design, Modeling, and Manufacture of Multiple Joint Solder Self-Assembled Micro-Electro-Mechanical Systems (MEMS)

    National Research Council Canada - National Science Library

    Kladitis, Paul

    2001-01-01

    .... This work is the first in the world to quantify or address the known entirety of major issues that go into realizing multiple joint solder self-assembled polysilicon surface micromachined MEMS...

  11. Gas separation membrane module assembly

    Science.gov (United States)

    Wynn, Nicholas P [Palo Alto, CA; Fulton, Donald A [Fairfield, CA

    2009-03-31

    A gas-separation membrane module assembly and a gas-separation process using the assembly. The assembly includes a set of tubes, each containing gas-separation membranes, arranged within a housing. The housing contains a tube sheet that divides the space within the housing into two gas-tight spaces. A permeate collection system within the housing gathers permeate gas from the tubes for discharge from the housing.

  12. Prospects for Simulating Macromolecular Surfactant Chemistry at the Ocean-Atmosphere Boundary

    Energy Technology Data Exchange (ETDEWEB)

    Elliott, S.; Burrows, Susannah M.; Deal, C.; Liu, Xiaohong; Long, M.; Ogunro, O.; Russell, Lynn M.; Wingenter, O.

    2014-05-01

    Biogenic lipids and polymers are surveyed for their ability to adsorb at the water-air interfaces associated with bubbles, marine microlayers and particles in the overlying boundary layer. Representative ocean biogeochemical regimes are defined in order to estimate local concentrations for the major macromolecular classes. Surfactant equilibria and maximum excess are then derived based on a network of model compounds. Relative local coverage and upward mass transport follow directly, and specific chemical structures can be placed into regional rank order. Lipids and denatured protein-like polymers dominate at the selected locations. The assigned monolayer phase states are variable, whether assessed along bubbles or at the atmospheric spray droplet perimeter. Since oceanic film compositions prove to be irregular, effects on gas and organic transfer are expected to exhibit geographic dependence as well. Moreover, the core arguments extend across the sea-air interface into aerosol-cloud systems. Fundamental nascent chemical properties including mass to carbon ratio and density depend strongly on the geochemical state of source waters. High surface pressures may suppress the Kelvin effect, and marine organic hygroscopicities are almost entirely unconstrained. While bubble adsorption provides a well-known means for transporting lipidic or proteinaceous material into sea spray, the same cannot be said of polysaccharides. Carbohydrates tend to be strongly hydrophilic so that their excess carbon mass is low despite stacked polymeric geometries. Since sugars are abundant in the marine aerosol, gel-based mechanisms may be required to achieve uplift. Uncertainties in the surfactant logic distill to a global scale dearth of information regarding two dimensional kinetics and equilibria. Nonetheless simulations are recommended, to initiate the process of systems level quantification.

  13. Prospects for simulating macromolecular surfactant chemistry at the ocean-atmosphere boundary

    Science.gov (United States)

    Elliott, S.; Burrows, S. M.; Deal, C.; Liu, X.; Long, M.; Ogunro, O.; Russell, L. M.; Wingenter, O.

    2014-05-01

    Biogenic lipids and polymers are surveyed for their ability to adsorb at the water-air interfaces associated with bubbles, marine microlayers and particles in the overlying boundary layer. Representative ocean biogeochemical regimes are defined in order to estimate local concentrations for the major macromolecular classes. Surfactant equilibria and maximum excess are then derived based on a network of model compounds. Relative local coverage and upward mass transport follow directly, and specific chemical structures can be placed into regional rank order. Lipids and denatured protein-like polymers dominate at the selected locations. The assigned monolayer phase states are variable, whether assessed along bubbles or at the atmospheric spray droplet perimeter. Since oceanic film compositions prove to be irregular, effects on gas and organic transfer are expected to exhibit geographic dependence as well. Moreover, the core arguments extend across the sea-air interface into aerosol-cloud systems. Fundamental nascent chemical properties including mass to carbon ratio and density depend strongly on the geochemical state of source waters. High surface pressures may suppress the Kelvin effect, and marine organic hygroscopicities are almost entirely unconstrained. While bubble adsorption provides a well-known means for transporting lipidic or proteinaceous material into sea spray, the same cannot be said of polysaccharides. Carbohydrates tend to be strongly hydrophilic so that their excess carbon mass is low despite stacked polymeric geometries. Since sugars are abundant in the marine aerosol, gel-based mechanisms may be required to achieve uplift. Uncertainties distill to a global scale dearth of information regarding two dimensional kinetics and equilibria. Nonetheless simulations are recommended, to initiate the process of systems level quantification.

  14. The use of workflows in the design and implementation of complex experiments in macromolecular crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Brockhauser, Sandor, E-mail: brockhauser@embl.fr [European Molecular Biology Laboratory, 6 Rue Jules Horowitz, BP 181, 38042 Grenoble (France); UJF–EMBL–CNRS, UMI 3265, 6 Rue Jules Horowitz, 38042 Grenoble CEDEX 9 (France); Svensson, Olof; Bowler, Matthew W. [European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, 38043 Grenoble (France); Nanao, Max [European Molecular Biology Laboratory, 6 Rue Jules Horowitz, BP 181, 38042 Grenoble (France); UJF–EMBL–CNRS, UMI 3265, 6 Rue Jules Horowitz, 38042 Grenoble CEDEX 9 (France); Gordon, Elspeth; Leal, Ricardo M. F.; Popov, Alexander; Gerring, Matthew [European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, 38043 Grenoble (France); McCarthy, Andrew A. [European Molecular Biology Laboratory, 6 Rue Jules Horowitz, BP 181, 38042 Grenoble (France); UJF–EMBL–CNRS, UMI 3265, 6 Rue Jules Horowitz, 38042 Grenoble CEDEX 9 (France); Gotz, Andy [European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, 38043 Grenoble (France); European Molecular Biology Laboratory, 6 Rue Jules Horowitz, BP 181, 38042 Grenoble (France)

    2012-08-01

    A powerful and easy-to-use workflow environment has been developed at the ESRF for combining experiment control with online data analysis on synchrotron beamlines. This tool provides the possibility of automating complex experiments without the need for expertise in instrumentation control and programming, but rather by accessing defined beamline services. The automation of beam delivery, sample handling and data analysis, together with increasing photon flux, diminishing focal spot size and the appearance of fast-readout detectors on synchrotron beamlines, have changed the way that many macromolecular crystallography experiments are planned and executed. Screening for the best diffracting crystal, or even the best diffracting part of a selected crystal, has been enabled by the development of microfocus beams, precise goniometers and fast-readout detectors that all require rapid feedback from the initial processing of images in order to be effective. All of these advances require the coupling of data feedback to the experimental control system and depend on immediate online data-analysis results during the experiment. To facilitate this, a Data Analysis WorkBench (DAWB) for the flexible creation of complex automated protocols has been developed. Here, example workflows designed and implemented using DAWB are presented for enhanced multi-step crystal characterizations, experiments involving crystal reorientation with kappa goniometers, crystal-burning experiments for empirically determining the radiation sensitivity of a crystal system and the application of mesh scans to find the best location of a crystal to obtain the highest diffraction quality. Beamline users interact with the prepared workflows through a specific brick within the beamline-control GUI MXCuBE.

  15. Novel use for polyvinylpyrrolidone as a macromolecular crowder for enhanced extracellular matrix deposition and cell proliferation.

    Science.gov (United States)

    Rashid, Rafi; Lim, Natalie Sheng Jie; Chee, Stella Min Ling; Png, Si Ning; Wohland, Thorsten; Raghunath, Michael

    2014-12-01

    Macromolecular crowding (MMC) is a biophysical effect that governs biochemical processes inside and outside of cells. Since standard cell culture media lack this effect, the physiological performance of differentiated and progenitor cells, including extracellular matrix (ECM) deposition, is impaired in vitro. To bring back physiological crowdedness to in vitro systems, we have previously introduced carbohydrate-based macromolecules to culture media and have achieved marked improvements with mixed MMC in terms of ECM deposition and differentiation of mesenchymal stem cells (MSCs). We show here that although this system is successful, it is limited, due to viscosity, to only 33% of the fractional volume occupancy (FVO) of full serum, which we calculated to have an FVO of approximately 54% v/v. We show here that full-serum FVO can be achieved using polyvinylpyrrolidone (PVP) 360 kDa. Under these conditions, ECM deposition in human fibroblasts and MSCs is on par, if not stronger than, with original MMC protocols using carbohydrates, but with a viscosity that is not significantly changed. In addition, we have found that the proliferation rate for bone marrow-derived MSCs and fibroblasts increases slightly in the presence of PVP360, similar to that observed with carbohydrate-based crowders. A palette of MMC compounds is now emerging that enables us to tune the crowdedness of culture media seamlessly from interstitial fluid (9% FVO), in which the majority of tissue cells might be based, to serum environments mimicking intravascular conditions. Despite identical FVO's, individual crowder size effects play a role and different cell types appear to have preferences in terms of FVO and the crowder that this is achieved with. However, in the quest of crowders that we have predicted to have a smoother regulatory approval path, PVP is a highly interesting compound, as it has been widely used in the medical and food industries and shows a novel promising use in cell culture and

  16. Improving the performance of a quadrupole time-of-flight instrument for macromolecular mass spectrometry

    NARCIS (Netherlands)

    Heuvel, van den R.H.H.; Duijn, van E.; Mazon, H.; Synowsky, S.A.; Lorenzen, K.; Versluis, C.; Brouns, S.J.J.; Langridge, D.; Oost, van der J.; Hoyes, J.; Heck, C.K.

    2006-01-01

    We modified and optimized a first generation quadrupole time-of-flight (Q-TOF) 1 to perform tandem mass spectrometry on macromolecular protein complexes. The modified instrument allows isolation and subsequent dissociation of high-mass protein complexes through collisions with argon molecules. The

  17. Isolation and chemical characterization of resistant macromolecular constituents in microalgae and marine sediments

    NARCIS (Netherlands)

    Gelin, F.

    1996-01-01

    The recognition of novel, insoluble and non-hydrolysable macromolecular constituents in protective tissues of fresh-water algae and higher plants has had a major impact on our understanding of the origin and fate of sedimentary organic matter (OM) in terrestrial and lacustrine deposits. The

  18. Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression

    DEFF Research Database (Denmark)

    Ma, Ding; Yang, Laurence; Fleming, Ronan M. T.

    2017-01-01

    Constraint-Based Reconstruction and Analysis (COBRA) is currently the only methodology that permits integrated modeling of Metabolism and macromolecular Expression (ME) at genome-scale. Linear optimization computes steady-state flux solutions to ME models, but flux values are spread over many...

  19. MMTF-An efficient file format for the transmission, visualization, and analysis of macromolecular structures.

    Science.gov (United States)

    Bradley, Anthony R; Rose, Alexander S; Pavelka, Antonín; Valasatava, Yana; Duarte, Jose M; Prlić, Andreas; Rose, Peter W

    2017-06-01

    Recent advances in experimental techniques have led to a rapid growth in complexity, size, and number of macromolecular structures that are made available through the Protein Data Bank. This creates a challenge for macromolecular visualization and analysis. Macromolecular structure files, such as PDB or PDBx/mmCIF files can be slow to transfer, parse, and hard to incorporate into third-party software tools. Here, we present a new binary and compressed data representation, the MacroMolecular Transmission Format, MMTF, as well as software implementations in several languages that have been developed around it, which address these issues. We describe the new format and its APIs and demonstrate that it is several times faster to parse, and about a quarter of the file size of the current standard format, PDBx/mmCIF. As a consequence of the new data representation, it is now possible to visualize structures with millions of atoms in a web browser, keep the whole PDB archive in memory or parse it within few minutes on average computers, which opens up a new way of thinking how to design and implement efficient algorithms in structural bioinformatics. The PDB archive is available in MMTF file format through web services and data that are updated on a weekly basis.

  20. Modeling macromolecular degradation of corn starch in a twin screw extruder

    NARCIS (Netherlands)

    Einde, van den R.M.; Veen, van der M.E.; Bosman, H.; Goot, van der A.J.; Boom, R.M.

    2005-01-01

    Macromolecular degradation of starch in a twin screw extruder was modeled. A shear cell having well-defined flow conditions described earlier was used to measure peak viscosity of corn starch melts at various moisture contents and temperatures. Shear rate and elongation rate distributions in the

  1. Interplay between the bacterial nucleoid protein H-NS and macromolecular crowding in compacting DNA

    NARCIS (Netherlands)

    Wintraecken, C.H.J.M.

    2012-01-01

      In this dissertation we discuss H-NS and its connection to nucleoid compaction and organization. Nucleoid formation involves a dramatic reduction in coil volume of the genomic DNA. Four factors are thought to influence coil volume: supercoiling, DNA charge neutralization, macromolecular

  2. Synergy of DNA-bending nucleoid proteins and macromolecular crowd-condensing DNA

    NARCIS (Netherlands)

    Bessa Ramos, E.; Wintraecken, C.H.J.M.; Geerling, A.C.M.; Vries, de R.J.

    2007-01-01

    Many prokaryotic nucleoid proteins bend DNA and form extended helical protein-DNA fibers rather than condensed structures. On the other hand, it is known that such proteins (such as bacterial HU) strongly promote DNA condensation by macromolecular crowding. Using theoretical arguments, we show that

  3. Integrated assembly and motion planning using regrasp graphs.

    Science.gov (United States)

    Wan, Weiwei; Harada, Kensuke

    2016-01-01

    This paper presents an integrated assembly and motion planning system to recursively find the assembly sequence and motions to assemble two objects with the help of a horizontal surface as the supporting fixture. The system is implemented in both assembly level and motion level. In the assembly level, the system checks all combinations of the assembly sequences and gets a set of candidates. Then, for each candidate assembly sequence, the system incrementally builds regrasp graphs and performs recursive search to find a pick-and-place motion in the motion level to manipulate the base object as well as to assemble the other object to the base. The system integrates the candidate assembly sequences computed in the assembly level incrementally and recursively with graph searching and motion planning in the motion level and plans the assembly sequences and motions integratedly for assembly tasks. Both simulation and real-world experiments are performed to demonstrate the efficacy of the integrated planning system.

  4. Multivalent Protein Assembly Using Monovalent Self-Assembling Building Blocks

    Directory of Open Access Journals (Sweden)

    Katja Petkau-Milroy

    2013-10-01

    Full Text Available 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 to streptavidin. Next to tetravalent streptavidin, monovalent streptavidin was used to study the protein assembly along the supramolecular polymer in detail without the interference of cross-linking. Upon self-assembly of the monovalent biotinylated discotics, multivalent proteins can be assembled along the supramolecular polymer. The concentration of discotics, which influences the length of the final polymers at the same time dictates the amount of assembled proteins.

  5. High-resolution cryo-electron microscopy on macromolecular complexes and cell organelles.

    Science.gov (United States)

    Hoenger, Andreas

    2014-03-01

    Cryo-electron microscopy techniques and computational 3-D reconstruction of macromolecular assemblies are tightly linked tools in modern structural biology. This symbiosis has produced vast amounts of detailed information on the structure and function of biological macromolecules. Typically, one of two fundamentally different strategies is used depending on the specimens and their environment. A: 3-D reconstruction based on repetitive and structurally identical unit cells that allow for averaging, and B: tomographic 3-D reconstructions where tilt-series between approximately ± 60 and ± 70° at small angular increments are collected from highly complex and flexible structures that are beyond averaging procedures, at least during the first round of 3-D reconstruction. Strategies of group A are averaging-based procedures and collect large number of 2-D projections at different angles that are computationally aligned, averaged together, and back-projected in 3-D space to reach a most complete 3-D dataset with high resolution, today often down to atomic detail. Evidently, success relies on structurally repetitive particles and an aligning procedure that unambiguously determines the angular relationship of all 2-D projections with respect to each other. The alignment procedure of small particles may rely on their packing into a regular array such as a 2-D crystal, an icosahedral (viral) particle, or a helical assembly. Critically important for cryo-methods, each particle will only be exposed once to the electron beam, making these procedures optimal for highest-resolution studies where beam-induced damage is a significant concern. In contrast, tomographic 3-D reconstruction procedures (group B) do not rely on averaging, but collect an entire dataset from the very same structure of interest. Data acquisition requires collecting a large series of tilted projections at angular increments of 1-2° or less and a tilt range of ± 60° or more. Accordingly, tomographic data

  6. General Assembly

    CERN Multimedia

    Staff Association

    2016-01-01

    5th April, 2016 – Ordinary General Assembly of the Staff Association! In the first semester of each year, the Staff Association (SA) invites its members to attend and participate in the Ordinary General Assembly (OGA). This year the OGA will be held on Tuesday, April 5th 2016 from 11:00 to 12:00 in BE Auditorium, Meyrin (6-2-024). During the Ordinary General Assembly, the activity and financial reports of the SA are presented and submitted for approval to the members. This is the occasion to get a global view on the activities of the SA, its financial management, and an opportunity to express one’s opinion, including taking part in the votes. Other points are listed on the agenda, as proposed by the Staff Council. Who can vote? Only “ordinary” members (MPE) of the SA can vote. Associated members (MPA) of the SA and/or affiliated pensioners have a right to vote on those topics that are of direct interest to them. Who can give his/her opinion? The Ordinary General Asse...

  7. Stabilization of Ostwald ripening in low molecular weight amino lipid nanoparticles for systemic delivery of siRNA therapeutics.

    Science.gov (United States)

    Gindy, Marian E; Feuston, Brad; Glass, Angela; Arrington, Leticia; Haas, R Matthew; Schariter, Joseph; Stirdivant, Steven M

    2014-11-03

    Lipid nanoparticles (LNPs) represent the most clinically advanced technology for the systemic delivery of therapeutic siRNA in vivo. Toward this end, a novel class of LNPs comprising low molecular weight (MW) ionizable amino lipids having asymmetric architecture was recently reported.1 LNPs of these amino lipids, termed asymmetric LNPs, were shown to be highly efficacious and well tolerated in vivo; advances were enabled by improved endosomal escape, coupled with enhanced amino lipid metabolism and clearance. In this work, we show that, in contrast to their desirable pharmacological performance, asymmetric LNPs present a significant pharmaceutical developability challenge, namely physical instability limiting extended shelf life. Using orthogonal characterization methods, we identify the mechanism of LNP instability as Ostwald ripening and establish it to be driven predominantly by the asymmetric amino lipid component. Through rational optimization of LNP physical and macromolecular properties, we are able to significantly attenuate or entirely eliminate the Ostwald ripening instability. Modulation of LNP size, for example, effectively halts particle growth. Similarly, optimization of LNP macromolecular packing through deliberate selection of structurally matched colipids significantly diminishes the rate of ripening. This later experimental observation is substantiated by molecular dynamics simulations of LNP self-assembly, which establish a quantitative dependence of LNP macromolecular order on colipid structure. In totality, the experimental and molecular dynamics outcomes of this work support the rational design of LNP physical and chemical properties leading to effective Ostwald ripening stabilization and enable the advance of asymmetric LNPs as a clinic-ready platform for siRNA therapeutics.

  8. A simplified and versatile system for the simultaneous expression of multiple siRNAs in mammalian cells using Gibson DNA Assembly.

    Science.gov (United States)

    Deng, Fang; Chen, Xiang; Liao, Zhan; Yan, Zhengjian; Wang, Zhongliang; Deng, Youlin; Zhang, Qian; Zhang, Zhonglin; Ye, Jixing; Qiao, Min; Li, Ruifang; Denduluri, Sahitya; Wang, Jing; Wei, Qiang; Li, Melissa; Geng, Nisha; Zhao, Lianggong; Zhou, Guolin; Zhang, Penghui; Luu, Hue H; Haydon, Rex C; Reid, Russell R; Yang, Tian; He, Tong-Chuan

    2014-01-01

    RNA interference (RNAi) denotes sequence-specific mRNA degradation induced by short interfering double-stranded RNA (siRNA) and has become a revolutionary tool for functional annotation of mammalian genes, as well as for development of novel therapeutics. The practical applications of RNAi are usually achieved by expressing short hairpin RNAs (shRNAs) or siRNAs in cells. However, a major technical challenge is to simultaneously express multiple siRNAs to silence one or more genes. We previously developed pSOS system, in which siRNA duplexes are made from oligo templates driven by opposing U6 and H1 promoters. While effective, it is not equipped to express multiple siRNAs in a single vector. Gibson DNA Assembly (GDA) is an in vitro recombination system that has the capacity to assemble multiple overlapping DNA molecules in a single isothermal step. Here, we developed a GDA-based pSOK assembly system for constructing single vectors that express multiple siRNA sites. The assembly fragments were generated by PCR amplifications from the U6-H1 template vector pB2B. GDA assembly specificity was conferred by the overlapping unique siRNA sequences of insert fragments. To prove the technical feasibility, we constructed pSOK vectors that contain four siRNA sites and three siRNA sites targeting human and mouse β-catenin, respectively. The assembly reactions were efficient, and candidate clones were readily identified by PCR screening. Multiple β-catenin siRNAs effectively silenced endogenous β-catenin expression, inhibited Wnt3A-induced β-catenin/Tcf4 reporter activity and expression of Wnt/β-catenin downstream genes. Silencing β-catenin in mesenchymal stem cells inhibited Wnt3A-induced early osteogenic differentiation and significantly diminished synergistic osteogenic activity between BMP9 and Wnt3A in vitro and in vivo. These findings demonstrate that the GDA-based pSOK system has been proven simplistic, effective and versatile for simultaneous expression of multiple

  9. Expert System analysis of non-fuel assembly hardware and spent fuel disassembly hardware: Its generation and recommended disposal

    Energy Technology Data Exchange (ETDEWEB)

    Williamson, Douglas Alan [Univ. of Florida, Gainesville, FL (United States)

    1991-01-01

    Almost all of the effort being expended on radioactive waste disposal in the United States is being focused on the disposal of spent Nuclear Fuel, with little consideration for other areas that will have to be disposed of in the same facilities. one area of radioactive waste that has not been addressed adequately because it is considered a secondary part of the waste issue is the disposal of the various Non-Fuel Bearing Components of the reactor core. These hardware components fall somewhat arbitrarily into two categories: Non-Fuel Assembly (NFA) hardware and Spent Fuel Disassembly (SFD) hardware. This work provides a detailed examination of the generation and disposal of NFA hardware and SFD hardware by the nuclear utilities of the United States as it relates to the Civilian Radioactive Waste Management Program. All available sources of data on NFA and SFD hardware are analyzed with particular emphasis given to the Characteristics Data Base developed by Oak Ridge National Laboratory and the characterization work performed by Pacific Northwest Laboratories and Rochester Gas & Electric. An Expert System developed as a portion of this work is used to assist in the prediction of quantities of NFA hardware and SFD hardware that will be generated by the United States` utilities. Finally, the hardware waste management practices of the United Kingdom, France, Germany, Sweden, and Japan are studied for possible application to the disposal of domestic hardware wastes. As a result of this work, a general classification scheme for NFA and SFD hardware was developed. Only NFA and SFD hardware constructed of zircaloy and experiencing a burnup of less than 70,000 MWD/MTIHM and PWR control rods constructed of stainless steel are considered Low-Level Waste. All other hardware is classified as Greater-ThanClass-C waste.

  10. Applied, theoretical modeling of space-based assembly, using expert system architecture for computer-aided engineering tool development

    Science.gov (United States)

    Jolly, Steven Douglas

    1992-01-01

    The challenges associated with constructing interplanetary spacecraft and space platforms in low earth orbit are such that it is imperative that comprehensive, preliminary process planning analyses be completed before committing funds for Phase B design (detail design, development). Phase A and 'pre-Phase A' design activities will commonly address engineering questions such as mission-design structural integrity, attitude control, thermal control, etc. But the questions of constructability, maintainability and reliability during the assembly phase usually go unaddressed until the more mature stages of design (or very often production) are reached. This is an unacceptable strategy for future space missions whether they be government or commercial ventures. After interviews with expert Aerospace and Construction industry planners a new methodology was formulated and a Blackboard Metaphor Knowledge-based Expert System synthesis model has been successfully developed which can decompose interplanetary vehicles into deliverable orbital subassemblies. Constraint propagation, including launch vehicle payload shroud envelope, is accomplished with heuristic and numerical algorithms including a unique adaptation of a reasoning technique used by Stanford researchers in terrestrial automated process planning. The model is a hybrid combination of rule and frame-based representations, designed to integrate into a Computer-Aided Engineering (CAE) environment. Emphasis is placed on the actual joining, rendezvous, and refueling of the orbiting, dynamic spacecraft. Significant results of this new methodology upon a large Mars interplanetary spacecraft (736,000 kg) designed by Boeing, show high correlation to manual decomposition and planning analysis studies, but at a fraction of the time, and with little user interaction. Such Computer-Aided Engineering (CAE) tools would greatly leverage the designers ability to assess constructability.

  11. Effect of Entrapped Solvent on the Evolution of Lateral Order in Self-Assembled P(S-r-MMA)/PS-b-PMMA Systems with Different Thicknesses.

    Science.gov (United States)

    Giammaria, Tommaso Jacopo; Ferrarese Lupi, Federico; Seguini, Gabriele; Sparnacci, Katia; Antonioli, Diego; Gianotti, Valentina; Laus, Michele; Perego, Michele

    2017-09-20

    Block copolymers (BCPs) are emerging as a cost-effective nanofabrication tool to complement conventional optical lithography because they self-assemble in highly ordered polymeric templates with well-defined sub-20-nm periodic features. In this context, cylinder-forming polystyrene-block-poly(methyl methacrylate) BCPs are revealed as an interesting material of choice because the orientation of the nanostructures with respect to the underlying substrate can be effectively controlled by a poly(styrene-random-methyl methacrylate) random copolymer (RCP) brush layer grafted to the substrate prior to BCP deposition. In this work, we investigate the self-assembly process and lateral order evolution in RCP + BCP systems consisting of cylinder-forming PS-b-PMMA (67 kg mol -1 , PS fraction of ∼70%) films with thicknesses of 30, 70, 100, and 130 nm deposited on RCP brush layers having thicknesses ranging from 2 to 20 nm. The self-assembly process is promoted by a rapid thermal processing machine operating at 250 °C for 300 s. The level of lateral order is determined by measuring the correlation length (ξ) in the self-assembled BCP films. Moreover, the amount of solvent (Φ) retained in the RCP + BCP systems is measured as a function of the thicknesses of the RCP and BCP layers, respectively. In the 30-nm-thick BCP films, an increase in Φ as a function of the thickness of the RCP brush layer significantly affects the self-assembly kinetics and the final extent of the lateral order in the BCP films. Conversely, no significant variations of ξ are observed in the 70-, 100-, and 130-nm-thick BCP films with increasing Φ.

  12. 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...

  13. Turbomachine blade assembly

    Energy Technology Data Exchange (ETDEWEB)

    Garcia Crespo, Andres Jose

    2016-11-01

    Embodiments of the present disclosure include a system comprising a turbomachine blade assembly having a blade portion, a shank portion, and a mounting portion, wherein the blade portion, the shank portion, and the mounting portion comprise a first plurality of plies extending from a tip of the airfoil to a base of the dovetail.

  14. Multi-Robot Assembly Strategies and Metrics

    Science.gov (United States)

    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

  15. Polymeric Biomaterials: Diverse Functions Enabled by Advances in Macromolecular Chemistry.

    Science.gov (United States)

    Liang, Yingkai; Li, Linqing; Scott, Rebecca A; Kiick, Kristi L

    2017-01-24

    Biomaterials have been extensively used to leverage beneficial outcomes in various therapeutic applications, such as providing spatial and temporal control over the release of therapeutic agents in drug delivery as well as engineering functional tissues and promoting the healing process in tissue engineering and regenerative medicine. This perspective presents important milestones in the development of polymeric biomaterials with defined structures and properties. Contemporary studies of biomaterial design have been reviewed with focus on constructing materials with controlled structure, dynamic functionality, and biological complexity. Examples of these polymeric biomaterials enabled by advanced synthetic methodologies, dynamic chemistry/assembly strategies, and modulated cell-material interactions have been highlighted. As the field of polymeric biomaterials continues to evolve with increased sophistication, current challenges and future directions for the design and translation of these materials are also summarized.

  16. Hand Controller Assembly

    Science.gov (United States)

    Bandera, Pablo (Inventor); Buchele, Paul (Inventor)

    2015-01-01

    A user input device for a vehicular electrical system is provided. The user input device includes a handle sized and shaped to be gripped by a human hand and a gimbal assembly within the handle. The gimbal assembly includes a first gimbal component, a second gimbal component coupled to the first gimbal component such that the second gimbal component is rotatable relative to the first gimbal component about a first axis, and a third gimbal component coupled to the second gimbal component such that the third gimbal component is rotatable relative to the second gimbal component about a second axis.

  17. Photovoltaic self-assembly.

    Energy Technology Data Exchange (ETDEWEB)

    Lavin, Judith; Kemp, Richard Alan; Stewart, Constantine A.

    2010-10-01

    This late-start LDRD was focused on the application of chemical principles of self-assembly on the ordering and placement of photovoltaic cells in a module. The drive for this chemical-based self-assembly stems from the escalating prices in the 'pick-and-place' technology currently used in the MEMS industries as the size of chips decreases. The chemical self-assembly principles are well-known on a molecular scale in other material science systems but to date had not been applied to the assembly of cells in a photovoltaic array or module. We explored several types of chemical-based self-assembly techniques, including gold-thiol interactions, liquid polymer binding, and hydrophobic-hydrophilic interactions designed to array both Si and GaAs PV chips onto a substrate. Additional research was focused on the modification of PV cells in an effort to gain control over the facial directionality of the cells in a solvent-based environment. Despite being a small footprint research project worked on for only a short time, the technical results and scientific accomplishments were significant and could prove to be enabling technology in the disruptive advancement of the microelectronic photovoltaics industry.

  18. Flow Accelerated Corrosion of Carbon Steel in the Feedwater System of PWR Plants - Behaviour of Welds and Weld Assemblies

    Science.gov (United States)

    Mansour, C.; Pavageau, E. M.; Faucher, A.; Inada, F.; Yoneda, K.; Miller, C.; Bretelle, J.-L.

    Flow Accelerated Corrosion (FAC) of carbon steel is a phenomenon that has been studied for many years. However, to date, the specific behavior of welds and weld assemblies of carbon steel towards this phenomenon has been scarcely examined. An experimental program of FAC of welds and weld assemblies is being conducted by EDF and CRIEPI. This paper describes the results obtained on the behavior of weld metal independently of its behavior in a weld assembly as well as the sensitivity to FAC of various weld assembly configurations. Tests are performed, at EDF, in the CIROCO loop which permits to follow the FAC rate by gammametry measurements, and at CRIEPI, in the PRINTEMPS loop where FAC is measured by laser displacement sensor. Welds are performed by two different methods: Submerged Arc Welding (SAW) and Gas Tungsten Arc Welding (GTAW). The influence of several parameters on FAC of welds is examined: welding method, chromium content and temperature. For weld assemblies, only the impact of chromium content is studied. All the tests are conducted in ammonia medium at pH 9.0 and oxygen concentration lower then 1 ppb. Chemical parameters, as the pH, the conductivity and oxygen concentration, are measured in situ during the test and surface characterizations are performed after the test. The results show that, with more than 0.15% chromium, no FAC is detected on the weld metal, which is similar to the base metal behaviour. For the same and lower chromium content, the two types of metal have the same FAC rate. Concerning the temperature effect, for both metals FAC rate decreases with temperature increase above 150°C. Below 150 °C, their behaviour seems to be different. For weld assemblies, the study of different configurations shows that the chromium content is the main parameter affecting the behaviour of the specimens. Additional tests and modeling studies will be conducted in order to complete the results.

  19. Subcritical Multiplication Parameters of the Accelerator-Driven System with 100 MeV Protons at the Kyoto University Critical Assembly

    OpenAIRE

    Jae-Yong Lim; Cheol Ho Pyeon; Takahiro Yagi; Tsuyoshi Misawa

    2012-01-01

    Basic experiments on the accelerator-driven system (ADS) at the Kyoto University Critical Assembly are carried out by combining a solid-moderated and -reflected core with the fixed-field alternating gradient accelerator. The reaction rates are measured by the foil activation method to obtain the subcritical multiplication parameters. The numerical calculations are conducted with the use of MCNPX and JENDL/HE-2007 to evaluate the reaction rates of activation foils set in the core region and at...

  20. Method to Assemble Genomic DNA Fragments or Genes on Human Artificial Chromosome with Regulated Kinetochore Using a Multi-Integrase System.

    Science.gov (United States)

    Lee, Nicholas C O; Kim, Jung-Hyun; Petrov, Nikolai S; Lee, Hee-Sheung; Masumoto, Hiroshi; Earnshaw, William C; Larionov, Vladimir; Kouprina, Natalay

    2018-01-19

    The production of cells capable of carrying multiple transgenes to Mb-size genomic loci has multiple applications in biomedicine and biotechnology. In order to achieve this goal, three key steps are required: (i) cloning of large genomic segments; (ii) insertion of multiple DNA blocks at a precise location and (iii) the capability to eliminate the assembled region from cells. In this study, we designed the iterative integration system (IIS) that utilizes recombinases Cre, ΦC31 and ΦBT1, and combined it with a human artificial chromosome (HAC) possessing a regulated kinetochore (alphoidtetO-HAC). We have demonstrated that the IIS-alphoidtetO-HAC system is a valuable genetic tool by reassembling a functional gene from multiple segments on the HAC. IIS-alphoidtetO-HAC has several notable advantages over other artificial chromosome-based systems. This includes the potential to assemble an unlimited number of genomic DNA segments; a DNA assembly process that leaves only a small insertion (<60 bp) scar between adjacent DNA, allowing genes reassembled from segments to be spliced correctly; a marker exchange system that also changes cell color, and counter-selection markers at each DNA insertion step, simplifying selection of correct clones; and presence of an error proofing mechanism to remove cells with misincorporated DNA segments, which improves the integrity of assembly. In addition, the IIS-alphoidtetO-HAC carrying a locus of interest is removable, offering the unique possibility to revert the cell line to its pretransformed state and compare the phenotypes of human cells with and without a functional copy of a gene(s). Thus, IIS-alphoidtetO-HAC allows investigation of complex biomedical pathways, gene(s) regulation, and has the potential to engineer synthetic chromosomes with a predetermined set of genes.

  1. Gastrointestinal host defence: importance of gut closure in control of macromolecular transport.

    Science.gov (United States)

    Walker, W A

    An important adaptation of the gastrointestinal tract to the extrauterine environment is its development of a mucosal barrier against the penetration of harmful substances (bacteria, toxins and antigens) present within the intestinal lumen. At birth, the newborn infant must be prepared to deal with bacterial colonization of the gut, with formation of toxic byproducts of bacteria and viruses (enterotoxins and endotoxins) and with the ingestion of antigens (milk proteins). These potentially noxious substances if allowed to penetrate the mucosal epithelial barrier under pathological conditions can cause inflammatory and allergic reactions which may result in gastrointestinal and systemic disease states. To combat the potential danger of invasion across the mucosal barrier the infant must develop an elaborate system of defence mechanisms within the lumen and on the luminal mucosal surface which act to control and maintain the epithelium as an impermeable barrier to uptake of macromolecular antigens. These defences include a unique immunological system adapted to function in the complicated milieu of the intestine as well as other non-immunological processes such as a gastric barrier, intestinal surface secretions, peristaltic movement and natural antibacterial substances (lysozyme, bile salts) which also help to provide maximum protection for the intestinal surface. Unfortunately, during the immediate postpartum period, particularly for premature and small-for-dates infants, this elaborate local defence system is incompletely developed. As a result of the delay in the maturation of the mucosal barrier newborn infants are particularly vulnerable to pathological penetration by harmful intraluminal substances. The consequences of altered defence are susceptibility to infection and the potential for hypersensitivity reactions and for formation of immune complexes. With these reactions comes the potential for developing life-threatening diseases such as necrotizing

  2. Flexibility damps macromolecular crowding effects on protein folding dynamics: Application to the murine prion protein (121-231)

    Science.gov (United States)

    Bergasa-Caceres, Fernando; Rabitz, Herschel A.

    2014-01-01

    A model of protein folding kinetics is applied to study the combined effects of protein flexibility and macromolecular crowding on protein folding rate and stability. It is found that the increase in stability and folding rate promoted by macromolecular crowding is damped for proteins with highly flexible native structures. The model is applied to the folding dynamics of the murine prion protein (121-231). It is found that the high flexibility of the native isoform of the murine prion protein (121-231) reduces the effects of macromolecular crowding on its folding dynamics. The relevance of these findings for the pathogenic mechanism are discussed.

  3. A Data-Driven Perspective on the Hierarchical Assembly of Molecular Structures.

    Science.gov (United States)

    Boninsegna, Lorenzo; Banisch, Ralf; Clementi, Cecilia

    2017-12-22

    Macromolecular systems are composed of a very large number of atomic degrees of freedom. There is strong evidence suggesting that structural changes occurring in large biomolecular systems at long time scale dynamics may be captured by models coarser than atomistic, although a suitable or optimal coarse-graining is a priori unknown. Here we propose a systematic approach to learning a coarse representation of a macromolecule from microscopic simulation data. In particular, the definition of effective coarse variables is achieved by partitioning the degrees of freedom both in the structural (physical) space and in the conformational space. The identification of groups of microscopic particles forming dynamical coherent states in different metastable states leads to a multiscale description of the system, in space and time. The application of this approach to the folding dynamics of two proteins provides a revised view of the classical idea of prestructured regions (foldons) that combine during a protein-folding process and suggests a hierarchical characterization of the assembly process of folded structures.

  4. Assembling consumption

    DEFF Research Database (Denmark)

    Assembling Consumption marks a definitive step in the institutionalisation of qualitative business research. By gathering leading scholars and educators who study markets, marketing and consumption through the lenses of philosophy, sociology and anthropology, this book clarifies and applies...... the investigative tools offered by assemblage theory, actor-network theory and non-representational theory. Clear theoretical explanation and methodological innovation, alongside empirical applications of these emerging frameworks will offer readers new and refreshing perspectives on consumer culture and market...... societies. This is an essential reading for both seasoned scholars and advanced students of markets, economies and social forms of consumption....

  5. Assembly, loading, and alignment of an analytical ultracentrifuge sample cell.

    Science.gov (United States)

    Balbo, Andrea; Zhao, Huaying; Brown, Patrick H; Schuck, Peter

    2009-11-05

    The analytical ultracentrifuge (AUC) is a powerful biophysical tool that allows us to record macromolecular sedimentation profiles during high speed centrifugation. When properly planned and executed, an AUC sedimentation velocity or sedimentation equilibrium experiment can reveal a great deal about a protein in regards to size and shape, sample purity, sedimentation coefficient, oligomerization states and protein-protein interactions. This technique, however, requires a rigorous level of technical attention. Sample cells hold a sectored center piece sandwiched between two window assemblies. They are sealed with a torque pressure of around 120-140 in/lbs. Reference buffer and sample are loaded into the centerpiece sectors and then after sealing, the cells are precisely aligned into a titanium rotor so that the optical detection systems scan both sample and reference buffer in the same radial path midline through each centerpiece sector while rotating at speeds of up to 60, 000 rpm and under very high vacuum Not only is proper sample cell assembly critical, sample cell components are very expensive and must be properly cared for to ensure they are in optimum working condition in order to avoid leaks and breakage during experiments. Handle windows carefully, for even the slightest crack or scratch can lead to breakage in the centrifuge. The contact between centerpiece and windows must be as tight as possible; i.e. no Newton s rings should be visible after torque pressure is applied. Dust, lint, scratches and oils on either the windows or the centerpiece all compromise this contact and can very easily lead to leaking of solutions from one sector to another or leaking out of the centerpiece all together. Not only are precious samples lost, leaking of solutions during an experiment will cause an imbalance of pressure in the cell that often leads to broken windows and centerpieces. In addition, plug gaskets and housing plugs must be securely in place to avoid solutions

  6. Investigation of Self-Assembly Processes for Chitosan-Based Coagulant-Flocculant Systems: A Mini-Review

    Directory of Open Access Journals (Sweden)

    Savi Bhalkaran

    2016-09-01

    Full Text Available The presence of contaminants in wastewater poses significant challenges to water treatment processes and environmental remediation. The use of coagulation-flocculation represents a facile and efficient way of removing charged particles from water. The formation of stable colloidal flocs is necessary for floc aggregation and, hence, their subsequent removal. Aggregation occurs when these flocs form extended networks through the self-assembly of polyelectrolytes, such as the amine-based polysaccharide (chitosan, which form polymer “bridges” in a floc network. The aim of this overview is to evaluate how the self-assembly process of chitosan and its derivatives is influenced by factors related to the morphology of chitosan (flocculant and the role of the solution conditions in the flocculation properties of chitosan and its modified forms. Chitosan has been used alone or in conjunction with a salt, such as aluminum sulphate, as an aid for the removal of various waterborne contaminants. Modified chitosan relates to grafted anionic or cationic groups onto the C-6 hydroxyl group or the amine group at C-2 on the glucosamine monomer of chitosan. By varying the parameters, such as molecular weight and the degree of deacetylation of chitosan, pH, reaction and settling time, dosage and temperature, self-assembly can be further investigated. This mini-review places an emphasis on the molecular-level details of the flocculation and the self-assembly processes for the marine-based biopolymer, chitosan.

  7. Fuel injection assembly for use in turbine engines and method of assembling same

    Science.gov (United States)

    Uhm, Jong Ho; Johnson, Thomas Edward

    2015-03-24

    A fuel injection assembly for use in a turbine engine is provided. The fuel injection assembly includes a plurality of tube assemblies, wherein each of the tube assemblies includes an upstream portion and a downstream portion. Each tube assembly includes a plurality of tubes that extend from the upstream portion to the downstream portion or from the upstream portion through the downstream portion. At least one injection system is coupled to at least one tube assembly of the plurality of tube assemblies. The injection system includes a fluid supply member that extends from a fluid source to the downstream portion of the tube assembly. The fluid supply member includes a first end portion located in the downstream portion of the tube assembly, wherein the first end portion has at least one first opening for channeling fluid through the tube assembly to facilitate reducing a temperature therein.

  8. Macromolecular Engineering: New Routes Towards the Synthesis of Well-??Defined Polyethers/Polyesters Co/Terpolymers with Different Architectures

    KAUST Repository

    Alamri, Haleema

    2016-05-18

    The primary objective of this research was to develop a new and efficient pathway for well-defined multicomponent homo/co/terpolymers of cyclic esters/ethers using an organocatalytic approach with an emphasis on the macromolecular engineering aspects of the overall synthesis. Macromolecular engineering (as discussed in the first chapter) of homo/copolymers refers to the specific tailoring of these materials for achieving an easy and reproducible synthesis that results in precise molecular characteristics, i.e. molecular weight and polydispersity, as well as specific structure and end?group choices. Precise control of these molecular characteristics will provide access to new materials that can be used for pre-targeted purposes such as biomedical applications. Among the most commonly used engineering materials are polyesters (biocompatible and biodegradable) and polyethers (biocompatible), either as homopolymers or when or copolymers with linear structures. The ability to create non-linear structures, for example stars, will open new horizons in the applications of these important polymeric materials. The second part of this thesis describes the synthesis of aliphatic polyesters, particularly polycaprolactone and polylactide, using a metal-free initiator/catalyst system. A phosphazene base (t?BuP2) was used as the catalyst for the ring-opening copolymerization of ?-aprolactone (??CL) and L,Lactide (LLA) at room temperature with a variety of protic initiators in different solvents. These studies provided important information for the design of a metal-free route toward the synthesis of polyester?based (bio) materials. The third part of the thesis describes a novel route for the one?pot synthesis of polyether-b polyester block copolymers with either a linear or a specific macromolecular architecture. Poly (styrene oxide)?b?poly(caprolactone)?b?poly(L,lactide) was prepared using this method with the goal of synthesizing poly(styrene oxide)-based materials since this

  9. Assembly and trafficking of box C/D and H/ACA snoRNPs.

    Science.gov (United States)

    Massenet, Séverine; Bertrand, Edouard; Verheggen, Céline

    2017-06-03

    Box C/D and box H/ACA snoRNAs are abundant non-coding RNAs that localize in the nucleolus and mostly function as guides for nucleotide modifications. While a large pool of snoRNAs modifies rRNAs, an increasing number of snoRNAs could also potentially target mRNAs. ScaRNAs belong to a family of specific RNAs that localize in Cajal bodies and that are structurally similar to snoRNAs. Most scaRNAs are involved in snRNA modification, while telomerase RNA, which contains H/ACA motifs, functions in telomeric DNA synthesis. In this review, we describe how box C/D and H/ACA snoRNAs are processed and assembled with core proteins to form functional RNP particles. Their biogenesis involve several transport factors that first direct pre-snoRNPs to Cajal bodies, where some processing steps are believed to take place, and then to nucleoli. Assembly of core proteins involves the HSP90/R2TP chaperone-cochaperone system for both box C/D and H/ACA RNAs, but also several factors specific for each family. These assembly factors chaperone unassembled core proteins, regulate the formation and disassembly of pre-snoRNP intermediates, and control the activity of immature particles. The AAA+ ATPase RUVBL1 and RUVBL2 belong to the R2TP co-chaperones and play essential roles in snoRNP biogenesis, as well as in the formation of other macro-molecular complexes. Despite intensive research, their mechanisms of action are still incompletely understood.

  10. Geometric reasoning about assembly tools

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, R.H.

    1997-01-01

    Planning for assembly requires reasoning about various tools used by humans, robots, or other automation to manipulate, attach, and test parts and subassemblies. This paper presents a general framework to represent and reason about geometric accessibility issues for a wide variety of such assembly tools. Central to the framework is a use volume encoding a minimum space that must be free in an assembly state to apply a given tool, and placement constraints on where that volume must be placed relative to the parts on which the tool acts. Determining whether a tool can be applied in a given assembly state is then reduced to an instance of the FINDPLACE problem. In addition, the author presents more efficient methods to integrate the framework into assembly planning. For tools that are applied either before or after their target parts are mated, one method pre-processes a single tool application for all possible states of assembly of a product in polynomial time, reducing all later state-tool queries to evaluations of a simple expression. For tools applied after their target parts are mated, a complementary method guarantees polynomial-time assembly planning. The author presents a wide variety of tools that can be described adequately using the approach, and surveys tool catalogs to determine coverage of standard tools. Finally, the author describes an implementation of the approach in an assembly planning system and experiments with a library of over one hundred manual and robotic tools and several complex assemblies.

  11. General Assembly

    CERN Multimedia

    Staff Association

    2015-01-01

    Mardi 5 mai à 11 h 00 Salle 13-2-005 Conformément aux statuts de l’Association du personnel, une Assemblée générale ordinaire est organisée une fois par année (article IV.2.1). Projet d’ordre du jour : 1- Adoption de l’ordre du jour. 2- Approbation du procès-verbal de l’Assemblée générale ordinaire du 22 mai 2014. 3- Présentation et approbation du rapport d’activités 2014. 4- Présentation et approbation du rapport financier 2014. 5- Présentation et approbation du rapport des vérificateurs aux comptes pour 2014. 6- Programme 2015. 7- Présentation et approbation du projet de budget 2015 et taux de cotisation pour 2015. 8- Pas de modifications aux Statuts de l'Association du personnel proposée. 9- Élections des membres de la Commission é...

  12. General assembly

    CERN Multimedia

    Staff Association

    2015-01-01

    Mardi 5 mai à 11 h 00 Salle 13-2-005 Conformément aux statuts de l’Association du personnel, une Assemblée générale ordinaire est organisée une fois par année (article IV.2.1). Projet d’ordre du jour : Adoption de l’ordre du jour. Approbation du procès-verbal de l’Assemblée générale ordinaire du 22 mai 2014. Présentation et approbation du rapport d’activités 2014. Présentation et approbation du rapport financier 2014. Présentation et approbation du rapport des vérificateurs aux comptes pour 2014. Programme 2015. Présentation et approbation du projet de budget 2015 et taux de cotisation pour 2015. Pas de modifications aux Statuts de l'Association du personnel proposée. Élections des membres de la Commission électorale. &am...

  13. General Assembly

    CERN Multimedia

    Staff Association

    2016-01-01

    Mardi 5 avril à 11 h 00 BE Auditorium Meyrin (6-2-024) Conformément aux statuts de l’Association du personnel, une Assemblée générale ordinaire est organisée une fois par année (article IV.2.1). Projet d’ordre du jour : Adoption de l’ordre du jour. Approbation du procès-verbal de l’Assemblée générale ordinaire du 5 mai 2015. Présentation et approbation du rapport d’activités 2015. Présentation et approbation du rapport financier 2015. Présentation et approbation du rapport des vérificateurs aux comptes pour 2015. Programme de travail 2016. Présentation et approbation du projet de budget 2016 Approbation du taux de cotisation pour 2017. Modifications aux Statuts de l'Association du personnel proposée. Élections des membres de la Commissio...

  14. General Assembly

    CERN Multimedia

    Staff Association

    2017-01-01

    Conformément aux statuts de l’Association du personnel, une Assemblée générale ordinaire est organisée une fois par année (article IV.2.1). Projet d’ordre du jour : Adoption de l’ordre du jour. Approbation du procès-verbal de l’Assemblée générale ordinaire du 5 avril 2016. Présentation et approbation du rapport d’activités 2016. Présentation et approbation du rapport financier 2016. Présentation et approbation du rapport des vérificateurs aux comptes pour 2016. Programme de travail 2017. Présentation et approbation du projet de budget 2017 Approbation du taux de cotisation pour 2018. Modifications aux Statuts de l'Association du personnel proposées. Élections des membres de la Commission électorale. Élections des vérifica...

  15. A nanoscale bio-inspired light-harvesting system developed from self-assembled alkyl-functionalized metallochlorin nano-aggregates

    KAUST Repository

    Ocakoǧlu, Kasim

    2014-01-01

    Self-assembled supramolecular organization of nano-structured biomimetic light-harvesting modules inside solid-state nano-templates can be exploited to develop excellent light-harvesting materials for artificial photosynthetic devices. We present here a hybrid light-harvesting system mimicking the chlorosomal structures of the natural photosynthetic system using synthetic zinc chlorin units (ZnChl-C6, ZnChl-C12 and ZnChl-C 18) that are self-aggregated inside the anodic aluminum oxide (AAO) nano-channel membranes. AAO nano-templates were modified with a TiO2 matrix and functionalized with long hydrophobic chains to facilitate the formation of supramolecular Zn-chlorin aggregates. The transparent Zn-chlorin nano-aggregates inside the alkyl-TiO2 modified AAO nano-channels have a diameter of ∼120 nm in a 60 μm length channel. UV-Vis studies and fluorescence emission spectra further confirm the formation of the supramolecular ZnChl aggregates from monomer molecules inside the alkyl-functionalized nano-channels. Our results prove that the novel and unique method can be used to produce efficient and stable light-harvesting assemblies for effective solar energy capture through transparent and stable nano-channel ceramic materials modified with bio-mimetic molecular self-assembled nano-aggregates. © 2014 the Partner Organisations.

  16. Metabolic growth rate control in Escherichia coli may be a consequence of subsaturation of the macromolecular biosynthetic apparatus with substrates and catalytic components.

    Science.gov (United States)

    Jensen, K F; Pedersen, S

    1990-06-01

    In this paper, the Escherichia coli cell is considered as a system designed for rapid growth, but limited by the medium. We propose that this very design causes the cell to become subsaturated with precursors and catalytic components at all levels of macromolecular biosynthesis and leads to a molecular sharing economy at a high level of competition inside the cell. Thus, the promoters compete with each other in the binding of a limited amount of free RNA polymerase and the ribosome binding sites on the mRNA chains compete with each other for the free ribosomes. The macromolecular chain elongation reactions sequester a considerable proportion of the total amount of RNA polymerase and ribosomes in the cells. We propose that the degree of subsaturation of the macromolecular biosynthetic apparatus renders a variable fraction of RNA polymerase and ribosomes unavailable for the initiation of new chain synthesis and that this, at least in part, determines the composition of the cell as a function of the growth rate. Thus, at rapid growth, the high speed of the elongation reactions enables the cell to increase the concentrations of free RNA polymerase and ribosomes for initiation purposes. Furthermore, it is proposed that the speed of RNA polymerase movement is adjusted to the performance speed of the ribosomes. Mechanistically, this adjustment of the coupling between transcription and translation involves transcriptional pause sites along the RNA chains, the adjustment of the saturation level of RNA polymerase with the nucleoside triphosphate substrates, and the concentration of ppGpp, which is known to inhibit RNA chain elongation. This model is able to explain the stringent response and the control of stable RNA and of ribosome synthesis in steady states and in shifts, as well as the rate of overall protein synthesis as a function of the growth rate.

  17. Design and assembly of an experimental laboratory for the study of atmosphere-plant interactions in the system of fumigation chambers.

    Science.gov (United States)

    Souza, S R; Pagliuso, J D

    2009-11-01

    An experimental laboratory was designed and assembled at the Botanical Institute of São Paulo, Brazil, in order to research atmosphere-plant interactions through the use of a system of fumigation chambers. A system of three "closed" fumigation chambers was designed to be used inside or outside the laboratory. The system was built to be used with a single pollutant or a mix of them. The innovation in this system is to allow chemical reactions inside the chambers that simulate atmospheric chemistry, especially photochemical processes involving high levels of ozone. Assessment of the performance and applicability of the system was based on the response of Nicotiana tabacum Bel W3 exposed to ozone produced alternatively by a generator and inside the chamber by reactions of its precursors. The results showed that the system can be well applied to the study of atmospheric chemistry interactions and the effects on plants.

  18. Field application. Selective stimulation of reservoirs or perforated intervals with use of coiled tubing equipped with real-time data communication system in combination with straddle packer assemblies

    Energy Technology Data Exchange (ETDEWEB)

    Oberascher, R.; Breimer, G. [GDF SUEZ E and P Deutschland GmbH, Lingen (Germany); Jonge, R.M. de [Baker Hughes (Netherlands)

    2013-08-01

    In two German gas wells a decline in production and wellhead pressures had been observed. Production logging data obtained by PLT surveys were evaluated, which showed that certain intervals within the reservoir section did not contribute, or showed a restricted contribution to the overall gas production. The restricted contribution was suspected to be caused by near-wellbore damage. To restore or enhance the production of the perforated intervals an acid treatment was considered in these wells in order to remove skin damage. To restore or enhance the production of the wells, an acid treatment of the perforated intervals was designed. For obtaining the required selective placement of the acid across the zones of interest, the use of coiled tubing (CT) in combination with a resettable straddle packer assembly was selected. The accuracy of the setting depth of the straddle packer was a critical issue for the execution of the well intervention operations. In order to obtain the required depth accuracy, the CT string was equipped with an intelligent CT communication system, which transfers real-time downhole data to surface. For the first time, a reservoir stimulation project was executed by combining CT equipped with a real-time data communication system (TeleCoil) and the Inflatable Straddle Acidizing Packer (ISAP) assembly. Inside the CT an encapsulated monoconductor cable was installed to transmit real-time data from the CT Bottom Hole Assembly (BHA) to surface. The BHA consists of a Casing Collar Locator (CCL) and downhole pressure and temperature gauges. Due to the protective jacket of the monoconductor cable, there are no restrictions in the use of different fluids in combination with the system. Information provided by the CCL monitoring tool ensures accurate depth correlations, whereas differential pressure measurements from the down-hole pressure gauges provide positive information about the setting and sealing conditions of the straddle packer assembly. The

  19. Light-Activated Hydrogel Formation via the Triggered Folding and Self-Assembly of a Designed Peptide

    Science.gov (United States)

    Haines, Lisa A.; Rajagopal, Karthikan; Ozbas, Bulent; Salick, Daphne A.; Pochan, Darrin J.; Schneider, Joel P.

    2009-01-01

    Photopolymerization can be used to construct materials with precise temporal and spatial resolution. Applications such as tissue engineering, drug delivery, the fabrication of microfluidic devices and the preparation of high-density cell arrays employ hydrogel materials that are often prepared by this technique. Current photopolymerization strategies used to prepare hydrogels employ photoinitiators, many of which are cytotoxic and require large macromolecular precursors that need to be functionalized with moieties capable of undergoing radical cross-linking reactions. We have developed a simple light-activated hydrogelation system that employs a designed peptide whose ability to self-assemble into hydrogel material is dependent on its intramolecular folded conformational state. An iterative design strategy afforded MAX7CNB, a photocaged peptide that, when dissolved in aqueous medium, remains unfolded and unable to self-assemble; a 2 wt % solution of freely soluble unfolded peptide is stable to ambient light and has the viscosity of water. Irradiation of the solution (260 < λ < 360 nm) releases the photocage and triggers peptide folding to produce amphiphilic β-hairpins that self-assemble into viscoelastic hydrogel material. Circular dichroic (CD) spectroscopy supports this folding and self-assembly mechanism, and oscillatory rheology shows that the resulting hydrogel is mechanically rigid ( G′ = 1000 Pa). Laser scanning confocal microscopy imaging of NIH 3T3 fibroblasts seeded onto the gel indicates that the gel surface is noncytotoxic, conducive to cell adhesion, and allows cell migration. Lastly, thymidine incorporation assays show that cells seeded onto decaged hydrogel proliferate at a rate equivalent to cells seeded onto a tissue culture-treated polystyrene control surface. PMID:16316249

  20. Satellite Power Systems (SPS) concept definition study. Volume 5: Transportation and operations analysis. [heavy lift launch and orbit transfer vehicles for orbital assembly

    Science.gov (United States)

    Hanley, G.

    1978-01-01

    The development of transportation systems to support the operations required for the orbital assembly of a 5-gigawatt satellite is discussed as well as the construction of a ground receiving antenna (rectenna). Topics covered include heavy lift launch vehicle configurations for Earth-to LEO transport; the use of chemical, nuclear, and electric orbit transfer vehicles for LEO to GEO operations; personnel transport systems; ground operations; end-to-end analysis of the construction, operation, and maintenance of the satellite and rectenna; propellant production and storage; and payload packaging.

  1. High-Resolution Macromolecular Structure Determination by MicroED, a cryo-EM Method

    Science.gov (United States)

    Rodriguez, J.A.; Gonen, T.

    2017-01-01

    Microelectron diffraction (MicroED) is a new cryo-electron microscopy (cryo-EM) method capable of determining macromolecular structures at atomic resolution from vanishingly small 3D crystals. MicroED promises to solve atomic resolution structures from even the tiniest of crystals, less than a few hundred nanometers thick. MicroED complements frontier advances in crystallography and represents part of the rebirth of cryo-EM that is making macromolecular structure determination more accessible for all. Here we review the concept and practice of MicroED, for both the electron microscopist and crystallographer. Where other reviews have addressed specific details of the technique (Hattne et al., 2015; Shi et al., 2016; Shi, Nannenga, Iadanza, & Gonen, 2013), we aim to provide context and highlight important features that should be considered when performing a MicroED experiment. PMID:27572734

  2. Local analysis of strains and rotations for macromolecular electron microscopy maps

    Energy Technology Data Exchange (ETDEWEB)

    Martin-Ramos, A.; Prieto, F.; Melero, R.; Martin-Benito, J.; Jonic, S.; Navas-Calvente, J.; Vargas, J.; Oton, J.; Abrishami, V.; Rosa-Trevin, J.L. de la; Gomez-Blanco, J.; Vilas, J.L.; Marabini, R.; Carazo, R.; Sorzano, C.O.S.

    2016-07-01

    Macromolecular complexes can be considered as molecular nano-machines that must have mobile parts in order to perform their physiological functions. The reordering of their parts is essential to execute their task. These rearrangements induce local strains and rotations which, after analyzing them, may provide relevant information about how the proteins perform their function. In this project these deformations of the macromolecular complexes are characterized, translating into a “mathematical language” the conformational changes of the complexes when they perform their function. Electron Microscopy (EM) volumes are analyzed using a method that uses B-splines as its basis functions. It is shown that the results obtained are consistent with the conformational changes described in their corresponding reference publications. (Author)

  3. Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Foadi, James [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Imperial College, London SW7 2AZ (United Kingdom); Aller, Pierre [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Alguel, Yilmaz; Cameron, Alex [Imperial College, London SW7 2AZ (United Kingdom); Axford, Danny; Owen, Robin L. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Armour, Wes [Oxford e-Research Centre (OeRC), Keble Road, Oxford OX1 3QG (United Kingdom); Waterman, David G. [Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA (United Kingdom); Iwata, So [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Imperial College, London SW7 2AZ (United Kingdom); Evans, Gwyndaf, E-mail: gwyndaf.evans@diamond.ac.uk [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom)

    2013-08-01

    A systematic approach to the scaling and merging of data from multiple crystals in macromolecular crystallography is introduced and explained. The availability of intense microbeam macromolecular crystallography beamlines at third-generation synchrotron sources has enabled data collection and structure solution from microcrystals of <10 µm in size. The increased likelihood of severe radiation damage where microcrystals or particularly sensitive crystals are used forces crystallographers to acquire large numbers of data sets from many crystals of the same protein structure. The associated analysis and merging of multi-crystal data is currently a manual and time-consuming step. Here, a computer program, BLEND, that has been written to assist with and automate many of the steps in this process is described. It is demonstrated how BLEND has successfully been used in the solution of a novel membrane protein.

  4. HTLV-1 Tax Induces Formation of the Active Macromolecular IKK Complex by Generating Lys63- and Met1-Linked Hybrid Polyubiquitin Chains.

    Science.gov (United States)

    Shibata, Yuri; Tokunaga, Fuminori; Goto, Eiji; Komatsu, Ginga; Gohda, Jin; Saeki, Yasushi; Tanaka, Keiji; Takahashi, Hirotaka; Sawasaki, Tatsuya; Inoue, Satoshi; Oshiumi, Hiroyuki; Seya, Tsukasa; Nakano, Hiroyasu; Tanaka, Yuetsu; Iwai, Kazuhiro; Inoue, Jun-Ichiro

    2017-01-01

    The Tax protein of human T-cell leukemia virus type 1 (HTLV-1) is crucial for the development of adult T-cell leukemia (ATL), a highly malignant CD4+ T cell neoplasm. Among the multiple aberrant Tax-induced effects on cellular processes, persistent activation of transcription factor NF-κB, which is activated only transiently upon physiological stimulation, is essential for leukemogenesis. We and others have shown that Tax induces activation of the IκB kinase (IKK) complex, which is a critical step in NF-κB activation, by generating Lys63-linked polyubiquitin chains. However, the molecular mechanism underlying Tax-induced IKK activation is controversial and not fully understood. Here, we demonstrate that Tax recruits linear (Met1-linked) ubiquitin chain assembly complex (LUBAC) to the IKK complex and that Tax fails to induce IKK activation in cells that lack LUBAC activity. Mass spectrometric analyses revealed that both Lys63-linked and Met1-linked polyubiquitin chains are associated with the IKK complex. Furthermore, treatment of the IKK-associated polyubiquitin chains with Met1-linked-chain-specific deubiquitinase (OTULIN) resulted in the reduction of high molecular weight polyubiquitin chains and the generation of short Lys63-linked ubiquitin chains, indicating that Tax can induce the generation of Lys63- and Met1-linked hybrid polyubiquitin chains. We also demonstrate that Tax induces formation of the active macromolecular IKK complex and that the blocking of Tax-induced polyubiquitin chain synthesis inhibited formation of the macromolecular complex. Taken together, these results lead us to propose a novel model in which the hybrid-chain-dependent oligomerization of the IKK complex triggered by Tax leads to trans-autophosphorylation-mediated IKK activation.

  5. Folding and assembly of hemoglobin monitored by electrospray mass spectrometry using an on-line dialysis system.

    Science.gov (United States)

    Boys, Brian L; Konermann, Lars

    2007-01-01

    The native structure of hemoglobin (Hb) comprises two alpha- and two beta-subunits, each of which carries a heme group. There appear to be no previous studies that report the in vitro folding and assembly of Hb from highly unfolded alpha- and beta-globin in a "one-pot" reaction. One difficulty that has to be overcome for studies of this kind is the tendency of Hb to aggregate during refolding. This work demonstrates that denaturation of Hb in 40% acetonitrile at pH 10.0 is reversible. A dialysis-mediated solvent change to a purely aqueous environment of pH 8.0 results in Hb refolding without any apparent aggregation. Fluorescence, Soret absorption, circular dichroism, and ESI mass spectra of the protein recorded before unfolding and after refolding are almost identical. By employing an externally pressurized dialysis cell that is coupled on-line to an ESI mass spectrometer, changes in heme binding behavior, protein conformation, and quaternary structure can be monitored as a function of time. The process occurs in a stepwise sequential manner, leading from monomeric alpha- and beta-globin to heterodimeric species, which then assemble into tetramers. Overall, this mechanism is consistent with previous studies employing the mixing of folded alpha- and beta-globin. However, some unexpected features are observed, e.g., a heme-deficient beta-globin dimer that represents an off-pathway intermediate. Monomeric beta-globin is capable of binding heme before forming a complex with an alpha-subunit. This observation suggests that holo-alpha-apo-beta globin does not represent an obligatory intermediate during Hb assembly, as had been proposed previously. The on-line dialysis/ESI-MS approach developed for this work represents a widely applicable tool for studying the folding and self-assembly of noncovalent biological complexes.

  6. Macromolecular coupling in seconds of triazolinedione end-functionalized polymers prepared by RAFT polymerization

    OpenAIRE

    Vandewalle, Stef; Billiet, Stijn; Driessen, Frank; Du Prez, Filip

    2016-01-01

    The ultrafast and additive-free triazolinedione-click reaction with electron rich (di)enes is a powerful method for the ultrafast ligation of polymer segments. A versatile method is described for the introduction of dickable TAD end groups in various polymer segments, using reversible addition-fragmentation chain transfer polymerization. These triazolinedione-functionalized prepolymers were subsequently used for macromolecular functionalization with a low molecular weight diene and block copo...

  7. Measurement and Interpretation of Diffuse Scattering in X-Ray Diffraction for Macromolecular Crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Wall, Michael E. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-10-16

    X-ray diffraction from macromolecular crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering reflects the mean electron density in the unit cells of the crystal. The diffuse scattering arises from correlations in the variations of electron density that may occur from one unit cell to another, and therefore contains information about collective motions in proteins.

  8. Folding dynamics of Trp-cage in the presence of chemical interference and macromolecular crowding. I.

    Science.gov (United States)

    Samiotakis, Antonios; Cheung, Margaret S

    2011-11-07

    Proteins fold and function in the crowded environment of the cell's interior. In the recent years it has been well established that the so-called "macromolecular crowding" effect enhances the folding stability of proteins by destabilizing their unfolded states for selected proteins. On the other hand, chemical and thermal denaturation is often used in experiments as a tool to destabilize a protein by populating the unfolded states when probing its folding landscape and thermodynamic properties. However, little is known about the complicated effects of these synergistic perturbations acting on the kinetic properties of proteins, particularly when large structural fluctuations, such as protein folding, have been involved. In this study, we have first investigated the folding mechanism of Trp-cage dependent on urea concentration by coarse-grained molecular simulations where the impact of urea is implemented into an energy function of the side chain and/or backbone interactions derived from the all-atomistic molecular dynamics simulations with urea through a Boltzmann inversion method. In urea solution, the folding rates of a model miniprotein Trp-cage decrease and the folded state slightly swells due to a lack of contact formation between side chains at the terminal regions. In addition, the equilibrium m-values of Trp-cage from the computer simulations are in agreement with experimental measurements. We have further investigated the combined effects of urea denaturation and macromolecular crowding on Trp-cage's folding mechanism where crowding agents are modeled as hard-spheres. The enhancement of folding rates of Trp-cage is most pronounced by macromolecular crowding effect when the extended conformations of Trp-cast dominate at high urea concentration. Our study makes quantitatively testable predictions on protein folding dynamics in a complex environment involving both chemical denaturation and macromolecular crowding effects.

  9. New methodologies at PF AR-NW12A: the implementation of high-pressure macromolecular crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Chavas, Leonard Michel Gabriel, E-mail: leonard.chavas@kek.jp [PF/IMSS/KEK, 1-1 Oho, Tsukuba, Ibaraki 300-0801 (Japan); Nagae, Tadayuki [Nagoya University, Nagoya, Aichi 464-8603 (Japan); Nagoya University, Nagoya, Aichi 464-8603 (Japan); Yamada, Hiroyuki [Nagoya University, Nagoya, Aichi 464-8603 (Japan); Watanabe, Nobuhisa [Nagoya University, Nagoya, Aichi 464-8603 (Japan); Nagoya University, Furo-cho Chikusa-ku, Nagoya, Aichi 464-8603 (Japan); Yamada, Yusuke; Hiraki, Masahiko; Matsugaki, Naohiro [PF/IMSS/KEK, 1-1 Oho, Tsukuba, Ibaraki 300-0801 (Japan)

    2013-11-01

    The evolution of AR-NW12A into a multi-purpose end-station with optional high-pressure crystallography is described. The macromolecular crystallography (MX) beamline AR-NW12A is evolving from its original design of high-throughput crystallography to a multi-purpose end-station. Among the various options to be implemented, great efforts were made in making available high-pressure MX (HPMX) at the beamline. High-pressure molecular biophysics is a developing field that attracts the interest of a constantly growing scientific community. A plethora of activities can benefit from high pressure, and investigations have been performed on its applicability to study multimeric complex assemblies, compressibility of proteins and their crystals, macromolecules originating from extremophiles, or even the trapping of higher-energy conformers for molecules of biological interest. Recent studies using HPMX showed structural hydrostatic-pressure-induced changes in proteins. The conformational modifications could explain the enzymatic mechanism differences between proteins of the same family, living at different environmental pressures, as well as the initial steps in the pressure-denaturation process that have been attributed to water penetration into the protein interior. To facilitate further HPMX, while allowing access to various individualized set-ups and experiments, the AR-NW12A sample environment has been revisited. Altogether, the newly added implementations will bring a fresh breath of life to AR-NW12A and allow the MX community to experiment in a larger set of fields related to structural biology.

  10. 24 CFR 3285.601 - Field assembly.

    Science.gov (United States)

    2010-04-01

    ... 24 Housing and Urban Development 5 2010-04-01 2010-04-01 false Field assembly. 3285.601 Section... § 3285.601 Field assembly. Home manufacturers must provide specific installation instructions for the proper field assembly of manufacturer-supplied and shipped loose ducts, plumbing, and fuel supply system...

  11. System Design and Implementation of the Detector Assembly of the Astro-H Soft X-Ray Spectrometer

    Science.gov (United States)

    Chiao, M. P.; Adams, J.; Goodwin, P.; Hobson, C.W.; Kelley, R. L.; Kilbourne, C. A.; McCammom, D.; McGuinness, D. S.; Moseley, S. J.; Porter, F. S.; hide

    2016-01-01

    The soft x-ray spectrometer (SXS) onboard Astro-H presents to the science community unprecedented capability (less than 7 eV at 6 keV) for high-resolution spectral measurements in the range of 0.5-12 keV to study extended celestial sources. At the heart of this SXS is the x-ray calorimeter spectrometer (XCS) where detectors (calorimeter array and anticoincidence detector) operate at 50 mK, the bias circuit operates at nominal 1.3 K, and the first stage amplifiers operateat 130 K, all within a nominal 20 cm envelope. The design of the detector assembly in this XCS originates from the Astro-E x-ray spectrometer (XRS) and lessons learned from Astro-E and Suzaku. After the production of our engineering model, additional changes were made in order to improve our flight assembly process for better reliability and overall performance. In this poster, we present the final design and implementation of the flight detector assembly, show comparison of parameters and performance to Suzakus XRS, and list susceptibilities to other subsystems as well as our lessons learned.

  12. Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination

    Science.gov (United States)

    Wlodawer, Alexander; Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz

    2014-01-01

    The number of macromolecular structures deposited in the Protein Data Bank now approaches 100 000, with the vast majority of them determined by crystallographic methods. Thousands of papers describing such structures have been published in the scientific literature, and 20 Nobel Prizes in chemistry or medicine have been awarded for discoveries based on macromolecular crystallography. New hardware and software tools have made crystallography appear to be an almost routine (but still far from being analytical) technique and many structures are now being determined by scientists with very limited experience in the practical aspects of the field. However, this apparent ease is sometimes illusory and proper procedures need to be followed to maintain high standards of structure quality. In addition, many noncrystallographers may have problems with the critical evaluation and interpretation of structural results published in the scientific literature. The present review provides an outline of the technical aspects of crystallography for less experienced practitioners, as well as information that might be useful for users of macromolecular structures, aiming to show them how to interpret (but not overinterpret) the information present in the coordinate files and in their description. A discussion of the extent of information that can be gleaned from the atomic coordinates of structures solved at different resolution is provided, as well as problems and pitfalls encountered in structure determination and interpretation. PMID:24034303

  13. The use of a mini-κ goniometer head in macromolecular crystallography diffraction experiments

    Energy Technology Data Exchange (ETDEWEB)

    Brockhauser, Sandor [European Molecular Biology Laboratory (EMBL), 6 Rue Jules Horowitz, 38042 Grenoble (France); UJF–EMBL–CNRS UMI 3265, 6 Rue Jules Horowitz, 38043 Grenoble (France); Ravelli, Raimond B. G. [Leiden University Medical Center (LUMC), PO Box 9600, 2300 RC Leiden (Netherlands); McCarthy, Andrew A., E-mail: andrewmc@embl.fr [European Molecular Biology Laboratory (EMBL), 6 Rue Jules Horowitz, 38042 Grenoble (France); UJF–EMBL–CNRS UMI 3265, 6 Rue Jules Horowitz, 38043 Grenoble (France)

    2013-07-01

    Hardware and software solutions for MX data-collection strategies using the EMBL/ESRF miniaturized multi-axis goniometer head are presented. Most macromolecular crystallography (MX) diffraction experiments at synchrotrons use a single-axis goniometer. This markedly contrasts with small-molecule crystallography, in which the majority of the diffraction data are collected using multi-axis goniometers. A novel miniaturized κ-goniometer head, the MK3, has been developed to allow macromolecular crystals to be aligned. It is available on the majority of the structural biology beamlines at the ESRF, as well as elsewhere. In addition, the Strategy for the Alignment of Crystals (STAC) software package has been developed to facilitate the use of the MK3 and other similar devices. Use of the MK3 and STAC is streamlined by their incorporation into online analysis tools such as EDNA. The current use of STAC and MK3 on the MX beamlines at the ESRF is discussed. It is shown that the alignment of macromolecular crystals can result in improved diffraction data quality compared with data obtained from randomly aligned crystals.

  14. Virtual Reality and Haptics for Product Assembly

    Directory of Open Access Journals (Sweden)

    Maria Teresa Restivo

    2012-01-01

    Full Text Available Haptics can significantly enhance the user's sense of immersion and interactivity. An industrial application of virtual reality and haptics for product assembly is described in this paper, which provides a new and low-cost approach for product assembly design, assembly task planning and assembly operation training. A demonstration of the system with haptics device interaction was available at the session of exp.at'11.

  15. Bacillus atrophaeus Outer Spore Coat Assembly and Ultrastructure

    Energy Technology Data Exchange (ETDEWEB)

    Plomp, M; Leighton, T J; Wheeler, K E; Pitesky, M E; Malkin, A J

    2005-11-21

    Our previous atomic force microscopy (AFM) studies successfully visualized native Bacillus atrophaeus spore coat ultrastructure and surface morphology. We have shown that the outer spore coat surface is formed by a crystalline array of {approx}11 nm thick rodlets, having a periodicity of {approx}8 nm. We present here further AFM ultrastructural investigations of air-dried and fully hydrated spore surface architecture. In the rodlet layer, planar and point defects, as well as domain boundaries, similar to those described for inorganic and macromolecular crystals, were identified. For several Bacillus species, rodlet structure assembly and architectural variation appear to be a consequence of species-specific nucleation and crystallization mechanisms that regulate the formation of the outer spore coat. We propose a unifying mechanism for nucleation and self-assembly of this crystalline layer on the outer spore coat surface.

  16. Glass-formers vs. Assemblers

    Science.gov (United States)

    Glotzer, Sharon

    2015-03-01

    In most instances, the formation of a glass signifies an inability of the constituents of a system to self-organize into a well-defined, thermodynamically preferred ordered structure. Thus good ''assemblers'' may make poor glass-formers, and good glass-formers tend to be poor assemblers. How good or bad a system is in assembling or vitrifying/jamming depends on many features of the constituent building blocks, including shape and interactions. In many cases, building blocks whose shapes make them good glass-formers can, through almost imperceptible perturbations, become good assemblers, and vice versa. We examine these issues through consideration of several model systems, including colloidal ''rocks'' and foldable nets. *with E.R. Chen, P. Damasceno, P. Dodd, M. Engel, A.S. Keys, D. Klotsa, E. Teich, and G. van Anders

  17. The Multinational Arabidopsis Steering Subcommittee for Proteomics Assembles the Largest Proteome Database Resource for Plant Systems Biology

    Energy Technology Data Exchange (ETDEWEB)

    Weckwerth, Wolfram; Baginsky, Sacha; Van Wijk, Klass; Heazlewood, Joshua; Millar, Harvey

    2009-12-01

    In the past 10 years, we have witnessed remarkable advances in the field of plant molecular biology. The rapid development of proteomic technologies and the speed with which these techniques have been applied to the field have altered our perception of how we can analyze proteins in complex systems. At nearly the same time, the availability of the complete genome for the model plant Arabidopsis thaliana was released; this effort provides an unsurpassed resource for the identification of proteins when researchers use MS to analyze plant samples. Recognizing the growth in this area, the Multinational Arabidopsis Steering Committee (MASC) established a subcommittee for A. thaliana proteomics in 2006 with the objective of consolidating databases, technique standards, and experimentally validated candidate genes and functions. Since the establishment of the Multinational Arabidopsis Steering Subcommittee for Proteomics (MASCP), many new approaches and resources have become available. Recently, the subcommittee established a webpage to consolidate this information (www.masc-proteomics.org). It includes links to plant proteomic databases, general information about proteomic techniques, meeting information, a summary of proteomic standards, and other relevant resources. Altogether, this website provides a useful resource for the Arabidopsis proteomics community. In the future, the website will host discussions and investigate the cross-linking of databases. The subcommittee members have extensive experience in arabidopsis proteomics and collectively have produced some of the most extensive proteomics data sets for this model plant (Table S1 in the Supporting Information has a list of resources). The largest collection of proteomics data from a single study in A. thaliana was assembled into an accessible database (AtProteome; http://fgcz-atproteome.unizh.ch/index.php) and was recently published by the Baginsky lab.1 The database provides links to major Arabidopsis online

  18. Leaching of organic acids from macromolecular organic matter by non-supercritical CO2

    Science.gov (United States)

    Sauer, P.; Glombitza, C.; Kallmeyer, J.

    2012-04-01

    The storage of CO2 in underground reservoirs is discussed controversly in the scientific literature. The worldwide search for suitable storage formations also considers coal-bearing strata. CO2 is already injected into seams for enhanced recovery of coal bed methane. However, the effects of increased CO2 concentration, especially on organic matter rich formations, are rarely investigated. The injected CO2 will dissolve in the pore water, causing a decrease in pH and resulting in acidic formation waters. Huge amounts of low molecular weight organic acids (LMWOAs) are chemically bound to the macromolecular matrix of sedimentary organic matter and may be liberated by hydrolysis, which is enhanced by the acidic porewater. Recent investigations outlined the importance of LMWOAs as a feedstock for microbial life in the subsurface [1]. Therefore, injection of CO2 into coal formations may result in enhanced nutrient supply for subsurface microbes. To investigate the effect of high concentrations of dissolved CO2 on the release of LMWOAs from coal we developed an inexpensive high-pressure high temperature system that allows manipulating the partial pressure of dissolved gases at pressures and temperatures up to 60 MPa and 120° C, respectively. In a reservoir vessel, gases are added to saturate the extraction medium to the desired level. Inside the extraction vessel hangs a flexible and inert PVDF sleeve (polyvinylidene fluoride, almost impermeable for gases), holding the sample and separating it from the pressure fluid. The flexibility of the sleeve allows for subsampling without loss of pressure. Coal samples from the DEBITS-1 well, Waikato Basin, NZ (R0 = 0.29, TOC = 30%). were extracted at 90° C and 5 MPa, either with pure or CO2-saturated water. Subsamples were taken at different time points during the extraction. The extracted LMWOAs such as formate, acetate and oxalate were analysed by ion chromatography. Yields of LMWOAs were higher with pure water than with CO2

  19. Macromolecular Coating Enables Tunable Selectivity in a Porous PDMS Matrix.

    Science.gov (United States)

    Winkeljann, Benjamin; Käsdorf, Benjamin T; Boekhoven, Job; Lieleg, Oliver

    2018-02-01

    Whether for laboratory use or clinical practice, many fields in Life Sciences require selective filtering. However, most existing filter systems lack the ability to easily tune their filtration behavior. Two key elements for efficient filtering are a high surface-to-volume ratio and the presence of suitable chemical groups which establish selectivity. In this study, an artificial PDMS-based capillary system with highly tunable selectivity properties is presented. The high surface-to-volume ratio of this filter system is generated by first embedding sugar fibers into a synthetic polymer matrix and then dissolving these fibers from the cured polymer. To functionalize this filter, the inner surface of the capillaries is coated with purified or synthetic macromolecules. Depending on the type of macromolecule used for filter functionalization, selective sieving is observed based on steric hindrance, electrostatic binding, electrostatic repulsion, or specific binding interactions. Furthermore, it is demonstrated that enzymes can be immobilized in the capillary system which allows for performing multiple cycles of enzymatic reactions with the same batch of enzymes and without the need to separate the enzymes from their reaction products. In addition to lab-scale filtration and enzyme immobilization applications demonstrated here, the functionalized porous PDMS matrix may also be used to test binding interactions between different molecules. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. The effect of macromolecular crowding on the structure of the protein complex superoxide dismutase

    Science.gov (United States)

    Rajapaksha Mudalige, Ajith Rathnaweera

    Biological environments contain between 7 - 40% macromolecules by volume. This reduces the available volume for macromolecules and elevates the osmotic pressure relative to pure water. Consequently, biological macromolecules in their native environments tend to adopt more compact and dehydrated conformations than those in vitro. This effect is referred to as macromolecular crowding and constitutes an important physical difference between native biological environments and the simple solutions in which biomolecules are usually studied. We used small angle scattering (SAS) to measure the effects of macromolecular crowding on the size of a protein complex, superoxide dismutase (SOD). Crowding was induced using 400 MW polyethylene glycol (PEG), triethylene glycol (TEG), methyl-alpha-glucoside (alpha-MG) and trimethylamine N-oxide (TMAO). Parallel small angle neutron scattering (SANS) and small angle X-ray scattering (SAXS) allowed us to unambiguously attribute apparent changes in radius of gyration to changes in the structure of SOD. For a 40% PEG solution, we find that the volume of SOD was reduced by 9%. SAS coupled with osmotic pressure measurements allowed us to estimate a compressibility modulus for SOD. We believe this to be the first time the osmotic compressibility of a protein complex was measured. Molecular Dynamics (MD) simulations are widely used to obtain insights on biomolecular processes. However, it is not clear whether MD is capable of predicting subtle effects of macromolecular crowding. We used our experimentally observed compressibility of SOD to evaluate the ability of MD to predict macromolecular crowding. Effects of macromolecular crowding due to PEG on SOD were modeled using an all atom MD simulation with the CHARMM forcefield and the crystallographically resolved structures of SOD and PEG. Two parallel MD simulations were performed for SOD in water and SOD in 40% PEG for over 150~ns. Over the period of the simulation the SOD structure in 40