Science.gov

Sample records for knotted reactor coupled

  1. Activated carbon-modified knotted reactor coupled to electrothermal atomic absorption spectrometry for sensitive determination of arsenic species in medicinal herbs and tea infusions

    NASA Astrophysics Data System (ADS)

    Grijalba, Alexander Castro; Martinis, Estefanía M.; Lascalea, Gustavo E.; Wuilloud, Rodolfo G.

    2015-01-01

    A flow injection system based on a modified polytetrafluoroethylene (PTFE) knotted reactor (KR) was developed for arsenite [As(III)] and arsenate [As(V)] species preconcentration and determination by electrothermal atomic absorption spectrometry (ETAAS). Activated carbon (AC) was immobilized on the inner walls of a PTFE KR by a thermal treatment. A significant increase in analyte retention was obtained with the AC-modified KR (100%) as compared to the regular PTFE KR (25%). The preconcentration method involved the on-line formation of As(III)-ammonium pyrrolidinedithiocarbamate (As-APDC) complex, followed by its adsorption onto the inner walls of the AC-modified KR. After analyte retention, the complex was eluted with acetone directly into the graphite furnace of ETAAS. The parameters affecting the flow injection system were evaluated with a full central composite face centered design with three center points. Under optimum conditions, a preconcentration factor of 200 was obtained with 10 ml of sample. The detection limit was 4 ng L- 1 and the relative standard deviation (RSD) for six replicate measurements at 0.2 μg L- 1 of As were 4.3% and 4.7% for As(III) and As(V), respectively. The developed methodology was highly selective towards As(III), while As(V), monomethylarsonic acid [MMA(V)] and dimethylarsinic [DMA(V)] were not retained in the AC-modified KR. The proposed method was successfully applied for As speciation analysis in infusions originated from medicinal herbs and tea.

  2. Fused fiber micro-knots.

    PubMed

    Shahal, Shir; Klein, Avi; Masri, Gilad; Fridman, Moti

    2016-06-10

    We present fusing of a fiber micro-knot by a CO2 laser beam. We demonstrate tuning of the coupling strength and tuning of the spectral resonance of the micro-knot by the fusing process. The experimental results reveal that fusing the fiber micro-knots increases the coupling efficiency and improves the robustness and the stability of the micro-knots. PMID:27409009

  3. Tying the knot with next-generation reactors: Can the industry afford a second marriage

    SciTech Connect

    Not Available

    1993-01-01

    This article examines the future of nuclear power beyond the year 2000. The nuclear industry just celebrated 50 years of nuclear technology, but no new plants have been ordered in the US since 1978 and some European countries are giving up on the nuclear option. This article discusses the four US advanced light-water reactor design and safety features, specific design features and parameters for the advanced designs, advanced designs from Europe, features utilities look for in a reactor, evolutionary versus passive designs, gaining public acceptance for new designs, and what alternatives are there to installing next-generation nuclear systems

  4. Ileosigmoid knotting.

    PubMed

    Mallick, I H; Winslet, M C

    2004-07-01

    Intestinal obstruction is a common cause of emergency surgical admission. The most frequent causes are well known and may often be safely treated conservatively in the first instance. The rarer causes of intestinal obstruction require prompt diagnosis and surgery if they are not to progress rapidly to strangulation and gangrene. One such cause is the ileosigmoid knotting, which is associated with a high morbidity and mortality. With increasing travel activity and population migration this condition is now being seen outside its original geographical sites of origin. This article focuses on the aetiology, pathophysiology, clinical features, investigations and the various surgical options for the management of the ileosigmoid knotting. Studies and case reports in English literature were identified by PubMed, ISIS, Embase and CAS searches between the years 1966-2004 using the following free text keywords: ileo- sigmoid knotting, ileosigmoid knot(ting), intestinal knot(ting), compound volvulus and double volvulus. All the reference lists were reviewed to retrieve additional articles. Aggressive resuscitation, prompt surgical relief of obstruction, appropriate antibiotics, accurate intra-operative assessment of the viability of the involved loops of intestine and the use of modern postoperative intensive care will help reduce the mortality and morbidity associated with this life threatening condition. PMID:15206962

  5. Three-dimensional printed knotted reactors enabling highly sensitive differentiation of silver nanoparticles and ions in aqueous environmental samples.

    PubMed

    Su, Cheng-Kuan; Hsieh, Meng-Hsuan; Sun, Yuh-Chang

    2016-03-31

    Whether silver nanoparticles (AgNPs) persist or release silver ions (Ag(+)) when discharged into a natural environment has remained an unresolved issue. In this study, we employed a low-cost stereolithographic three-dimensional printing (3DP) technology to fabricate the angle-defined knotted reactors (KRs) to construct a simple differentiation scheme for quantitative assessment of Ag(+) ions and AgNPs in municipal wastewater samples. We chose xanthan/phosphate-buffered saline as a dispersion medium for in situ stabilization of the two silver species, while also facilitating their extraction from complicated wastewater matrices. After method optimization, we measured extraction efficiencies of 54.5 and 32.3% for retaining Ag(+) ions and AgNPs, respectively, in the printed KR (768-turn), with detection limits (DLs) of 0.86 and 0.52 ng L(-1) when determining Ag(+) ions and AgNPs, respectively (sample run at pH 11 without a rinse solution), and 0.86 ng L(-1) when determining Ag(+) ions alone (sample run at pH 12 with a 1.5-mL rinse solution). The proposed scheme is tolerant of the wastewater matrix and provides more reliable differentiation between Ag(+)/AgNPs than does a conventional filtration method. The concept and applicability of adopting 3DP technology to renew traditional KR devices were evidently proven by means of these significantly improved analytical performance. Our analytical data suggested that the concentrations of Ag(+) ions and AgNPs in the tested industrial wastewater sample were both higher than those in domestic wastewater, implying that industrial activity might be a main source of environmental silver species, rather than domestic discharge from AgNP-containing products. PMID:26965333

  6. Subknots in ideal knots, random knots, and knotted proteins

    PubMed Central

    Rawdon, Eric J.; Millett, Kenneth C.; Stasiak, Andrzej

    2015-01-01

    We introduce disk matrices which encode the knotting of all subchains in circular knot configurations. The disk matrices allow us to dissect circular knots into their subknots, i.e. knot types formed by subchains of the global knot. The identification of subknots is based on the study of linear chains in which a knot type is associated to the chain by means of a spatially robust closure protocol. We characterize the sets of observed subknot types in global knots taking energy-minimized shapes such as KnotPlot configurations and ideal geometric configurations. We compare the sets of observed subknots to knot types obtained by changing crossings in the classical prime knot diagrams. Building upon this analysis, we study the sets of subknots in random configurations of corresponding knot types. In many of the knot types we analyzed, the sets of subknots from the ideal geometric configurations are found in each of the hundreds of random configurations of the same global knot type. We also compare the sets of subknots observed in open protein knots with the subknots observed in the ideal configurations of the corresponding knot type. This comparison enables us to explain the specific dispositions of subknots in the analyzed protein knots. PMID:25753957

  7. Oligothiophene catenanes and knots: a theoretical study.

    PubMed

    Fomine, Serguei; Guadarrama, Patricia

    2006-08-24

    Oligothiophene [2]catenanes and knots containing up to 28 thiophene units have been studied at the BHandHLYP/3-21G level of theory. Small knots (less than 22 thiophene units) and [2]catenanes (less than 18 thiophene units) are strained molecules. Larger knots and [2]catenanes are almost strain-free. [2]Catenanes and knots having less than 18 and 24 units, respectively, show transversal electronic coupling destroying one-dimensionality of molecules reflecting in smaller band gaps compared to larger knots and catenanes. Ionization potentials of knots and catenanes are always higher compared to that of lineal oligomers due to less effective conjugation. Polaron formation in catenanes is delocalized only over one ring, leaving another intact. In the case of a knot containing 22 thiophene units, estimated polaron delocalization is 8 to 9 repeating units. PMID:16913684

  8. A Midsummer Knot's Dream

    ERIC Educational Resources Information Center

    Henrich, A.; MacNaughton, N.; Narayan, S.; Pechenik, O.; Silversmith, R.; Townsend, J.

    2011-01-01

    We introduce playing games on the shadows of knots and demonstrate two novel games, namely, "To Knot or Not to Knot" and "Much Ado about Knotting." We discuss winning strategies for these games on certain families of knot shadows and go on to suggest variations of these games for further study.

  9. Coupling Schemes for Multiphysics Reactor Simulation

    SciTech Connect

    Vijay Mahadeven; Jean Ragusa

    2007-11-01

    This report documents the progress of the student Vijay S. Mahadevan from the Nuclear Engineering Department of Texas A&M University over the summer of 2007 during his visit to the INL. The purpose of his visit was to investigate the physics-based preconditioned Jacobian-free Newton-Krylov method applied to physics relevant to nuclear reactor simulation. To this end he studied two test problems that represented reaction-diffusion and advection-reaction. These two test problems will provide the basis for future work in which neutron diffusion, nonlinear heat conduction, and a twophase flow model will be tightly coupled to provide an accurate model of a BWR core.

  10. IET. Coupling station. Man holds flexible couplers to reactor Dolly ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    IET. Coupling station. Man holds flexible couplers to reactor Dolly and HTRE rig. Date: April 22, 1955. INEEL negative no. 55-1010 - Idaho National Engineering Laboratory, Test Area North, Scoville, Butte County, ID

  11. Coupled IVPs to Investigate a Nuclear Reactor Poison Burn Up

    SciTech Connect

    Faghihi, F.

    2009-09-09

    A set of coupled IVPs that describe the change rate of an important poison, in a nuclear reactor, has been written herein. Specifically, in this article, we have focused on the samarium-149 (as a poison) burnup in a desired pressurized water nuclear reactor and its concentration are given using our MATLAB-linked 'solver'.

  12. COUPLED FAST-THERMAL POWER BREEDER REACTOR

    DOEpatents

    Avery, R.

    1961-07-18

    A nuclear reactor having a region operating predominantly on fast neutrons and another region operating predominantly on slow neutrons is described. The fast region is a plutonium core and the slow region is a natural uranium blanket around the core. Both of these regions are free of moderator. A moderating reflector surrounds the uranium blanket. The moderating material and thickness of the reflector are selected so that fissions in the uranium blanket make a substantial contribution to the reactivity of the reactor.

  13. Coupled reactor kinetics and heat transfer model for heat pipe cooled reactors

    NASA Astrophysics Data System (ADS)

    Wright, Steven A.; Houts, Michael

    2001-02-01

    Heat pipes are often proposed as cooling system components for small fission reactors. SAFE-300 and STAR-C are two reactor concepts that use heat pipes as an integral part of the cooling system. Heat pipes have been used in reactors to cool components within radiation tests (Deverall, 1973); however, no reactor has been built or tested that uses heat pipes solely as the primary cooling system. Heat pipe cooled reactors will likely require the development of a test reactor to determine the main differences in operational behavior from forced cooled reactors. The purpose of this paper is to describe the results of a systems code capable of modeling the coupling between the reactor kinetics and heat pipe controlled heat transport. Heat transport in heat pipe reactors is complex and highly system dependent. Nevertheless, in general terms it relies on heat flowing from the fuel pins through the heat pipe, to the heat exchanger, and then ultimately into the power conversion system and heat sink. A system model is described that is capable of modeling coupled reactor kinetics phenomena, heat transfer dynamics within the fuel pins, and the transient behavior of heat pipes (including the melting of the working fluid). This paper focuses primarily on the coupling effects caused by reactor feedback and compares the observations with forced cooled reactors. A number of reactor startup transients have been modeled, and issues such as power peaking, and power-to-flow mismatches, and loading transients were examined, including the possibility of heat flow from the heat exchanger back into the reactor. This system model is envisioned as a tool to be used for screening various heat pipe cooled reactor concepts, for designing and developing test facility requirements, for use in safety evaluations, and for developing test criteria for in-pile and out-of-pile test facilities. .

  14. Oxidative coupling of methane using inorganic membrane reactor

    SciTech Connect

    Ma, Y.H.; Moser, W.R.; Dixon, A.G.

    1995-12-31

    The goal of this research is to improve the oxidative coupling of methane in a catalytic inorganic membrane reactor. A specific target is to achieve conversion of methane to C{sub 2} hydrocarbons at very high selectivity and relatively higher yields than in fixed bed reactors by controlling the oxygen supply through the membrane. A membrane reactor has the advantage of precisely controlling the rate of delivery of oxygen to the catalyst. This facility permits balancing the rate of oxidation and reduction of the catalyst. In addition, membrane reactors minimize the concentration of gas phase oxygen thus reducing non selective gas phase reactions, which are believed to be a main route for formation of CO{sub x} products. Such gas phase reactions are a cause for decreased selectivity in oxidative coupling of methane in conventional flow reactors. Membrane reactors could also produce higher product yields by providing better distribution of the reactant gases over the catalyst than the conventional plug flow reactors. Modeling work which aimed at predicting the observed experimental trends in porous membrane reactors was also undertaken in this research program.

  15. Reactor modeling of the oxidative coupling of methane in membranes reactors

    SciTech Connect

    Lu, Y.; Ramachandra, A.; Ma, Y.H.

    1994-12-31

    A reactor model has been developed to analyze the performance of membrane reactors for the high temperature oxidative coupling of methane and to compare their operation with fixed bed reactors. Three reactor configurations of the shell and tube type were this study: a conventional fixed bed reactor, a tubular porous membrane reactor, dense membrane reactor. For the membrane reactors, oxygen is fed on the shell side and methane into the tube side, and the catalyst is present only inside the tube. Both streams are diluted with helium and the feed ratio is maintained at a methane to oxygen ratio of 2:1 for all three configurations. The ratio of the volumetric flow rate of each reactant to the amount of catalyst is kept the same for the three configurations. Kinetic equations for the oxidative coupling of methane have been taken from the simplified mechanism on Li/MgO proposed by Tung and Lobban, where C{sub 2}H{sub 6}, CO{sub 2} and H{sub 2}O are the reaction products considered. The modeling study indicates an improved performance of the membrane reactors over the conventional packed bed reactor. For the porous membrane reactor, a 4 angstrom pore size membrane gives higher C{sub 2}H{sub 6} selectivities and C{sub 2}H{sub 6} yields than a 40 Angstrom pore size membrane. For the dense membrane reactor, a lower oxygen permeability gives higher C{sub 2}H{sub 6} yield. Of the three types of reactors, the dense membrane reactor offers the highest C{sub 2}H{sub 6} yields but a longer reactor length is needed because of the lower permeation rate of oxygen from the shell to the tube side, and hence the lower oxygen partial pressure and lower reaction rate on the tube side.

  16. OXIDATIVE COUPLING OF METHANE USING INORGANIC MEMBRANE REACTORS

    SciTech Connect

    Dr. Y.H. Ma; Dr. W.R. Moser; Dr. A.G. Dixon; Dr. A.M. Ramachandra; Dr. Y. Lu; C. Binkerd

    1998-04-01

    The objective of this research is to study the oxidative coupling of methane in catalytic inorganic membrane reactors. A specific target is to achieve conversion of methane to C{sub 2} hydrocarbons at very high selectivity and higher yields than in conventional non-porous, co-feed, fixed bed reactors by controlling the oxygen supply through the membrane. A membrane reactor has the advantage of precisely controlling the rate of delivery of oxygen to the catalyst. This facility permits balancing the rate of oxidation and reduction of the catalyst. In addition, membrane reactors minimize the concentration of gas phase oxygen thus reducing non selective gas phase reactions, which are believed to be a main route for the formation of CO{sub x} products. Such gas phase reactions are a cause of decreased selectivity in the oxidative coupling of methane in conventional flow reactors. Membrane reactors could also produce higher product yields by providing better distribution of the reactant gases over the catalyst than the conventional plug flow reactors. Membrane reactor technology also offers the potential for modifying the membranes both to improve catalytic properties as well as to regulate the rate of the permeation/diffusion of reactants through the membrane to minimize by-product generation. Other benefits also exist with membrane reactors, such as the mitigation of thermal hot-spots for highly exothermic reactions such as the oxidative coupling of methane. The application of catalytically active inorganic membranes has potential for drastically increasing the yield of reactions which are currently limited by either thermodynamic equilibria, product inhibition, or kinetic selectivity.

  17. Nuclear reactor remote disconnect control rod coupling indicator

    DOEpatents

    Vuckovich, Michael

    1977-01-01

    A coupling indicator for use with nuclear reactor control rod assemblies which have remotely disengageable couplings between the control rod and the control rod drive shaft. The coupling indicator indicates whether the control rod and the control rod drive shaft are engaged or disengaged. A resistive network, utilizing magnetic reed switches, senses the position of the control rod drive mechanism lead screw and the control rod position indicating tube, and the relative position of these two elements with respect to each other is compared to determine whether the coupling is engaged or disengaged.

  18. Nonionic micellar liquid chromatography coupled to immobilized enzyme reactors.

    PubMed

    Tomer, S; Dorsey, J G; Berthod, A

    2001-07-20

    Immobilized enzyme reactors are used as post-column reactors to modify the detectability of analytes. An immobilized amino acid oxidase reactor was prepared and coupled to an immobilized peroxidase reactor to detect low level of amino acids by fluorescence of the homovanilic dimer produced. A cholesterol oxidase reactor was prepared to detect cholesterol and metabolites by 241 nm UV absorbance of the enone produced. The preparation of the porous glass beads with the immobilized enzymes is described. Micellar liquid chromatography is used with non-ionic micellar phases to separate the amino acids or cholesterol derivatives. It is demonstrated that the non ionic Brij 35 micellar phases are very gentle for the enzyme activity allowing the reactor activity to remain at a higher level and for a much longer time than with hydro-organic classical chromatographic mobile phases or aqueous buffers. The coupling of nonionic micellar phases with enzymatic detection gave limits of detection of 32 pmol (4.8 ng injected) of methionine and 50 pmol (19 ng injected) of 20alpha-hydroxy cholesterol. The immobilized enzyme reactors could be used continuously for a week without losing their activity. It is shown that the low efficiency obtained with micellar liquid chromatography is compensated by the possibility offered by the technique to easily adjust selectivity. PMID:11510562

  19. Parity in knot theory

    SciTech Connect

    Manturov, Vassily O

    2010-06-29

    In this work we study knot theories with a parity property for crossings: every crossing is declared to be even or odd according to a certain preassigned rule. If this rule satisfies a set of simple axioms related to the Reidemeister moves, then certain simple invariants solving the minimality problem can be defined, and invariant maps on the set of knots can be constructed. The most important example of a knot theory with parity is the theory of virtual knots. Using the parity property arising from Gauss diagrams we show that even a gross simplification of the theory of virtual knots, namely, the theory of free knots, admits simple and highly nontrivial invariants. This gives a solution to a problem of Turaev, who conjectured that all free knots are trivial. In this work we show that free knots are generally not invertible, and provide invariants which detect the invertibility of free knots. The passage to ordinary virtual knots allows us to strengthen known invariants (such as the Kauffman bracket) using parity considerations. We also discuss other examples of knot theories with parity. Bibliography: 27 items.

  20. [DNA knots and strong triviality].

    PubMed

    Torisu, Ichiro

    2009-06-01

    A circle embedded in 3-space without self-intersection is called a knot. A knot is a mathematical object according to topology. Knot theory studies how complicated a given knot is, or whether it is trivial. Any knot can be represented by a diagram with above and below information at the crossings. Then a knot obtained by replacing the information at one crossing is generally another knot. This operation is called a crossing change. A crossing change is an important notion in knot theory. In this article, we survey the strong triviality of knots, which is one of the multi-crossing changes. PMID:19530562

  1. Knot theory realizations in nematic colloids.

    PubMed

    Čopar, Simon; Tkalec, Uroš; Muševič, Igor; Žumer, Slobodan

    2015-02-10

    Nematic braids are reconfigurable knots and links formed by the disclination loops that entangle colloidal particles dispersed in a nematic liquid crystal. We focus on entangled nematic disclinations in thin twisted nematic layers stabilized by 2D arrays of colloidal particles that can be controlled with laser tweezers. We take the experimentally assembled structures and demonstrate the correspondence of the knot invariants, constructed graphs, and surfaces associated with the disclination loop to the physically observable features specific to the geometry at hand. The nematic nature of the medium adds additional topological parameters to the conventional results of knot theory, which couple with the knot topology and introduce order into the phase diagram of possible structures. The crystalline order allows the simplified construction of the Jones polynomial and medial graphs, and the steps in the construction algorithm are mirrored in the physics of liquid crystals. PMID:25624467

  2. Knot theory realizations in nematic colloids

    PubMed Central

    Čopar, Simon; Tkalec, Uroš; Muševič, Igor; Žumer, Slobodan

    2015-01-01

    Nematic braids are reconfigurable knots and links formed by the disclination loops that entangle colloidal particles dispersed in a nematic liquid crystal. We focus on entangled nematic disclinations in thin twisted nematic layers stabilized by 2D arrays of colloidal particles that can be controlled with laser tweezers. We take the experimentally assembled structures and demonstrate the correspondence of the knot invariants, constructed graphs, and surfaces associated with the disclination loop to the physically observable features specific to the geometry at hand. The nematic nature of the medium adds additional topological parameters to the conventional results of knot theory, which couple with the knot topology and introduce order into the phase diagram of possible structures. The crystalline order allows the simplified construction of the Jones polynomial and medial graphs, and the steps in the construction algorithm are mirrored in the physics of liquid crystals. PMID:25624467

  3. Tightly Coupled Multiphysics Algorithm for Pebble Bed Reactors

    SciTech Connect

    HyeongKae Park; Dana Knoll; Derek Gaston; Richard Martineau

    2010-10-01

    We have developed a tightly coupled multiphysics simulation tool for the pebble-bed reactor (PBR) concept, a type of Very High-Temperature gas-cooled Reactor (VHTR). The simulation tool, PRONGHORN, takes advantages of the Multiphysics Object-Oriented Simulation Environment library, and is capable of solving multidimensional thermal-fluid and neutronics problems implicitly with a Newton-based approach. Expensive Jacobian matrix formation is alleviated via the Jacobian-free Newton-Krylov method, and physics-based preconditioning is applied to minimize Krylov iterations. Motivation for the work is provided via analysis and numerical experiments on simpler multiphysics reactor models. We then provide detail of the physical models and numerical methods in PRONGHORN. Finally, PRONGHORN's algorithmic capability is demonstrated on a number of PBR test cases.

  4. Localized patterns in homogeneous networks of diffusively coupled reactors

    NASA Astrophysics Data System (ADS)

    Moore, Peter K.; Horsthemke, Werner

    2005-06-01

    We study the influence of network topology on instabilities of the homogeneous steady state of diffusively coupled, monostable nonlinear cells. A particular focus are diffusion-induced instabilities, i.e., Turing instabilities. We present various theorems that make it possible to determine analytically the stability properties of networks with arbitrary topologies and general monostable dynamics of the individual cells. This work aims in particular to determine those topologies that will give rise to localized stationary patterns. Specific examples focus on well-stirred chemical reactors. The reactors are coupled by diffusion-like mass transfer, and the kinetics is given by the Lengyel-Epstein model, a two-variable scheme for the chlorine dioxide-iodine-malonic acid reaction.

  5. Coupled simulation of the reactor core using CUPID/MASTER

    SciTech Connect

    Lee, J. R.; Cho, H. K.; Yoon, H. Y.; Jeong, J. J.

    2012-07-01

    The CUPID is a component-scale thermal hydraulics code which is aimed for the analysis of transient two-phase flows in nuclear reactor components such as the reactor vessel, steam generator, containment. This code adopts a three-dimensional, transient, two-phase and three-field model, and includes physical models and correlations of the interfacial mass, momentum, and energy transfer for the closure. In the present paper, a multi-physics simulation was performed by coupling CUPID with a three dimensional neutron kinetics code, MASTER. MASTER is merged into CUPID as a dynamic link library (DLL). The APR1400 reactor core during a control rod drop/ejection accident was simulated as an example by adopting a porous media approach to employ a fuel assembly. The following sections present the numerical modeling for the reactor core, coupling of the kinetics code, and the simulation results. And also, a preliminary study for multi-scale simulation between CUPID and system-scaled thermal hydraulics code, MARS will be introduced as well. (authors)

  6. Root-knot nematodes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although root-knot nematodes (Meloidogyne species) can reduce crop yields worldwide, methods for their identification are often difficult to implement. This review summarizes the diagnostic morphological and molecular features for distinguishing the ten major previously described root-knot nematode ...

  7. Lattice invariants for knots

    SciTech Connect

    Janse Van Rensburg, E.J.

    1996-12-31

    The geometry of polygonal knots in the cubic lattice may be used to define some knot invariants. One such invariant is the minimal edge number, which is the minimum number of edges necessary (and sufficient) to construct a lattice knot of given type. In addition, one may also define the minimal (unfolded) surface number, and the minimal (unfolded) boundary number; these are the minimum number of 2-cells necessary to construct an unfolded lattice Seifert surface of a given knot type in the lattice, and the minimum number of edges necessary in a lattice knot to guarantee the existence of an unfolded lattice Seifert surface. In addition, I derive some relations amongst these invariants. 8 refs., 5 figs., 2 tabs.

  8. Tying quantum knots

    NASA Astrophysics Data System (ADS)

    Hall, D. S.; Ray, M. W.; Tiurev, K.; Ruokokoski, E.; Gheorghe, A. H.; Möttönen, M.

    2016-05-01

    As topologically stable objects in field theories, knots have been put forward to explain various persistent phenomena in systems ranging from atoms and molecules to cosmic textures in the universe. Recent experiments have reported the observation of knots in different classical contexts. However, no experimental observation of knots has yet been reported in quantum matter. Here we demonstrate the experimental creation and detection of knot solitons in the order parameter of a spinor Bose-Einstein condensate. The observed texture corresponds to a topologically nontrivial element of the third homotopy group and exhibits the celebrated Hopf fibration, which unites many seemingly unrelated physical phenomena. Our work calls for future studies of the stability and dynamics knot solitons in the quantum regime.

  9. Untying knots in proteins.

    PubMed

    Sułkowska, Joanna I; Sułkowski, Piotr; Szymczak, Piotr; Cieplak, Marek

    2010-10-13

    A shoelace can be readily untied by pulling its ends rather than its loops. Attempting to untie a native knot in a protein can also succeed or fail depending on where one pulls. However, thermal fluctuations induced by the surrounding water affect conformations stochastically and may add to the uncertainty of the outcome. When the protein is pulled by the termini, the knot can only get tightened, and any attempt at untying results in failure. We show that, by pulling specific amino acids, one may easily retract a terminal segment of the backbone from the knotting loop and untangle the knot. At still other amino acids, the outcome of pulling can go either way. We study the dependence of the untying probability on the way the protein is grasped, the pulling speed, and the temperature. Elucidation of the mechanisms underlying this dependence is critical for a successful experimental realization of protein knot untying. PMID:20857930

  10. Knot Theory with Young Children

    ERIC Educational Resources Information Center

    Handa, Yuichi; Mattman, Thomas

    2008-01-01

    There are many interesting explorations that can be done in knot theory, the study of mathematical knots. This article offers some knot theory activities that are appropriate for elementary grade children. These activities teach some basic concepts from knot theory as a natural extension of commonly-taught geometric ideas. (Contains 10 figures.)

  11. Multiple steady states in coupled flow tank reactors

    NASA Astrophysics Data System (ADS)

    Hunt, Katharine L. C.; Kottalam, J.; Hatlee, Michael D.; Ross, John

    1992-05-01

    Coupling between continuous-flow, stirred tank reactors (CSTR's), each having multiple steady states, can produce new steady states with different concentrations of the chemical species in each of the coupled tanks. In this work, we identify a kinetic potential ψ that governs the deterministic time evolution of coupled tank reactors, when the reaction mechanism permits a single-variable description of the states of the individual tanks; examples include the iodate-arsenous acid reaction, a cubic model suggested by Noyes, and two quintic models. Stable steady states correspond to minima of ψ, and unstable steady states to maxima or saddle points; marginally stable states typically correspond to saddle-node points. We illustrate the variation in ψ due to changes in the rate constant for external material intake (k0) and for exchange between tanks (kx). For fixed k0 values, we analyze the changes in numbers and types of steady states as kx increases from zero. We show that steady states disappear by pairwise coalescence; we also show that new steady states may appear with increasing kx, when the reaction mechanism is sufficiently complex. For fixed initial conditions, the steady state ultimately reached in a mixing experiment may depend on the exchange rate constant as a function of time, kx(t) : Adiabatic mixing is obtained in the limit of slow changes in kx(t) and instantaneous mixing in the limit as kx(t)→∞ while t remains small. Analyses based on the potential ψ predict the outcome of mixing experiments for arbitrary kx(t). We show by explicit counterexamples that a prior theory developed by Noyes does not correctly predict the instability points or the transitions between steady states of coupled tanks, to be expected in mixing experiments. We further show that the outcome of such experiments is not connected to the relative stability of steady states in individual tank reactors. We find that coupling may effectively stabilize the tanks. We provide

  12. On universal knot polynomials

    NASA Astrophysics Data System (ADS)

    Mironov, A.; Mkrtchyan, R.; Morozov, A.

    2016-02-01

    We present a universal knot polynomials for 2- and 3-strand torus knots in adjoint representation, by universalization of appropriate Rosso-Jones formula. According to universality, these polynomials coincide with adjoined colored HOMFLY and Kauffman polynomials at SL and SO/Sp lines on Vogel's plane, respectively and give their exceptional group's counterparts on exceptional line. We demonstrate that [m,n]=[n,m] topological invariance, when applicable, take place on the entire Vogel's plane. We also suggest the universal form of invariant of figure eight knot in adjoint representation, and suggest existence of such universalization for any knot in adjoint and its descendant representations. Properties of universal polynomials and applications of these results are discussed.

  13. CRDIAC: Coupled Reactor Depletion Instrument with Automated Control

    SciTech Connect

    Steven K. Logan

    2012-08-01

    When modeling the behavior of a nuclear reactor over time, it is important to understand how the isotopes in the reactor will change, or transmute, over that time. This is especially important in the reactor fuel itself. Many nuclear physics modeling codes model how particles interact in the system, but do not model this over time. Thus, another code is used in conjunction with the nuclear physics code to accomplish this. In our code, Monte Carlo N-Particle (MCNP) codes and the Multi Reactor Transmutation Analysis Utility (MRTAU) were chosen as the codes to use. In this way, MCNP would produce the reaction rates in the different isotopes present and MRTAU would use cross sections generated from these reaction rates to determine how the mass of each isotope is lost or gained. Between these two codes, the information must be altered and edited for use. For this, a Python 2.7 script was developed to aid the user in getting the information in the correct forms. This newly developed methodology was called the Coupled Reactor Depletion Instrument with Automated Controls (CRDIAC). As is the case in any newly developed methodology for modeling of physical phenomena, CRDIAC needed to be verified against similar methodology and validated against data taken from an experiment, in our case AFIP-3. AFIP-3 was a reduced enrichment plate type fuel tested in the ATR. We verified our methodology against the MCNP Coupled with ORIGEN2 (MCWO) method and validated our work against the Post Irradiation Examination (PIE) data. When compared to MCWO, the difference in concentration of U-235 throughout Cycle 144A was about 1%. When compared to the PIE data, the average bias for end of life U-235 concentration was about 2%. These results from CRDIAC therefore agree with the MCWO and PIE data, validating and verifying CRDIAC. CRDIAC provides an alternative to using ORIGEN-based methodology, which is useful because CRDIAC's depletion code, MRTAU, uses every available isotope in its depletion

  14. PFC Abatement in Capacitevely-Coupled Plasma Reactor

    NASA Astrophysics Data System (ADS)

    Porshnev, P. I.; Alaoui, M.; Diamant, Stela; Francis, Terry; Raoux, Sebastien; Woolston, Mike

    2001-10-01

    A low-pressure plasma reactor, was developed to reduce PFC emissions of dielectric etch tools, is a point-of-use environmentally and economically sound solution. Generally, local electric fields in capacitively-coupled (CC) plasmas are higher than in inductively-coupled (IC) plasmas. As a result, electron energy distributions in CC plasmas have more pronounced high-energy part compared to the ones in IC plasmas. This is particularly important for effective breaking of the strong C-F bonds, which dissociation potentials are observably higher than the average electron energy. CC plasma in the Pegasys (Plasma Exhaust Gas Abatement SYStem) reactor was found to be in so-called g-regime, in which ionization is provided with secondary emission electrons. Though in these plasmas, the majority of electrons still reside in plasma bulk, the most important discharge characteristics, in particular, the abatement efficiency, are determined by highly-energetic electrons from sheath zones. With water being added to the incoming gas mixture, better than 95% destruction removal efficiency of the PFCs has been achieved for all dielectric etch applications. CC plasma-based abatement significantly differs from existing abatement methods, especially combustion and catalytic oxidation, which are much less environmentally friendly and economically viable.

  15. Simple Coupling of Reactor Physics Effects and Uncertain Nuances

    Energy Science and Technology Software Center (ESTSC)

    2012-08-27

    The "Simple Coupling of Reactor Physics Effects and Uncertain Nuances" (SCORPEUN) code is a simple r-z 1-group neutron diffusion code where each r-mesh is coupled to a single-flow-channel model that represents all flow-channels in that r-mesh. This 1-D model assesses q=m*Cp*deletaT for each z-mesh in that channel. This flow channel model is then coupled to a simple 1-D heat conduction model for ascertaining the peak center-line fuel temperature in a hypothetical pin assigned to thatmore » flow channel. The code has property lookup capability for water, Na, Zirc, HT9, metalic fuel, oxide fuel, etc. It has linear interpolation features for micro-scopic cross-sections with respect to coolant density and fuel temperature. ***This last feature has not been fully tested and may need development***. The interpolated microscopic cross-sections are then combined (using the water density from the T/H calculation) to generate macroscopic diffusion coefficient, removal cross-section and nu-sigmaF for each r-z mesh of the neutron diffusion code.« less

  16. Simple Coupling of Reactor Physics Effects and Uncertain Nuances

    SciTech Connect

    Bays, Samuel

    2012-08-27

    The "Simple Coupling of Reactor Physics Effects and Uncertain Nuances" (SCORPEUN) code is a simple r-z 1-group neutron diffusion code where each r-mesh is coupled to a single-flow-channel model that represents all flow-channels in that r-mesh. This 1-D model assesses q=m*Cp*deletaT for each z-mesh in that channel. This flow channel model is then coupled to a simple 1-D heat conduction model for ascertaining the peak center-line fuel temperature in a hypothetical pin assigned to that flow channel. The code has property lookup capability for water, Na, Zirc, HT9, metalic fuel, oxide fuel, etc. It has linear interpolation features for micro-scopic cross-sections with respect to coolant density and fuel temperature. ***This last feature has not been fully tested and may need development***. The interpolated microscopic cross-sections are then combined (using the water density from the T/H calculation) to generate macroscopic diffusion coefficient, removal cross-section and nu-sigmaF for each r-z mesh of the neutron diffusion code.

  17. Knot theory in understanding proteins.

    PubMed

    Mishra, Rama; Bhushan, Shantha

    2012-12-01

    This paper aims to enthuse mathematicians, especially topologists, knot theorists and geometers to examine problems in the study of proteins. We have highlighted those advances and breakthroughs in knot theory that directly and indirectly help in understanding proteins. We have discussed the phenomena of knotting of protein backbone. This paper also provides a few open questions for knot theorists, the answers to which will help in further understanding of proteins. PMID:22105789

  18. pKNOT v.2: the protein KNOT web server.

    PubMed

    Lai, Yan-Long; Chen, Chih-Chieh; Hwang, Jenn-Kang

    2012-07-01

    Knotted proteins have recently received lots of attention due to their interesting topological novelty as well as its puzzling folding mechanisms. We previously published a pKNOT server, which provides a structural database of knotted proteins, analysis tools for detecting and analyzing knotted regions from structures as well as a Java-based 3D graphics viewer for visualizing knotted structures. However, there lacks a convenient platform performing similar tasks directly from 'protein sequences'. In the current version of the web server, referred to as pKNOT v.2, we implement a homology modeling tool such that the server can now accept protein sequences in addition to 3D structures or Protein Data Bank (PDB) IDs and return knot analysis. In addition, we have updated the database of knotted proteins from the current PDB with a combination of automatic and manual procedure. We believe that the updated pKNOT server with its extended functionalities will provide better service to biologists interested in the research of knotted proteins. The pKNOT v.2 is available from http://pknot.life.nctu.edu.tw/. PMID:22693223

  19. Methane coupling by membrane reactor. Quarterly technical progress report, December 25, 1993--March 24, 1994

    SciTech Connect

    Not Available

    1994-06-15

    A comparison study was made between a quartz tube non-porous packed bed reactor and a 40 Angstrom pore size porous VYCOR membrane reactor using two different methane coupling catalysts. Comparisons of reactor performance of the two reactors were made on the basis of amount of methane converted, C{sub 2} selectivities and the total C{sub 2} yields. Identical flow and temperature conditions were maintained for the two reactor systems for this study. These studies appear to indicate that improved performance can be obtained in VYCOR membrane reactors. The product stream from the tube side effluent of the porous VYCOR membrane reactor was superior to that from the quartz tube non-porous reactor in terms of improved C{sub 2} selectivity. At the present stage of research, the total effluent from the membrane reactor compared slightly less favorably to the effluent from a non-porous reactor, but studies are continuing on devising a reactor configuration which increases methane throughput in the tube side of the membrane reactor which is expected to demonstrate the overall superiority of the membrane reactor. Simulation results obtained by doing a parameter study for different reactor systems showed that, for the methane coupling reaction, where the desired product formation had a lower kinetic order with respect to oxygen, improved C{sub 2} yields could be achieved in membrane reactors if the residence times were sufficiently high.

  20. Linked and knotted chimera filaments in oscillatory systems.

    PubMed

    Lau, Hon Wai; Davidsen, Jörn

    2016-07-01

    While the existence of stable knotted and linked vortex lines has been established in many experimental and theoretical systems, their existence in oscillatory systems and systems with nonlocal coupling has remained elusive. Here, we present strong numerical evidence that stable knots and links such as trefoils and Hopf links do exist in simple, complex, and chaotic oscillatory systems if the coupling between the oscillators is neither too short ranged nor too long ranged. In this case, effective repulsive forces between vortex lines in knotted and linked structures stabilize curvature-driven shrinkage observed for single vortex rings. In contrast to real fluids and excitable media, the vortex lines correspond to scroll wave chimeras [synchronized scroll waves with spatially extended (tubelike) unsynchronized filaments], a prime example of spontaneous synchrony breaking in systems of identical oscillators. In the case of complex oscillatory systems, this leads to a topological superstructure combining knotted filaments and synchronization defect sheets. PMID:27575065

  1. Linked and knotted chimera filaments in oscillatory systems

    NASA Astrophysics Data System (ADS)

    Lau, Hon Wai; Davidsen, Jörn

    2016-07-01

    While the existence of stable knotted and linked vortex lines has been established in many experimental and theoretical systems, their existence in oscillatory systems and systems with nonlocal coupling has remained elusive. Here, we present strong numerical evidence that stable knots and links such as trefoils and Hopf links do exist in simple, complex, and chaotic oscillatory systems if the coupling between the oscillators is neither too short ranged nor too long ranged. In this case, effective repulsive forces between vortex lines in knotted and linked structures stabilize curvature-driven shrinkage observed for single vortex rings. In contrast to real fluids and excitable media, the vortex lines correspond to scroll wave chimeras [synchronized scroll waves with spatially extended (tubelike) unsynchronized filaments], a prime example of spontaneous synchrony breaking in systems of identical oscillators. In the case of complex oscillatory systems, this leads to a topological superstructure combining knotted filaments and synchronization defect sheets.

  2. Physics in knots

    SciTech Connect

    Holz, D.; Wheeler, J.A.; Kheyfets, A.; Miller, W.A.

    1992-08-01

    In this report the authors work out the relevant it-form-bit means to measure spacetime curvature. Also described are the essential new features of the knot description of gravity and the one index loop variable and the Einstein tensor. (LSP)

  3. Physics in knots

    SciTech Connect

    Holz, D.; Wheeler, J.A. . Dept. of Physics); Kheyfets, A. . Dept. of Mathematics); Miller, W.A. )

    1992-01-01

    In this report the authors work out the relevant it-form-bit means to measure spacetime curvature. Also described are the essential new features of the knot description of gravity and the one index loop variable and the Einstein tensor. (LSP)

  4. Coupled Monte Carlo neutronics and thermal hydraulics for power reactors

    SciTech Connect

    Bernnat, W.; Buck, M.; Mattes, M.; Zwermann, W.; Pasichnyk, I.; Velkov, K.

    2012-07-01

    The availability of high performance computing resources enables more and more the use of detailed Monte Carlo models even for full core power reactors. The detailed structure of the core can be described by lattices, modeled by so-called repeated structures e.g. in Monte Carlo codes such as MCNP5 or MCNPX. For cores with mainly uniform material compositions, fuel and moderator temperatures, there is no problem in constructing core models. However, when the material composition and the temperatures vary strongly a huge number of different material cells must be described which complicate the input and in many cases exceed code or memory limits. The second problem arises with the preparation of corresponding temperature dependent cross sections and thermal scattering laws. Only if these problems can be solved, a realistic coupling of Monte Carlo neutronics with an appropriate thermal-hydraulics model is possible. In this paper a method for the treatment of detailed material and temperature distributions in MCNP5 is described based on user-specified internal functions which assign distinct elements of the core cells to material specifications (e.g. water density) and temperatures from a thermal-hydraulics code. The core grid itself can be described with a uniform material specification. The temperature dependency of cross sections and thermal neutron scattering laws is taken into account by interpolation, requiring only a limited number of data sets generated for different temperatures. Applications will be shown for the stationary part of the Purdue PWR benchmark using ATHLET for thermal- hydraulics and for a generic Modular High Temperature reactor using THERMIX for thermal- hydraulics. (authors)

  5. A coupled chemical burster: The chlorine dioxide-iodide reaction in two flow reactors

    NASA Astrophysics Data System (ADS)

    Dolnik, Milos; Epstein, Irving R.

    1993-01-01

    The dynamical behavior of the chlorine dioxide-iodide reaction has been studied in a system consisting of two continuous flow stirred tank reactors (CSTRs). The reactors are coupled by computer monitoring of the electrochemical potential in each reactor, which is then used to control the input into the other reactor. Two forms of coupling are employed: reciprocally triggered, exponentially decreasing stimulation, and alternating mass exchange. The reaction, which exhibits oscillatory and excitable behavior in a single CSTR, displays neuronlike bursting behavior with both forms of coupling. Reciprocal stimulation yields bursting in both reactors, while with alternating mass exchange, bursting is observed in one reactor and complex oscillation in the other. A simple model of the reaction gives good agreement between the experimental observations and numerical simulations.

  6. Methane coupling by membrane reactor. Quarterly technical progress report: June 25, 1993--September 24, 1993

    SciTech Connect

    Ma, Yi Hua

    1993-10-28

    Several membranes have been investigated for use in a membrane reactor. Porous VYCOR has been tested for permeability changes with temperature. Three-sectional VYCOR membranes, with a porous central section, have been fabricated and tested in the experimental setup. Catalysts for methane coupling have been reviewed in the literature and five catalysts have been selected. Modeling studies of the methane oxidative coupling reaction in different reactor configurations shows higher C{sub 2} selectivity and yield with membrane reactors as compared to conventional packed bed reactors.

  7. k/not theory.

    PubMed

    Chowdhry, M

    2000-01-01

    SUMMARY This paper discusses the role of the personal experience in the writing process. Using a personal/journal writing style the author charts the journey of a recent play Skin into Rainbows from first draft to production. The author plays with the constructs of writing and juxtapositions these against a form of Knot Theory to measure their value, playing with math and language techniques in a search for truth. PMID:24802683

  8. Metastable Tight Knots in DNA

    NASA Astrophysics Data System (ADS)

    Dai, Liang; Renner, C. Benjamin; Doyle, Patrick

    2015-03-01

    Knotted structures can spontaneously occur in polymers such as DNA and proteins, and the formation of knots affects biological functions, mechanical strength and rheological properties. In this work, we calculate the equilibrium size distribution of trefoil knots in linear DNA using off-lattice simulations. We observe metastable knots on DNA, as predicted by Grosberg and Rabin. Furthermore, we extend their theory to incorporate the finite width of chains and show an agreement between our simulations and the modified theory for real chains. Our results suggest localized knots spontaneously occur in long DNA and the contour length in the knot ranges from 600 to 1800 nm. This research was supported by the National Research Foundation Singapore through the Singapore MIT Alliance for Research and Technology's research program in BioSystems and Micromechanics, the National Science Foundation (Grant No. 1335938).

  9. Dynamic loading of surgical knots.

    PubMed

    Brouwers, J E; Oosting, H; de Haas, D; Klopper, P J

    1991-12-01

    Lately, many suture materials have been introduced. Their physical characteristics in combination with knots are not well known. In this study, seven knots (square--1=1, 2=1, 2=1-S and 1=1=1--and sliding--SxSxS, S=S parallel S and 1-S parallel S parallel S) made in seven suture materials (plain catgut, Dexon [polyglycolic acid)] Maxon [polyglyconate], PDS [polydiaxone], Vicryl [polyglactine 910], Mersilene [polyester fiber], Prolene [polypropylene] were tested dynamically to ascertain tensile strength. The knots were classified as "predominantly breaking" (PB) and "predominantly slipping" (PS). A new method for statistical analysis, the Kaplan-Meier survival estimate, was introduced. Square knots provided good mechanical results but did not prevent slippage completely. Most sliding knots were weak. The 1=1=1 knot was superior. PS knots (1=1, 2=1, SxSxS and S=S parallel S) were unsuitable for surgical practice in monofilament or coated multifilament suture materials. The classification PB and PS knots gave an easy impression of the knot holding capacities. Application of the Kaplan-Meier estimate resulted in a more realistic analysis than classical methods. PMID:1948600

  10. Network topology and Turing instabilities in small arrays of diffusively coupled reactors

    NASA Astrophysics Data System (ADS)

    Horsthemke, Werner; Lam, Kwan; Moore, Peter K.

    2004-08-01

    We study the effect of the network structure on the diffusion-induced instability to nonuniform steady states in arrays of diffusively coupled reactors. The kinetics is given by the Lengyel-Epstein model, and we derive the conditions for Turing instabilities in all arrays of two, three, and four reactors.

  11. How superfluid vortex knots untie

    NASA Astrophysics Data System (ADS)

    Kleckner, Dustin; Kauffman, Louis H.; Irvine, William T. M.

    2016-07-01

    Knots and links often occur in physical systems, including shaken strands of rope and DNA (ref. ), as well as the more subtle structure of vortices in fluids and magnetic fields in plasmas. Theories of fluid flows without dissipation predict these tangled structures persist, constraining the evolution of the flow much like a knot tied in a shoelace. This constraint gives rise to a conserved quantity known as helicity, offering both fundamental insights and enticing possibilities for controlling complex flows. However, even small amounts of dissipation allow knots to untie by means of `cut-and-splice’ operations known as reconnections. Despite the potentially fundamental role of these reconnections in understanding helicity--and the stability of knotted fields more generally--their effect is known only for a handful of simple knots. Here we study the evolution of 322 elemental knots and links in the Gross-Pitaevskii model for a superfluid, and find that they universally untie. We observe that the centreline helicity is partially preserved even as the knots untie, a remnant of the perfect helicity conservation predicted for idealized fluids. Moreover, we find that the topological pathways of untying knots have simple descriptions in terms of minimal two-dimensional knot diagrams, and tend to concentrate in states which are twisted in only one direction. These results have direct analogies to previous studies of simple knots in several systems, including DNA recombination and classical fluids. This similarity in the geometric and topological evolution suggests there are universal aspects in the behaviour of knots in dissipative fields.

  12. High-resolution coupled physics solvers for analysing fine-scale nuclear reactor design problems

    PubMed Central

    Mahadevan, Vijay S.; Merzari, Elia; Tautges, Timothy; Jain, Rajeev; Obabko, Aleksandr; Smith, Michael; Fischer, Paul

    2014-01-01

    An integrated multi-physics simulation capability for the design and analysis of current and future nuclear reactor models is being investigated, to tightly couple neutron transport and thermal-hydraulics physics under the SHARP framework. Over several years, high-fidelity, validated mono-physics solvers with proven scalability on petascale architectures have been developed independently. Based on a unified component-based architecture, these existing codes can be coupled with a mesh-data backplane and a flexible coupling-strategy-based driver suite to produce a viable tool for analysts. The goal of the SHARP framework is to perform fully resolved coupled physics analysis of a reactor on heterogeneous geometry, in order to reduce the overall numerical uncertainty while leveraging available computational resources. The coupling methodology and software interfaces of the framework are presented, along with verification studies on two representative fast sodium-cooled reactor demonstration problems to prove the usability of the SHARP framework. PMID:24982250

  13. High-resolution coupled physics solvers for analysing fine-scale nuclear reactor design problems.

    PubMed

    Mahadevan, Vijay S; Merzari, Elia; Tautges, Timothy; Jain, Rajeev; Obabko, Aleksandr; Smith, Michael; Fischer, Paul

    2014-08-01

    An integrated multi-physics simulation capability for the design and analysis of current and future nuclear reactor models is being investigated, to tightly couple neutron transport and thermal-hydraulics physics under the SHARP framework. Over several years, high-fidelity, validated mono-physics solvers with proven scalability on petascale architectures have been developed independently. Based on a unified component-based architecture, these existing codes can be coupled with a mesh-data backplane and a flexible coupling-strategy-based driver suite to produce a viable tool for analysts. The goal of the SHARP framework is to perform fully resolved coupled physics analysis of a reactor on heterogeneous geometry, in order to reduce the overall numerical uncertainty while leveraging available computational resources. The coupling methodology and software interfaces of the framework are presented, along with verification studies on two representative fast sodium-cooled reactor demonstration problems to prove the usability of the SHARP framework. PMID:24982250

  14. Pseudohaptic interaction with knot diagrams

    NASA Astrophysics Data System (ADS)

    Weng, Jianguang; Zhang, Hui

    2012-07-01

    To make progress in understanding knot theory, we need to interact with the projected representations of mathematical knots, which are continuous in three dimensions (3-D) but significantly interrupted in the projective images. One way to achieve such a goal is to design an interactive system that allows us to sketch two-dimensional (2-D) knot diagrams by taking advantage of a collision-sensing controller and explore their underlying smooth structures through a continuous motion. Recent advances of interaction techniques have been made that allow progress in this direction. Pseudohaptics that simulate haptic effects using pure visual feedback can be used to develop such an interactive system. We outline one such pseudohaptic knot diagram interface. Our interface derives from the familiar pencil-and-paper process of drawing 2-D knot diagrams and provides haptic-like sensations to facilitate the creation and exploration of knot diagrams. A centerpiece of the interaction model simulates a physically reactive mouse cursor, which is exploited to resolve the apparent conflict between the continuous structure of the actual smooth knot and the visual discontinuities in the knot diagram representation. Another value in exploiting pseudohaptics is that an acceleration (or deceleration) of the mouse cursor (or surface locator) can be used to indicate the slope of the curve (or surface) of which the projective image is being explored. By exploiting these additional visual cues, we proceed to a full-featured extension to a pseudohaptic four-dimensional (4-D) visualization system that simulates the continuous navigation on 4-D objects and allows us to sense the bumps and holes in the fourth dimension. Preliminary tests of the software show that main features of the interface overcome some expected perceptual limitations in our interaction with 2-D knot diagrams of 3-D knots and 3-D projective images of 4-D mathematical objects.

  15. Periodic forces trigger knot untying during translocation of knotted proteins.

    PubMed

    Szymczak, Piotr

    2016-01-01

    Proteins need to be unfolded when translocated through the pores in mitochondrial and other cellular membranes. Knotted proteins, however, might get stuck during this process, jamming the pore, since the diameter of the pore is smaller than the size of maximally tightened knot. The jamming probability dramatically increases as the magnitude of the driving force exceeds a critical value, Fc. In this numerical study, we show that for deep knots Fc lies below the force range over which molecular import motors operate, which suggest that in these cases the knots will tighten and block the pores. Next, we show how such topological traps might be prevented by using a pulling protocol of a repetitive, on-off character. Such a repetitive pulling is biologically relevant, since the mitochondrial import motor, like other molecular motors transforms chemical energy into directed motions via nucleotide-hydrolysis-mediated conformational changes, which are cyclic in character. PMID:26996878

  16. Periodic forces trigger knot untying during translocation of knotted proteins

    NASA Astrophysics Data System (ADS)

    Szymczak, Piotr

    2016-03-01

    Proteins need to be unfolded when translocated through the pores in mitochondrial and other cellular membranes. Knotted proteins, however, might get stuck during this process, jamming the pore, since the diameter of the pore is smaller than the size of maximally tightened knot. The jamming probability dramatically increases as the magnitude of the driving force exceeds a critical value, Fc. In this numerical study, we show that for deep knots Fc lies below the force range over which molecular import motors operate, which suggest that in these cases the knots will tighten and block the pores. Next, we show how such topological traps might be prevented by using a pulling protocol of a repetitive, on-off character. Such a repetitive pulling is biologically relevant, since the mitochondrial import motor, like other molecular motors transforms chemical energy into directed motions via nucleotide-hydrolysis-mediated conformational changes, which are cyclic in character.

  17. Periodic forces trigger knot untying during translocation of knotted proteins

    PubMed Central

    Szymczak, Piotr

    2016-01-01

    Proteins need to be unfolded when translocated through the pores in mitochondrial and other cellular membranes. Knotted proteins, however, might get stuck during this process, jamming the pore, since the diameter of the pore is smaller than the size of maximally tightened knot. The jamming probability dramatically increases as the magnitude of the driving force exceeds a critical value, Fc. In this numerical study, we show that for deep knots Fc lies below the force range over which molecular import motors operate, which suggest that in these cases the knots will tighten and block the pores. Next, we show how such topological traps might be prevented by using a pulling protocol of a repetitive, on-off character. Such a repetitive pulling is biologically relevant, since the mitochondrial import motor, like other molecular motors transforms chemical energy into directed motions via nucleotide-hydrolysis-mediated conformational changes, which are cyclic in character. PMID:26996878

  18. Knot invariants from Virasoro related representation and pretzel knots

    NASA Astrophysics Data System (ADS)

    Galakhov, D.; Melnikov, D.; Mironov, A.; Morozov, A.

    2015-10-01

    We remind the method to calculate colored Jones polynomials for the plat representations of knot diagrams from the knowledge of modular transformation (monodromies) of Virasoro conformal blocks with insertions of degenerate fields. As an illustration we use a rich family of pretzel knots, lying on a surface of arbitrary genus g, which was recently analyzed by the evolution method. Further generalizations can be to generic Virasoro modular transformations, provided by integral kernels, which can lead to the Hikami invariants.

  19. Methane coupling by membrane reactor. Quarterly technical progress report, June 25, 1994--September 24, 1994

    SciTech Connect

    Ma, Yi Hua

    1995-01-04

    This quarterly report describes results from the experimental studies on oxidative coupling of methane, oxygen conducting perovskite dense membrane synthesis and modeling studies of the methane coupling reaction. The focus of the experimental study is to explore the effects of varying catalyst loading, varying methane to oxygen ratios and feed conditions when the oxygen conversion is much less than 100%. Results from these studies help in understanding the effects of various parameters controlling methane coupling. Dense membrane synthesis and characterization results are presented which describe new approaches to the synthesis and characterization of these membranes. The modeling results described in this report present a theoretical fit to the experimental data on oxidative coupling of methane in fixed bed reactors. The parameters from the fit are used to predict the trends in experimental data obtained from VYCOR membrane reactors. The predicted trends are based on a theoretical model employing simplified methane coupling kinetics.

  20. Methane coupling by membrane reactor. Quarterly technical progress report, September 25, 1995--December 24, 1995

    SciTech Connect

    1996-03-15

    The performance of the third type of catalytic membrane reactor configuration, with catalyst deposited in the membrane and no catalyst or inert materials in the tube side, was evaluated. The C{sub 2} selectivity obtained was about 10% due to the gas phase reaction in the empty tube side of the reactor. The membrane reactor with an oxygen-permeable dense membrane has been built. The use of a dense membrane will eliminate the loss of hydrocarbon from the tube side to the shell side, as observed in the Vycor glass membrane reactor. Also, air can be used as the oxygen source without contaminating the product. La/MgO was synthesized and will be used as the catalyst for the dense membrane reactor. This catalyst was reported in the literature to show significant improvement of C{sub 2} selectivity and yield for oxidative coupling of methane in a packed-bed reactor by using the operation mode of staged-feed of oxygen. A reactor mode for methane oxidative coupling in reactors with both distributed oxygen feed and C{sub 2} product removal was developed based on the general model of cross-flow reactors reported in the last quarterly report. A distributed oxygen feed could give rise to much higher C{sub 2} yield than the co-feed reactor as long as the space time is long enough. In the case of a two-membrane reactor, where oxygen is supplied by one membrane and products are removed through the other membrane, a high separation factor of C{sub 2} product to methane for the product-removal membrane is critical to achieve high C{sub 2} yield.

  1. Optimal Coupling of a Nuclear Reactor and a Thermal Desalination Plant

    SciTech Connect

    Caruso, G.; Naviglio, A.; Nisan, S.; Bielak, B.; Cinotti, L.; Humphries, J.R.; Martins, N.; Volpi, L.

    2002-07-01

    The present study, performed in the framework of the EURODESAL Project (5. EU FWP), deals with the analysis of the 'optimum' coupling of a PWR and of a HTGR plant with a thermal desalination plant, based on the Multiple Effects process. The reference reactors are the AP600 and the PWR900 as Pressurized reactors and the GT-MHR as Gas reactor. The calculations performed show that there are several technical solutions allowing to couple PWRs and GRs to a ME desalination plant. The optimization criteria concern the technical feasibility of the coupling, producing the maximum quantity of fresh water at the lower cost, without unacceptable reduction of the electrical power produced and without undue health hazard for population. (authors)

  2. Effects of Knots on Protein Folding Properties

    PubMed Central

    Soler, Miguel A.; Faísca, Patrícia F. N.

    2013-01-01

    This work explores the impact of knots, knot depth and motif of the threading terminus in protein folding properties (kinetics, thermodynamics and mechanism) via extensive Monte Carlo simulations of lattice models. A knotted backbone has no effect on protein thermodynamic stability but it may affect key aspects of folding kinetics. In this regard, we found clear evidence for a functional advantage of knots: knots enhance kinetic stability because a knotted protein unfolds at a distinctively slower rate than its unknotted counterpart. However, an increase in knot deepness does not necessarily lead to more effective changes in folding properties. In this regard, a terminus with a non-trivial conformation (e.g. hairpin) can have a more dramatic effect in enhancing kinetic stability than knot depth. Nevertheless, our results suggest that the probability of the denatured ensemble to keep knotted is higher for proteins with deeper knots, indicating that knot depth plays a role in determining the topology of the denatured state. Refolding simulations starting from denatured knotted conformations show that not every knot is able to nucleate folding and further indicate that the formation of the knotting loop is a key event in the folding of knotted trefoils. They also show that there are specific native contacts within the knotted core that are crucial to keep a native knotting loop in denatured conformations which otherwise have no detectable structure. The study of the knotting mechanism reveals that the threading of the knotting loop generally occurs towards late folding in conformations that exhibit a significant degree of structural consolidation. PMID:24023962

  3. Tightening of Knots in Proteins

    NASA Astrophysics Data System (ADS)

    Sułkowska, Joanna I.; Sułkowski, Piotr; Szymczak, P.; Cieplak, Marek

    2008-02-01

    We perform theoretical studies of stretching of 20 proteins with knots within a coarse-grained model. The knot’s ends are found to jump to well defined sequential locations that are associated with sharp turns, whereas in homopolymers they diffuse around and eventually slide off. The waiting times of the jumps are increasingly stochastic as the temperature is raised. Knots typically do not return to their native locations when a protein is released after stretching.

  4. Neutronic/Thermalhydraulic Coupling Technigues for Sodium Cooled Fast Reactor Simulations

    SciTech Connect

    Jean Ragusa; Andrew Siegel; Jean-Michel Ruggieri

    2010-09-28

    The objective of this project was to test new coupling algorithms and enable efficient and scalable multi-physics simulations of advanced nuclear reactors, with considerations regarding the implementation of such algorithms in massively parallel environments. Numerical tests were carried out to verify the proposed approach and the examples included some reactor transients. The project was directly related to the Sodium Fast Reactor program element of the Generation IV Nuclear Energy Systems Initiative and the Advanced Fuel cycle Initiative, and, supported the requirement of high-fidelity simulation as a mean of achieving the goals of the presidential Global Nuclear Energy Partnership (GNEP) vision.

  5. Continuous flow Sonogashira C-C coupling using a heterogeneous palladium-copper dual reactor.

    PubMed

    Tan, Li-Min; Sem, Zhi-Yu; Chong, Wei-Yuan; Liu, Xiaoqian; Hendra; Kwan, Wei Lek; Lee, Chi-Lik Ken

    2013-01-01

    We report the development of a heterogeneous catalyst system on continuous flow chemistry. A palladium (Pd) coated tubular reactor was placed in line with copper (Cu) tubing using a continuous flow platform, and a Sonogashira C-C coupling reaction was used to evaluate the performance. The reactions were favorably carried out in the Cu reactor, catalyzed by the traces of leached Pd from the Pd reactor. The leached Pd and Cu were trapped with a metal scavaging resin at the back-end of the continuous flow system, affording a genuine approach toward green chemistry. PMID:23248977

  6. Knot theory and statistical mechanics

    SciTech Connect

    Jones, V.F.R. )

    1990-11-01

    Certain algebraic relations used to solve models in statistical mechanics were key to describing a mathematical property of knots known as a polynomial invariant. This connection, tenuous at first, has since developed into a significant flow of ideas. The appearance of such common ground is not atypical of recent developments in mathematics and physics--ideas from different fields interact and produce unexpected results. Indeed, the discovery of the connection between knots and statistical mechanics passed through a theory intimately related to the mathematical structure of quantum physics. This theory, called von Neumann algebras, is distinguished by the idea of continuous dimensionality. Spaces typically have dimensions that are natural numbers, such as 2, 3 or 11, but in von Neumann algebras dimensions such as 2 or {pi} are equally possible. This possibility for continuous dimension played a key role in joining knot theory and statistical mechanics. In another direction, the knot invariants were soon found to occur in quantum field theory. Indeed, Edward Witten of the Institute for Advanced Study in Princeton, N.J., has shown that topological quantum field theory provides a natural way of expressing the new ideas about knots. This advance, in turn, has allowed a beautiful generalization about the invariants of knots in more complicated three-dimensional spaces known as three-manifolds, in which space itself may contain holes and loops.

  7. Specification of the Advanced Burner Test Reactor Multi-Physics Coupling Demonstration Problem

    SciTech Connect

    Shemon, E. R.; Grudzinski, J. J.; Lee, C. H.; Thomas, J. W.; Yu, Y. Q.

    2015-12-21

    This document specifies the multi-physics nuclear reactor demonstration problem using the SHARP software package developed by NEAMS. The SHARP toolset simulates the key coupled physics phenomena inside a nuclear reactor. The PROTEUS neutronics code models the neutron transport within the system, the Nek5000 computational fluid dynamics code models the fluid flow and heat transfer, and the DIABLO structural mechanics code models structural and mechanical deformation. The three codes are coupled to the MOAB mesh framework which allows feedback from neutronics, fluid mechanics, and mechanical deformation in a compatible format.

  8. A coupled nuclear reactor thermal energy storage system for enhanced load following operation

    NASA Astrophysics Data System (ADS)

    Alameri, Saeed A.

    Nuclear power plants usually provide base-load electric power and operate most economically at a constant power level. In an energy grid with a high fraction of renewable energy sources, future nuclear reactors may be subject to significantly variable power demands. These variable power demands can negatively impact the effective capacity factor of the reactor and result in severe economic penalties. Coupling the reactor to a large Thermal Energy Storage (TES) block will allow the reactor to better respond to variable power demands. In the system described in this thesis, a Prismatic-core Advanced High Temperature Reactor (PAHTR) operates at constant power with heat provided to a TES block that supplies power as needed to a secondary energy conversion system. The PAHTR is designed to have a power rating of 300 MW th, with 19.75 wt% enriched Tri-Structural-Isotropic UO 2 fuel and a five year operating cycle. The passive molten salt TES system will operate in the latent heat region with an energy storage capacity of 150 MWd. Multiple smaller TES blocks are used instead of one large block to enhance the efficiency and maintenance complexity of the system. A transient model of the coupled reactor/TES system is developed to study the behavior of the system in response to varying load demands. The model uses six-delayed group point kinetics and decay heat models coupled to thermal-hydraulic and heat transfer models of the reactor and TES system. Based on the transient results, the preferred TES design consists of 1000 blocks, each containing 11000 LiCl phase change material tubes. A safety assessment of major reactor events demonstrates the inherent safety of the coupled system. The loss of forced circulation study determined the minimum required air convection heat removal rate from the reactor core and the lowest possible reduced primary flow rate that can maintain the reactor in a safe condition. The loss of ultimate heat sink study demonstrated the ability of the TES

  9. Capacitively coupled RF diamond-like-carbon reactor

    DOEpatents

    Devlin, David James; Coates, Don Mayo; Archuleta, Thomas Arthur; Barbero, Robert Steven

    2000-01-01

    A process of coating a non-conductive fiber with diamond-like carbon, including passing a non-conductive fiber between a pair of parallel metal grids within a reaction chamber, introducing a hydrocarbon gas into the reaction chamber, forming a plasma within the reaction chamber for a sufficient period of time whereby diamond-like carbon is formed upon the non-conductive fiber, is provided together with a reactor chamber for deposition of diamond-like carbon upon a non-conductive fiber, including a vacuum chamber, a cathode assembly including a pair of electrically isolated opposingly parallel metal grids spaced apart at a distance of less than about 1 centimeter, an anode, a means of introducing a hydrocarbon gas into said vacuum chamber, and a means of generating a plasma within said vacuum chamber.

  10. Coupled edge-core model of fusion reactor

    NASA Astrophysics Data System (ADS)

    Zagórski, R.; Kulinski, S.; Scholz, M.

    1997-10-01

    A model has been developed which is capable to describe in a self consistent way the plasma dynamics in the centre and edge region of a fusion reactor. The core plasma is treated in the frame of the 0D model in which an empirical scaling law for the energy confinement time is included. The model accounts for energy losses due to Bremsstrahlung and line radiation as well as alpha particle heating. A 1D analytical model for plasma and impurity transport outside the last close magnetic surface (LCMS) is applied. The model accounts for the strong gradients of the plasma parameters along the magnetic field lines in the divertor. The sputtering phenomena at the plate and radiating cooling by injected impurities are treated self consistently in the model. The model has been used to investigate operating regimes of the ignition experiment. Analysis have been performed for different first wall materials (C, Ni, Mo, W) for ITER like tokamak.

  11. Capacitively coupled RF diamond-like-carbon reactor

    SciTech Connect

    Devlin, D.J.; Coates, D.M.; Archuleta, T.A.; Barbero, R.S.

    2000-03-14

    A process of coating a non-conductive fiber with diamond-like carbon, including passing a non-conductive fiber between a pair of parallel metal grids within a reaction chamber, introducing a hydrocarbon gas into the reaction chamber, forming a plasma within the reaction chamber for a sufficient period of time whereby diamond-like carbon is formed upon the non-conductive fiber, is provided together with a reactor chamber for deposition of diamond-like carbon upon a non-conductive fiber, including a vacuum chamber, a cathode assembly including a pair of electrically isolated opposingly parallel metal grids spaced apart at a distance of less than about 1 centimeter, an anode, a means of introducing a hydrocarbon gas into said vacuum chamber, and a means of generating a plasma within said vacuum chamber.

  12. Stabilizing effect of knots on proteins

    PubMed Central

    Sułkowska, Joanna I.; Sułkowski, Piotr; Szymczak, P.; Cieplak, Marek

    2008-01-01

    Molecular dynamics studies within a coarse-grained, structure-based model were used on two similar proteins belonging to the transcarbamylase family to probe the effects of the knot in the native structure of a protein. The first protein, N-acetylornithine transcarbamylase, contains no knot, whereas human ormithine transcarbamylase contains a trefoil knot located deep within the sequence. In addition, we also analyzed a modified transferase with the knot removed by the appropriate change of a knot-making crossing of the protein chain. The studies of thermally and mechanically induced unfolding processes suggest a larger intrinsic stability of the protein with the knot. PMID:19064918

  13. Stabilizing effect of knots on proteins.

    PubMed

    Sułkowska, Joanna I; Sulkowski, Piotr; Szymczak, P; Cieplak, Marek

    2008-12-16

    Molecular dynamics studies within a coarse-grained, structure-based model were used on two similar proteins belonging to the transcarbamylase family to probe the effects of the knot in the native structure of a protein. The first protein, N-acetylornithine transcarbamylase, contains no knot, whereas human ormithine transcarbamylase contains a trefoil knot located deep within the sequence. In addition, we also analyzed a modified transferase with the knot removed by the appropriate change of a knot-making crossing of the protein chain. The studies of thermally and mechanically induced unfolding processes suggest a larger intrinsic stability of the protein with the knot. PMID:19064918

  14. Universal Racah matrices and adjoint knot polynomials: Arborescent knots

    NASA Astrophysics Data System (ADS)

    Mironov, A.; Morozov, A.

    2016-04-01

    By now it is well established that the quantum dimensions of descendants of the adjoint representation can be described in a universal form, independent of a particular family of simple Lie algebras. The Rosso-Jones formula then implies a universal description of the adjoint knot polynomials for torus knots, which in particular unifies the HOMFLY (SUN) and Kauffman (SON) polynomials. For E8 the adjoint representation is also fundamental. We suggest to extend the universality from the dimensions to the Racah matrices and this immediately produces a unified description of the adjoint knot polynomials for all arborescent (double-fat) knots, including twist, 2-bridge and pretzel. Technically we develop together the universality and the "eigenvalue conjecture", which expresses the Racah and mixing matrices through the eigenvalues of the quantum R-matrix, and for dealing with the adjoint polynomials one has to extend it to the previously unknown 6 × 6 case. The adjoint polynomials do not distinguish between mutants and therefore are not very efficient in knot theory, however, universal polynomials in higher representations can probably be better in this respect.

  15. Assessement of Codes and Standards Applicable to a Hydrogen Production Plant Coupled to a Nuclear Reactor

    SciTech Connect

    M. J. Russell

    2006-06-01

    This is an assessment of codes and standards applicable to a hydrogen production plant to be coupled to a nuclear reactor. The result of the assessment is a list of codes and standards that are expected to be applicable to the plant during its design and construction.

  16. A Numerical Model for Coupling of Neutron Diffusion and Thermomechanics in Fast Burst Reactors

    SciTech Connect

    Samet Y. Kadioglu; Dana A. Knoll; Cassiano De Oliveira

    2008-11-01

    We develop a numerical model for coupling of neutron diffusion adn termomechanics in order to stimulate transient behavior of a fast burst reactor. The problem involves solving a set of non-linear different equations which approximate neutron diffusion, temperature change, and material behavior. With this equation set we will model the transition from a supercritical to subcritical state and possible mechanical vibration.

  17. Spontaneous knotting of an agitated string.

    PubMed

    Raymer, Dorian M; Smith, Douglas E

    2007-10-16

    It is well known that a jostled string tends to become knotted; yet the factors governing the "spontaneous" formation of various knots are unclear. We performed experiments in which a string was tumbled inside a box and found that complex knots often form within seconds. We used mathematical knot theory to analyze the knots. Above a critical string length, the probability P of knotting at first increased sharply with length but then saturated below 100%. This behavior differs from that of mathematical self-avoiding random walks, where P has been proven to approach 100%. Finite agitation time and jamming of the string due to its stiffness result in lower probability, but P approaches 100% with long, flexible strings. We analyzed the knots by calculating their Jones polynomials via computer analysis of digital photos of the string. Remarkably, almost all were identified as prime knots: 120 different types, having minimum crossing numbers up to 11, were observed in 3,415 trials. All prime knots with up to seven crossings were observed. The relative probability of forming a knot decreased exponentially with minimum crossing number and Möbius energy, mathematical measures of knot complexity. Based on the observation that long, stiff strings tend to form a coiled structure when confined, we propose a simple model to describe the knot formation based on random "braid moves" of the string end. Our model can qualitatively account for the observed distribution of knots and dependence on agitation time and string length. PMID:17911269

  18. On ambiguity in knot polynomials for virtual knots

    NASA Astrophysics Data System (ADS)

    Morozov, A.; Morozov, And.; Popolitov, A.

    2016-06-01

    We claim that HOMFLY polynomials for virtual knots, defined with the help of the matrix-model recursion relations, contain more parameters, than just the usual q and A =qN. These parameters preserve topological invariance and do not show up in the case of ordinary (non-virtual) knots and links. They are most conveniently observed in the hypercube formalism: then they substitute q-dimensions of certain fat graphs, which are not constrained by recursion and can be chosen arbitrarily. The number of these new topological invariants seems to grow fast with the number of non-virtual crossings: 0, 1, 1, 5, 15, 91, 784, 9160, ... This number can be decreased by imposing the factorization requirement for composites, in addition to topological invariance - still freedom remains. None of these new parameters, however, appears in HOMFLY for Kishino unknot, which thus remains unseparated from the ordinary unknots even by this enriched set of knot invariants.

  19. New Invariants in the Theory of Knots.

    ERIC Educational Resources Information Center

    Kauffman, Louis H.

    1988-01-01

    A diagrammatic approach to invariants of knots is the focus. Connections with graph theory, physics, and other topics are included, along with an explanation of how proofs of some old conjectures about alternating knots emerge from this work. (MNS)

  20. Relation between strings and ribbon knots

    SciTech Connect

    Ahmed, E. Mansoura Univ. ); El-Rifai, E.A. ); Abdellatif, R.A. )

    1991-02-01

    A ribbon knot can be representation as the propagation of an open string in (Euclidean) space-time. By imposing physical conditions plus an ansatz on the string scattering amplitude. The authors get invariant polynomials of ribbon knots which correspond to Jones and Wadati et al. polynomials for ordinary knots. Motivated by the string scattering vertices, they derive an algebra which is a generalization of Hecke and Murakami-Birman-Wenzel (BMW) algebras of knots.

  1. Relation between strings and ribbon knots

    NASA Astrophysics Data System (ADS)

    Ahmed, E.; El-Rifai, E. A.; Abdellatif, R. A.

    1991-02-01

    A ribbon knot can be represented as the propagation of an open string in (Euclidean) space-time. By imposing physical conditions plus an ansatz on the string scattering amplitude, we get invariant polynomials of ribbon knots which correspond to Jones and Wadati et al. polynomials for ordinary knots. Motivated by the string scattering vertices, we derive an algebra which is a generalization of Hecke and Murakami-Birman-Wenzel (BMW) algebras of knots.

  2. Second IBEX Map Unties the Knot

    NASA Video Gallery

    One of the clear features visible in the IBEX maps is an apparent knot in the ribbon. The second map showed that the knot in the ribbon somehow spread out. It is as if the knot in the ribbon was li...

  3. Knotted stents: Case report and outcome analysis

    PubMed Central

    Lee, Ha Na; Hwang, Hokyeong

    2015-01-01

    A knotted ureteral stent is an extremely rare condition, with fewer than 20 cases reported in the literature; however, it is difficult to treat. We report a case in which a folded Terumo guidewire was successfully used to remove a knotted stent percutaneously without anesthesia. We also review the current literature on predisposing factors and management strategies for knotted ureteral stents. PMID:25964843

  4. Osiris: A Modern, High-Performance, Coupled, Multi-Physics Code For Nuclear Reactor Core Analysis

    SciTech Connect

    Procassini, R J; Chand, K K; Clouse, C J; Ferencz, R M; Grandy, J M; Henshaw, W D; Kramer, K J; Parsons, I D

    2007-02-26

    To meet the simulation needs of the GNEP program, LLNL is leveraging a suite of high-performance codes to be used in the development of a multi-physics tool for modeling nuclear reactor cores. The Osiris code project, which began last summer, is employing modern computational science techniques in the development of the individual physics modules and the coupling framework. Initial development is focused on coupling thermal-hydraulics and neutral-particle transport, while later phases of the project will add thermal-structural mechanics and isotope depletion. Osiris will be applicable to the design of existing and future reactor systems through the use of first-principles, coupled physics models with fine-scale spatial resolution in three dimensions and fine-scale particle-energy resolution. Our intent is to replace an existing set of legacy, serial codes which require significant approximations and assumptions, with an integrated, coupled code that permits the design of a reactor core using a first-principles physics approach on a wide range of computing platforms, including the world's most powerful parallel computers. A key research activity of this effort deals with the efficient and scalable coupling of physics modules which utilize rather disparate mesh topologies. Our approach allows each code module to use a mesh topology and resolution that is optimal for the physics being solved, and employs a mesh-mapping and data-transfer module to effect the coupling. Additional research is planned in the area of scalable, parallel thermal-hydraulics, high-spatial-accuracy depletion and coupled-physics simulation using Monte Carlo transport.

  5. The elusive quest for RNA knots.

    PubMed

    Burton, Aaron S; Di Stefano, Marco; Lehman, Niles; Orland, Henri; Micheletti, Cristian

    2016-02-01

    Physical entanglement, and particularly knots arise spontaneously in equilibrated polymers that are sufficiently long and densely packed. Biopolymers are no exceptions: knots have long been known to occur in proteins as well as in encapsidated viral DNA. The rapidly growing number of RNA structures has recently made it possible to investigate the incidence of physical knots in this type of biomolecule, too. Strikingly, no knots have been found to date in the known RNA structures. In this Point of View Article we discuss the absence of knots in currently available RNAs and consider the reasons why knots in RNA have not yet been found, despite the expectation that they should exist in Nature. We conclude by singling out a number of RNA sequences that, based on the properties of their predicted secondary structures, are good candidates for knotted RNAs. PMID:26828280

  6. The elusive quest for RNA knots

    PubMed Central

    Burton, Aaron S.; Di Stefano, Marco; Lehman, Niles; Orland, Henri; Micheletti, Cristian

    2016-01-01

    ABSTRACT Physical entanglement, and particularly knots arise spontaneously in equilibrated polymers that are sufficiently long and densely packed. Biopolymers are no exceptions: knots have long been known to occur in proteins as well as in encapsidated viral DNA. The rapidly growing number of RNA structures has recently made it possible to investigate the incidence of physical knots in this type of biomolecule, too. Strikingly, no knots have been found to date in the known RNA structures. In this Point of View Article we discuss the absence of knots in currently available RNAs and consider the reasons why knots in RNA have not yet been found, despite the expectation that they should exist in Nature. We conclude by singling out a number of RNA sequences that, based on the properties of their predicted secondary structures, are good candidates for knotted RNAs. PMID:26828280

  7. Enhanced c2 yields from methane oxidative coupling by means of a separative chemical reactor.

    PubMed

    Tonkovich, A L; Carr, R W; Aris, R

    1993-10-01

    Of the processes for converting natural gas into a more useful chemical feedstock, the oxidative coupling of methane to form ethane and ethylene (C(2)) has perhaps been the most intensively investigated in recent years, but it has proved extremely difficult to obtain C(2) yields in excess of 20 to 25%. Methane oxidative coupling was carried out in a separative chemical reactor that simulated a countercurrent chromatographic moving-bed. This reaction gives 65% methane conversion, 80% C(2) selectivity, and a C(2) yield slightly better than 50% with Sm(2)O(3) catalyst at approximately 1000 K. PMID:17841868

  8. Physics-based multiscale coupling for full core nuclear reactor simulation

    SciTech Connect

    Gaston, Derek R.; Permann, Cody J.; Peterson, John W.; Slaughter, Andrew E.; Andrš, David; Wang, Yaqi; Short, Michael P.; Perez, Danielle M.; Tonks, Michael R.; Ortensi, Javier; Zou, Ling; Martineau, Richard C.

    2015-10-01

    Numerical simulation of nuclear reactors is a key technology in the quest for improvements in efficiency, safety, and reliability of both existing and future reactor designs. Historically, simulation of an entire reactor was accomplished by linking together multiple existing codes that each simulated a subset of the relevant multiphysics phenomena. Recent advances in the MOOSE (Multiphysics Object Oriented Simulation Environment) framework have enabled a new approach: multiple domain-specific applications, all built on the same software framework, are efficiently linked to create a cohesive application. This is accomplished with a flexible coupling capability that allows for a variety of different data exchanges to occur simultaneously on high performance parallel computational hardware. Examples based on the KAIST-3A benchmark core, as well as a simplified Westinghouse AP-1000 configuration, demonstrate the power of this new framework for tackling—in a coupled, multiscale manner—crucial reactor phenomena such as CRUD-induced power shift and fuel shuffle. 2014 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-SA license

  9. Physics-based multiscale coupling for full core nuclear reactor simulation

    DOE PAGESBeta

    Gaston, Derek R.; Permann, Cody J.; Peterson, John W.; Slaughter, Andrew E.; Andrš, David; Wang, Yaqi; Short, Michael P.; Perez, Danielle M.; Tonks, Michael R.; Ortensi, Javier; et al

    2015-10-01

    Numerical simulation of nuclear reactors is a key technology in the quest for improvements in efficiency, safety, and reliability of both existing and future reactor designs. Historically, simulation of an entire reactor was accomplished by linking together multiple existing codes that each simulated a subset of the relevant multiphysics phenomena. Recent advances in the MOOSE (Multiphysics Object Oriented Simulation Environment) framework have enabled a new approach: multiple domain-specific applications, all built on the same software framework, are efficiently linked to create a cohesive application. This is accomplished with a flexible coupling capability that allows for a variety of different datamore » exchanges to occur simultaneously on high performance parallel computational hardware. Examples based on the KAIST-3A benchmark core, as well as a simplified Westinghouse AP-1000 configuration, demonstrate the power of this new framework for tackling—in a coupled, multiscale manner—crucial reactor phenomena such as CRUD-induced power shift and fuel shuffle. 2014 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-SA license« less

  10. A preliminary assessment of a radiatively coupled in-core thermionic space reactor

    NASA Astrophysics Data System (ADS)

    Marshall, Albert C.; King, Donald B.; Wilson, Volney C.; Houts, Michael G.

    1997-01-01

    A radiatively-coupled in-core thermionic space reactor is proposed that may offer a number of economic and performance benefits. This design combines the advantages of fuel loading after conducting non-nuclear system tests (characteristic of a single-cell design) with the performance benefits of a multi-cell design. Permitting full system tests without nuclear fuel can significantly reduce testing costs while improving reliability of the flight system. In addition, the approach permits the entire system to be transported to the launch site without nuclear fuel. Consequently, program planners can avoid the expensive development of a large shipping cask, or the potential costly completion of system assembly at the launch site. The concept uses a fast reactor as the power source; therefore, the development of a moderator capable of long operational times and high temperature is unnecessary. A fast reactor also permits the use of refractory materials without a significant critical mass penalty from resonance capture of neutrons. The high operating temperature permitted by refractory materials and multi-cell performance improvements will increase system efficiency and reduce radiator surface area requirements. The combination of higher efficiency and reduced radiator area can reduce system size and mass, resulting in launch cost savings. A conceptual design of the reactor power system has been completed. The RSMASS-D model was used to estimate a mass optimized system configuration. System mass predictions for the proposed concept compare favorably to mass predictions for alternative space reactor power system approaches.

  11. Coupling a Supercritical Carbon Dioxide Brayton Cycle to a Helium-Cooled Reactor.

    SciTech Connect

    Middleton, Bobby; Pasch, James Jay; Kruizenga, Alan Michael; Walker, Matthew

    2016-01-01

    This report outlines the thermodynamics of a supercritical carbon dioxide (sCO2) recompression closed Brayton cycle (RCBC) coupled to a Helium-cooled nuclear reactor. The baseline reactor design for the study is the AREVA High Temperature Gas-Cooled Reactor (HTGR). Using the AREVA HTGR nominal operating parameters, an initial thermodynamic study was performed using Sandia's deterministic RCBC analysis program. Utilizing the output of the RCBC thermodynamic analysis, preliminary values of reactor power and of Helium flow rate through the reactor were calculated in Sandia's HelCO2 code. Some research regarding materials requirements was then conducted to determine aspects of corrosion related to both Helium and to sCO2 , as well as some mechanical considerations for pressures and temperatures that will be seen by the piping and other components. This analysis resulted in a list of materials-related research items that need to be conducted in the future. A short assessment of dry heat rejection advantages of sCO2> Brayton cycles was also included. This assessment lists some items that should be investigated in the future to better understand how sCO2 Brayton cycles and nuclear can maximally contribute to optimizing the water efficiency of carbon free power generation

  12. Factorization of colored knot polynomials at roots of unity

    NASA Astrophysics Data System (ADS)

    Kononov, Ya.; Morozov, A.

    2015-07-01

    HOMFLY polynomials are the Wilson-loop averages in Chern-Simons theory and depend on four variables: the closed line (knot) in 3d space-time, representation R of the gauge group SU (N) and exponentiated coupling constant q. From analysis of a big variety of different knots we conclude that at q, which is a 2m-th root of unity, q2m = 1, HOMFLY polynomials in symmetric representations [ r ] satisfy recursion identity: Hr+m =Hr ṡHm for any A =qN, which is a generalization of the property Hr = H1r for special polynomials at m = 1. We conjecture a further generalization to arbitrary representation R, which, however, is checked only for torus knots. Next, Kashaev polynomial, which arises from HR at q2 = e 2 πi / | R |, turns equal to the special polynomial with A substituted by A| R |, provided R is a single-hook representations (including arbitrary symmetric) - what provides a q - A dual to the similar property of Alexander polynomial. All this implies non-trivial relations for the coefficients of the differential expansions, which are believed to provide reasonable coordinates in the space of knots - existence of such universal relations means that these variables are still not unconstrained.

  13. Reactor physics studies for the Advanced Fuel Cycle Initiative (AFCI) Reactor-Accelerator Coupling Experiments (RACE) Project

    NASA Astrophysics Data System (ADS)

    Stankovskiy, Evgeny Yuryevich

    In the recently completed RACE Project of the AFCI, accelerator-driven subcritical systems (ADS) experiments were conducted to develop technology of coupling accelerators to nuclear reactors. In these experiments electron accelerators induced photon-neutron reactions in heavy-metal targets to initiate fission reactions in ADS. Although the Idaho State University (ISU) RACE ADS was constructed only to develop measurement techniques for advanced experiments, many reactor kinetics experiments were conducted there. In the research reported in this dissertation, a method was developed to calculate kinetics parameters for measurement and calculation of the reactivity of ADS, a safety parameter that is necessary for control and monitoring of power production. Reactivity is measured in units of fraction of delayed versus prompt neutron from fission, a quantity that cannot be directly measured in far-subcritical reactors such as the ISU RACE configuration. A new technique is reported herein to calculate it accurately and to predict kinetic behavior of a far-subcritical ADS. Experiments conducted at ISU are first described and experimental data are presented before development of the kinetic theory used in the new computational method. Because of the complexity of the ISU ADS, the Monte-Carlo method as applied in the MCNP code is most suitable for modeling reactor kinetics. However, the standard method of calculating the delayed neutron fraction produces inaccurate values. A new method was developed and used herein to evaluate actual experiments. An advantage of this method is that its efficiency is independent of the fission yield of delayed neutrons, which makes it suitable for fuel with a minor actinide component (e.g. transmutation fuels). The implementation of this method is based on a correlated sampling technique which allows the accurate evaluation of delayed and prompt neutrons. The validity of the obtained results is indicated by good agreement between experimental

  14. Development of a coupling code for PWR reactor cavity radiation streaming calculation

    SciTech Connect

    Zheng, Z.; Wu, H.; Cao, L.; Zheng, Y.; Zhang, H.; Wang, M.

    2012-07-01

    PWR reactor cavity radiation streaming is important for the safe of the personnel and equipment, thus calculation has to be performed to evaluate the neutron flux distribution around the reactor. For this calculation, the deterministic codes have difficulties in fine geometrical modeling and need huge computer resource; and the Monte Carlo codes require very long sampling time to obtain results with acceptable precision. Therefore, a coupling method has been developed to eliminate the two problems mentioned above in each code. In this study, we develop a coupling code named DORT2MCNP to link the Sn code DORT and Monte Carlo code MCNP. DORT2MCNP is used to produce a combined surface source containing top, bottom and side surface simultaneously. Because SDEF card is unsuitable for the combined surface source, we modify the SOURCE subroutine of MCNP and compile MCNP for this application. Numerical results demonstrate the correctness of the coupling code DORT2MCNP and show reasonable agreement between the coupling method and the other two codes (DORT and MCNP). (authors)

  15. Biomechanical evaluation of the Nice knot

    PubMed Central

    Hill, Shannon W.; Chapman, Christopher R.; Adeeb, Samer; Duke, Kajsa; Beaupre, Lauren; Bouliane, Martin J.

    2016-01-01

    Background: The Nice knot is a bulky double-stranded knot. Biomechanical data supporting its use as well as the number of half hitches required to ensure knot security is lacking. Materials and Methods: Nice knots with, one, two, or three half-hitches were compared with the surgeon's and Tennessee slider knots with three half hitches. Each knot was tied 10 times around a fixed diameter using four different sutures: FiberWire (Arthrex, Naples, FL), Ultrabraid (Smith and Nephew, Andover, MA), Hi-Fi (ConMed Linvatec, Largo, FL) and Force Fiber (Teleflex Medical OEM, Gurnee, IL). Cyclic testing was performed for 10 min between 10N and 45N, resulting in approximately 1000 cycles. Displacement from an initial 10N load was recorded. Knots surviving cyclic testing were subjected to a load to failure test at a rate of 60 mm/min. Load at clinical failure: 3 mm slippage or opening of the suture loop was recorded. Bulk, mode of ultimate failure, opening of the loop past clinical failure, was also recorded. Results: During cyclic testing, the Nice knots with one or more half-hitches performed the best, slipping significantly less than the surgeon's and Tennessee Slider (P < 0.002). After one half-hitch, the addition of half-hitches did not significantly improve Nice knot performance during cyclic testing (P > 0.06). The addition of half-hitches improved the strength of the Nice knot during the force to failure test, however after two half-hitches, increase of strength was not significant (P = 0.59). While FiberWire was the most bulky of the sutures tested, it also performed the best, slipping the least. Conclusion: The Nice knot, especially using FiberWire, is biomechanically superior to the surgeon's and Tennessee slider knots. Two half hitches are recommended to ensure adequate knot security. PMID:26980985

  16. KnotPad: Visualizing and Exploring Knot Theory with Fluid Reidemeister Moves.

    PubMed

    Zhang, Hui; Weng, Jianguang; Jing, Lin; Zhong, Yiwen

    2012-12-01

    We present KnotPad, an interactive paper-like system for visualizing and exploring mathematical knots; we exploit topological drawing and math-aware deformation methods in particular to enable and enrich our interactions with knot diagrams. Whereas most previous efforts typically employ physically based modeling to simulate the 3D dynamics of knots and ropes, our tool offers a Reidemeister move based interactive environment that is much closer to the topological problems being solved in knot theory, yet without interfering with the traditional advantages of paper-based analysis and manipulation of knot diagrams. Drawing knot diagrams with many crossings and producing their equivalent is quite challenging and error-prone. KnotPad can restrict user manipulations to the three types of Reidemeister moves, resulting in a more fluid yet mathematically correct user experience with knots. For our principal test case of mathematical knots, KnotPad permits us to draw and edit their diagrams empowered by a family of interactive techniques. Furthermore, we exploit supplementary interface elements to enrich the user experiences. For example, KnotPad allows one to pull and drag on knot diagrams to produce mathematically valid moves. Navigation enhancements in KnotPad provide still further improvement: by remembering and displaying the sequence of valid moves applied during the entire interaction, KnotPad allows a much cleaner exploratory interface for the user to analyze and study knot equivalence. All these methods combine to reveal the complex spatial relationships of knot diagrams with a mathematically true and rich user experience. PMID:26357111

  17. KnotProt: a database of proteins with knots and slipknots

    PubMed Central

    Jamroz, Michal; Niemyska, Wanda; Rawdon, Eric J.; Stasiak, Andrzej; Millett, Kenneth C.; Sułkowski, Piotr; Sulkowska, Joanna I.

    2015-01-01

    The protein topology database KnotProt, http://knotprot.cent.uw.edu.pl/, collects information about protein structures with open polypeptide chains forming knots or slipknots. The knotting complexity of the cataloged proteins is presented in the form of a matrix diagram that shows users the knot type of the entire polypeptide chain and of each of its subchains. The pattern visible in the matrix gives the knotting fingerprint of a given protein and permits users to determine, for example, the minimal length of the knotted regions (knot's core size) or the depth of a knot, i.e. how many amino acids can be removed from either end of the cataloged protein structure before converting it from a knot to a different type of knot. In addition, the database presents extensive information about the biological functions, families and fold types of proteins with non-trivial knotting. As an additional feature, the KnotProt database enables users to submit protein or polymer chains and generate their knotting fingerprints. PMID:25361973

  18. Method for coupled three-dimensional analysis of reactor vessel blowdowns with internal structures. [PWR

    SciTech Connect

    Silling, S.A.; Gross, M.B.; Santee, G.E. Jr.; Chang, F.H.

    1981-01-01

    The STEALTH 3D and WHAMSE 3D computer codes have been combined to perform three-dimensional coupled fluid/structure calculations of the blowdown response of a pressure vessel with internal structures typical of a pressurized water reactor. The fluid/structure coupling, which is performed cycle by cycle during a calculation, is described. The coupled fluid/structure code, STEALTH/WHAMSE 3D, has been used to simulate the decompression of test V31.1 from the HDR blowdown test series. Calculations of fluid pressure, differential fluid pressure and hoop strain compare favorably with the experimental data from test V31.1. The computed peak axial stain compares less favorably with the experimental data, probably due to coarseness of the structural grid. 14 refs.

  19. Commercial-Scale Performance Predictions for High-Temperature Electrolysis Plants Coupled to Three Advanced Reactor Types

    SciTech Connect

    M. G. McKellar; J. E. O'Brien; J. S. Herring

    2007-09-01

    This report presents results of system analyses that have been developed to assess the hydrogen production performance of commercial-scale high-temperature electrolysis (HTE) plants driven by three different advanced reactor – power-cycle combinations: a high-temperature helium cooled reactor coupled to a direct Brayton power cycle, a supercritical CO2-cooled reactor coupled to a direct recompression cycle, and a sodium-cooled fast reactor coupled to a Rankine cycle. The system analyses were performed using UniSim software. The work described in this report represents a refinement of previous analyses in that the process flow diagrams include realistic representations of the three advanced reactors directly coupled to the power cycles and integrated with the high-temperature electrolysis process loops. In addition, this report includes parametric studies in which the performance of each HTE concept is determined over a wide range of operating conditions. Results of the study indicate that overall thermal-to- hydrogen production efficiencies (based on the low heating value of the produced hydrogen) in the 45 - 50% range can be achieved at reasonable production rates with the high-temperature helium cooled reactor concept, 42 - 44% with the supercritical CO2-cooled reactor and about 33 - 34% with the sodium-cooled reactor.

  20. Simulating High Flux Isotope Reactor Core Thermal-Hydraulics via Interdimensional Model Coupling

    SciTech Connect

    Travis, Adam R

    2014-05-01

    A coupled interdimensional model is presented for the simulation of the thermal-hydraulic characteristics of the High Flux Isotope Reactor core at Oak Ridge National Laboratory. The model consists of two domains a solid involute fuel plate and the surrounding liquid coolant channel. The fuel plate is modeled explicitly in three-dimensions. The coolant channel is approximated as a twodimensional slice oriented perpendicular to the fuel plate s surface. The two dimensionally-inconsistent domains are linked to one another via interdimensional model coupling mechanisms. The coupled model is presented as a simplified alternative to a fully explicit, fully three-dimensional model. Involute geometries were constructed in SolidWorks. Derivations of the involute construction equations are presented. Geometries were then imported into COMSOL Multiphysics for simulation and modeling. Both models are described in detail so as to highlight their respective attributes in the 3D model, the pursuit of an accurate, reliable, and complete solution; in the coupled model, the intent to simplify the modeling domain as much as possible without affecting significant alterations to the solution. The coupled model was created with the goal of permitting larger portions of the reactor core to be modeled at once without a significant sacrifice to solution integrity. As such, particular care is given to validating incorporated model simplifications. To the greatest extent possible, the decrease in solution time as well as computational cost are quantified versus the effects such gains have on the solution quality. A variant of the coupled model which sufficiently balances these three solution characteristics is presented alongside the more comprehensive 3D model for comparison and validation.

  1. Development of Pressurized Water Reactor Integrated Safety Analysis Methodology Using Multilevel Coupling Algorithm

    SciTech Connect

    Ziabletsev, Dmitri; Avramova, Maria; Ivanov, Kostadin

    2004-11-15

    The subchannel code COBRA-TF has been introduced for an evaluation of thermal margins on the local pin-by-pin level in a pressurized water reactor. The coupling of COBRA-TF with TRAC-PF1/NEM is performed by providing from TRAC to COBRA-TF axial and radial thermal-hydraulic boundary conditions and relative pin-power profiles, obtained with the pin power reconstruction model of the nodal expansion method (NEM). An efficient algorithm for coupling of the subchannel code COBRA-TF with TRAC-PF1/NEM in the parallel virtual machine environment was developed addressing the issues of time synchronization, data exchange, spatial overlays, and coupled convergence. Local feedback modeling on the pin level was implemented into COBRA-TF, which enabled updating the local form functions and the recalculation of the pin powers in TRAC-PF1/NEM after obtaining the local feedback parameters. The coupled TRAC-PF1/NEM/COBRA-TF code system was tested on the rod ejection accident and main steam line break benchmark problems. In both problems, the local results are closer than before the introduced multilevel coupling to the corresponding critical limits. This fact indicates that the assembly average results tend to underestimate the accident consequences in terms of local safety margins. The capability of local safety evaluation, performed simultaneously (online) with coupled global three-dimensional neutron kinetics/thermal-hydraulic calculations, is introduced and tested. The obtained results demonstrate the importance of the current work.

  2. DNA Knots: Theory and Experiments

    NASA Astrophysics Data System (ADS)

    Sumners, D. W.

    Cellular DNA is a long, thread-like molecule with remarkably complex topology. Enzymes that manipulate the geometry and topology of cellular DNA perform many vital cellular processes (including segregation of daughter chromosomes, gene regulation, DNA repair, and generation of antibody diversity). Some enzymes pass DNA through itself via enzyme-bridged transient breaks in the DNA; other enzymes break the DNA apart and reconnect it to different ends. In the topological approach to enzymology, circular DNA is incubated with an enzyme, producing an enzyme signature in the form of DNA knots and links. By observing the changes in DNA geometry (supercoiling) and topology (knotting and linking) due to enzyme action, the enzyme binding and mechanism can often be characterized. This paper will discuss some personal research history, and the tangle model for the analysis of site-specific recombination experiments on circular DNA.

  3. Modeling and temperature regulation of a thermally coupled reactor system via internal model control strategy

    SciTech Connect

    Lee, S.Y.; Coronella, C.J.; Bhadkamkar, A.S.; Seader, J.D.

    1993-12-01

    A two-stage, thermally coupled fluidized-bed reactor system has been developed for energy-efficient conversion of tar-sand bitumen to synthetic crude oil. Modeling and temperature control of a system are addressed in this study. A process model and transfer function are determined by a transient response technique and the reactor temperature are controlled by PI controllers with tuning settings determined by an internal model control (IMC) strategy. Using the IMC tuning method, sufficiently good control performance was experimentally observed without lengthy on-line tuning. It is shown that IMC strategy provides a means to directly use process knowledge to make a control decision. Although this control method allows for fine tuning by adjusting a single tuning parameter, it is not easy to determine the optimal value of this tuning parameter, which must be specified by the user. A novel method is presented to evaluate that parameter, which must be specified by the user. A novel method is presented to evaluate that parameter in this study. It was selected based on the magnitude of elements on the off-diagonal of the relative gain array to account for the effect of thermal coupling on control performance. It is shown that this method provides stable and fast control of reactor temperatures. By successfully decoupling the system, a simple method of extending the IMC tuning technique to multiinput/multioutput systems is obtained.

  4. Characteristic length of the knotting probability revisited

    NASA Astrophysics Data System (ADS)

    Uehara, Erica; Deguchi, Tetsuo

    2015-09-01

    We present a self-avoiding polygon (SAP) model for circular DNA in which the radius of impermeable cylindrical segments corresponds to the screening length of double-stranded DNA surrounded by counter ions. For the model we evaluate the probability for a generated SAP with N segments having a given knot K through simulation. We call it the knotting probability of a knot K with N segments for the SAP model. We show that when N is large the most significant factor in the knotting probability is given by the exponentially decaying part exp(-N/NK), where the estimates of parameter NK are consistent with the same value for all the different knots we investigated. We thus call it the characteristic length of the knotting probability. We give formulae expressing the characteristic length as a function of the cylindrical radius rex, i.e. the screening length of double-stranded DNA.

  5. Vortex knots in tangled quantum eigenfunctions.

    PubMed

    Taylor, Alexander J; Dennis, Mark R

    2016-01-01

    Tangles of string typically become knotted, from macroscopic twine down to long-chain macromolecules such as DNA. Here, we demonstrate that knotting also occurs in quantum wavefunctions, where the tangled filaments are vortices (nodal lines/phase singularities). The probability that a vortex loop is knotted is found to increase with its length, and a wide gamut of knots from standard tabulations occur. The results follow from computer simulations of random superpositions of degenerate eigenstates of three simple quantum systems: a cube with periodic boundaries, the isotropic three-dimensional harmonic oscillator and the 3-sphere. In the latter two cases, vortex knots occur frequently, even in random eigenfunctions at relatively low energy, and are constrained by the spatial symmetries of the modes. The results suggest that knotted vortex structures are generic in complex three-dimensional wave systems, establishing a topological commonality between wave chaos, polymers and turbulent Bose-Einstein condensates. PMID:27468801

  6. Vortex knots in tangled quantum eigenfunctions

    PubMed Central

    Taylor, Alexander J.; Dennis, Mark R.

    2016-01-01

    Tangles of string typically become knotted, from macroscopic twine down to long-chain macromolecules such as DNA. Here, we demonstrate that knotting also occurs in quantum wavefunctions, where the tangled filaments are vortices (nodal lines/phase singularities). The probability that a vortex loop is knotted is found to increase with its length, and a wide gamut of knots from standard tabulations occur. The results follow from computer simulations of random superpositions of degenerate eigenstates of three simple quantum systems: a cube with periodic boundaries, the isotropic three-dimensional harmonic oscillator and the 3-sphere. In the latter two cases, vortex knots occur frequently, even in random eigenfunctions at relatively low energy, and are constrained by the spatial symmetries of the modes. The results suggest that knotted vortex structures are generic in complex three-dimensional wave systems, establishing a topological commonality between wave chaos, polymers and turbulent Bose–Einstein condensates. PMID:27468801

  7. Vortex knots in tangled quantum eigenfunctions

    NASA Astrophysics Data System (ADS)

    Taylor, Alexander J.; Dennis, Mark R.

    2016-07-01

    Tangles of string typically become knotted, from macroscopic twine down to long-chain macromolecules such as DNA. Here, we demonstrate that knotting also occurs in quantum wavefunctions, where the tangled filaments are vortices (nodal lines/phase singularities). The probability that a vortex loop is knotted is found to increase with its length, and a wide gamut of knots from standard tabulations occur. The results follow from computer simulations of random superpositions of degenerate eigenstates of three simple quantum systems: a cube with periodic boundaries, the isotropic three-dimensional harmonic oscillator and the 3-sphere. In the latter two cases, vortex knots occur frequently, even in random eigenfunctions at relatively low energy, and are constrained by the spatial symmetries of the modes. The results suggest that knotted vortex structures are generic in complex three-dimensional wave systems, establishing a topological commonality between wave chaos, polymers and turbulent Bose-Einstein condensates.

  8. The condensate from torus knots

    NASA Astrophysics Data System (ADS)

    Gorsky, A.; Milekhin, A.; Sopenko, N.

    2015-09-01

    We discuss recently formulated instanton-torus knot duality in Ω-deformed 5D SQED on {{R}}^4× {S}^1 focusing at the microscopic aspects of the condensate formation in the instanton ensemble. Using the chain of dualities and geometric transitions we embed the SQED with a surface defect into the SU(2) SQCD with N f = 4 and identify the numbers ( n, m) of the torus T n, m knot as instanton charge and electric charge. The HOMFLY torus knot invariants in the fundamental representation provide entropic factor in the condensate of the massless flavor counting the degeneracy of the instanton-W-boson web with instanton and electric numbers ( n, m) but different spin and flavor content. Using the inverse geometrical transition we explain how our approach is related to the evaluation of the HOMFLY invariants in terms of Wilson loop in 3d CS theory. The reduction to 4D theory is briefly considered and some analogy with baryon vertex is conjectured.

  9. Lunar electric power systems utilizing the SP-100 reactor coupled to dynamic conversion systems

    NASA Astrophysics Data System (ADS)

    Harty, Richard B.; Durand, Richard E.; Mason, Lee S.

    1991-09-01

    An integration study was performed by coupling an SP-100 reactor to either a Brayton or Stirling power conversion subsystem. The application was for a surface power system to supply power requirements to a lunar base. A power level of 550 kWe was selected based on the NASA Space Exploration Initiative 90-day study. Reliability studies were initially performed to determine optimum power-conversion redundancy. This study resulted in selecting three operating engines and one standby unit. Integratiaon-design studies indicated that either the Brayton or Stirling power conversion subsystem could be integrated with the SP-100 reactor. The Stirling system had an integration advantage because of smaller piping size and fewer components. The Stirling engine, however, is more complex and heavier than the Brayton rotating unit, which tends to offset the Stirling integration advantage. From a performance consideration, the Brayton had a 9-percent mass advantage and the Stirling a 50-percent radiator-area advantage.

  10. Knots and nonorientable surfaces in chiral nematics

    PubMed Central

    Machon, Thomas; Alexander, Gareth P.

    2013-01-01

    Knots and knotted fields enrich physical phenomena ranging from DNA and molecular chemistry to the vortices of fluid flows and textures of ordered media. Liquid crystals provide an ideal setting for exploring such topological phenomena through control of their characteristic defects. The use of colloids in generating defects and knotted configurations in liquid crystals has been demonstrated for spherical and toroidal particles and shows promise for the development of novel photonic devices. Extending this existing work, we describe the full topological implications of colloids representing nonorientable surfaces and use it to construct torus knots and links of type (p,2) around multiply twisted Möbius strips. PMID:23940365

  11. An assessment of coupling algorithms for nuclear reactor core physics simulations

    NASA Astrophysics Data System (ADS)

    Hamilton, Steven; Berrill, Mark; Clarno, Kevin; Pawlowski, Roger; Toth, Alex; Kelley, C. T.; Evans, Thomas; Philip, Bobby

    2016-04-01

    This paper evaluates the performance of multiphysics coupling algorithms applied to a light water nuclear reactor core simulation. The simulation couples the k-eigenvalue form of the neutron transport equation with heat conduction and subchannel flow equations. We compare Picard iteration (block Gauss-Seidel) to Anderson acceleration and multiple variants of preconditioned Jacobian-free Newton-Krylov (JFNK). The performance of the methods are evaluated over a range of energy group structures and core power levels. A novel physics-based approximation to a Jacobian-vector product has been developed to mitigate the impact of expensive on-line cross section processing steps. Numerical simulations demonstrating the efficiency of JFNK and Anderson acceleration relative to standard Picard iteration are performed on a 3D model of a nuclear fuel assembly. Both criticality (k-eigenvalue) and critical boron search problems are considered.

  12. An assessment of coupling algorithms for nuclear reactor core physics simulations

    DOE PAGESBeta

    Hamilton, Steven; Berrill, Mark; Clarno, Kevin; Pawlowski, Roger; Toth, Alex; Kelley, C. T.; Evans, Thomas; Philip, Bobby

    2016-04-01

    Here we evaluate the performance of multiphysics coupling algorithms applied to a light water nuclear reactor core simulation. The simulation couples the k-eigenvalue form of the neutron transport equation with heat conduction and subchannel flow equations. We compare Picard iteration (block Gauss–Seidel) to Anderson acceleration and multiple variants of preconditioned Jacobian-free Newton–Krylov (JFNK). The performance of the methods are evaluated over a range of energy group structures and core power levels. A novel physics-based approximation to a Jacobian-vector product was developed to mitigate the impact of expensive on-line cross section processing steps. Numerical simulations demonstrating the efficiency of JFNK andmore » Anderson acceleration relative to standard Picard iteration are performed on a 3D model of a nuclear fuel assembly. Finally, both criticality (k-eigenvalue) and critical boron search problems are considered.« less

  13. Optimization of coupled multiphysics methodology for safety analysis of pebble bed modular reactor

    NASA Astrophysics Data System (ADS)

    Mkhabela, Peter Tshepo

    The research conducted within the framework of this PhD thesis is devoted to the high-fidelity multi-physics (based on neutronics/thermal-hydraulics coupling) analysis of Pebble Bed Modular Reactor (PBMR), which is a High Temperature Reactor (HTR). The Next Generation Nuclear Plant (NGNP) will be a HTR design. The core design and safety analysis methods are considerably less developed and mature for HTR analysis than those currently used for Light Water Reactors (LWRs). Compared to LWRs, the HTR transient analysis is more demanding since it requires proper treatment of both slower and much longer transients (of time scale in hours and days) and fast and short transients (of time scale in minutes and seconds). There is limited operation and experimental data available for HTRs for validation of coupled multi-physics methodologies. This PhD work developed and verified reliable high fidelity coupled multi-physics models subsequently implemented in robust, efficient, and accurate computational tools to analyse the neutronics and thermal-hydraulic behaviour for design optimization and safety evaluation of PBMR concept The study provided a contribution to a greater accuracy of neutronics calculations by including the feedback from thermal hydraulics driven temperature calculation and various multi-physics effects that can influence it. Consideration of the feedback due to the influence of leakage was taken into account by development and implementation of improved buckling feedback models. Modifications were made in the calculation procedure to ensure that the xenon depletion models were accurate for proper interpolation from cross section tables. To achieve this, the NEM/THERMIX coupled code system was developed to create the system that is efficient and stable over the duration of transient calculations that last over several tens of hours. Another achievement of the PhD thesis was development and demonstration of full-physics, three-dimensional safety analysis

  14. Sedimentation of macroscopic rigid knots and its relation to gel electrophoretic mobility of DNA knots.

    PubMed

    Weber, Cédric; Carlen, Mathias; Dietler, Giovanni; Rawdon, Eric J; Stasiak, Andrzej

    2013-01-01

    We address the general question of the extent to which the hydrodynamic behaviour of microscopic freely fluctuating objects can be reproduced by macrosopic rigid objects. In particular, we compare the sedimentation speeds of knotted DNA molecules undergoing gel electrophoresis to the sedimentation speeds of rigid stereolithographic models of ideal knots in both water and silicon oil. We find that the sedimentation speeds grow roughly linearly with the average crossing number of the ideal knot configurations, and that the correlation is stronger within classes of knots. This is consistent with previous observations with DNA knots in gel electrophoresis. PMID:23346349

  15. Sedimentation of macroscopic rigid knots and its relation to gel electrophoretic mobility of DNA knots

    PubMed Central

    Weber, Cédric; Carlen, Mathias; Dietler, Giovanni; Rawdon, Eric J.; Stasiak, Andrzej

    2013-01-01

    We address the general question of the extent to which the hydrodynamic behaviour of microscopic freely fluctuating objects can be reproduced by macrosopic rigid objects. In particular, we compare the sedimentation speeds of knotted DNA molecules undergoing gel electrophoresis to the sedimentation speeds of rigid stereolithographic models of ideal knots in both water and silicon oil. We find that the sedimentation speeds grow roughly linearly with the average crossing number of the ideal knot configurations, and that the correlation is stronger within classes of knots. This is consistent with previous observations with DNA knots in gel electrophoresis. PMID:23346349

  16. Viscous effects on motion and heating of electrons in inductively coupled plasma reactors

    SciTech Connect

    Chang, C.H.; Bose, D.

    1999-10-01

    A transport model is developed for nonlocal effects on motion and heating of electrons in inductively coupled plasma reactors. The model is based on the electron momentum equation derived from the Boltzmann equation, retaining anisotropic stress components which in fact are viscous stresses. The resulting model consists of transport equations for the magnitude of electron velocity oscillation and terms representing energy dissipation due to viscous stresses in the electron energy equation. In this model, electrical current is obtained in a nonlocal manner due to viscous effects, instead of Ohm's law or the electron momentum equation without viscous effects, while nonlocal heating of electrons is represented by the viscous dissipation. Computational results obtained by two-dimensional numerical simulations show that nonlocal determination of electrical current indeed is important, and viscous dissipation becomes an important electron heating mechanism at low pressures. It is suspected that viscous dissipation in inductively coupled plasma reactors in fact represents stochastic heating of electrons, and this possibility is exploited by discussing physical similarities between stochastic heating and energy dissipation due to the stress tensor.

  17. Cr(VI) reduction coupled with anaerobic oxidation of methane in a laboratory reactor.

    PubMed

    Lu, Yong-Ze; Fu, Liang; Ding, Jing; Ding, Zhao-Wei; Li, Na; Zeng, Raymond J

    2016-10-01

    The process of anaerobic oxidation of methane (AOM) is globally important because of its contribution to the carbon cycle in the environment. Besides, microorganisms play important roles in the environmental fate of chromium. However, there have been no studies to date on the interaction between methane and chromium in batch reactor systems. In this study, biological Cr(VI) reduction was investigated using methane as the sole electron donor. Isotopic (13)CH4 in the batch experiments and long-term performance in the reactor demonstrated that Cr(VI) reduction is coupled with methane oxidation. High-throughput sequencing of the 16S rRNA genes demonstrated that the microbial community had changed substantially after Cr(VI) reduction. The populations of ANME-2d archaea were enhanced, and they became the only predominant AOM-related microbe. Interestingly, other bacteria with significant increases in abundance were not reported as having the ability to reduce Cr(VI). According to these results, two mechanisms were proposed: 1) Cr(VI) is reduced by ANME-2d alone; 2) Cr(VI) is reduced by unknown Cr(VI)-reducing microbes coupled with ANME-2d. This study revealed the potential relationship between Cr(VI) reduction and CH4 oxidation, and extended our knowledge of the relationship between the AOM process and biogeochemical cycles. PMID:27395029

  18. Knot theory and quantum gravity

    SciTech Connect

    Rovelli, C.; Smolin, L.

    1988-09-05

    A new represenatation for quantum general relativity is described, which is defined in terms of functionals of sets of loops in three-space. In this representation exact solutions of the quantum constraints may be obtained. This result is related to the simplification of the constraints in Ashtekar's new formalism. We give in closed form the general solution of the diffeomorphisms constraint and a large class of solutions of the full set of constraints. These are classified by the knot and link classes of the spatial three-manifold.

  19. Knots, BPS States, and Algebraic Curves

    NASA Astrophysics Data System (ADS)

    Garoufalidis, Stavros; Kucharski, Piotr; Sułkowski, Piotr

    2016-08-01

    We analyze relations between BPS degeneracies related to Labastida-Mariño-Ooguri-Vafa (LMOV) invariants and algebraic curves associated to knots. We introduce a new class of such curves, which we call extremal A-polynomials, discuss their special properties, and determine exact and asymptotic formulas for the corresponding (extremal) BPS degeneracies. These formulas lead to nontrivial integrality statements in number theory, as well as to an improved integrality conjecture, which is stronger than the known M-theory integrality predictions. Furthermore, we determine the BPS degeneracies encoded in augmentation polynomials and show their consistency with known colored HOMFLY polynomials. Finally, we consider refined BPS degeneracies for knots, determine them from the knowledge of super-A-polynomials, and verify their integrality. We illustrate our results with twist knots, torus knots, and various other knots with up to 10 crossings.

  20. Knots, BPS States, and Algebraic Curves

    NASA Astrophysics Data System (ADS)

    Garoufalidis, Stavros; Kucharski, Piotr; Sułkowski, Piotr

    2016-07-01

    We analyze relations between BPS degeneracies related to Labastida-Mariño-Ooguri-Vafa (LMOV) invariants and algebraic curves associated to knots. We introduce a new class of such curves, which we call extremal A-polynomials, discuss their special properties, and determine exact and asymptotic formulas for the corresponding (extremal) BPS degeneracies. These formulas lead to nontrivial integrality statements in number theory, as well as to an improved integrality conjecture, which is stronger than the known M-theory integrality predictions. Furthermore, we determine the BPS degeneracies encoded in augmentation polynomials and show their consistency with known colored HOMFLY polynomials. Finally, we consider refined BPS degeneracies for knots, determine them from the knowledge of super-A-polynomials, and verify their integrality. We illustrate our results with twist knots, torus knots, and various other knots with up to 10 crossings.

  1. A pseudo-haptic knot diagram interface

    NASA Astrophysics Data System (ADS)

    Zhang, Hui; Weng, Jianguang; Hanson, Andrew J.

    2011-01-01

    To make progress in understanding knot theory, we will need to interact with the projected representations of mathematical knots which are of course continuous in 3D but significantly interrupted in the projective images. One way to achieve such a goal would be to design an interactive system that allows us to sketch 2D knot diagrams by taking advantage of a collision-sensing controller and explore their underlying smooth structures through a continuous motion. Recent advances of interaction techniques have been made that allow progress to be made in this direction. Pseudo-haptics that simulates haptic effects using pure visual feedback can be used to develop such an interactive system. This paper outlines one such pseudo-haptic knot diagram interface. Our interface derives from the familiar pencil-and-paper process of drawing 2D knot diagrams and provides haptic-like sensations to facilitate the creation and exploration of knot diagrams. A centerpiece of the interaction model simulates a "physically" reactive mouse cursor, which is exploited to resolve the apparent conflict between the continuous structure of the actual smooth knot and the visual discontinuities in the knot diagram representation. Another value in exploiting pseudo-haptics is that an acceleration (or deceleration) of the mouse cursor (or surface locator) can be used to indicate the slope of the curve (or surface) of whom the projective image is being explored. By exploiting these additional visual cues, we proceed to a full-featured extension to a pseudo-haptic 4D visualization system that simulates the continuous navigation on 4D objects and allows us to sense the bumps and holes in the fourth dimension. Preliminary tests of the software show that main features of the interface overcome some expected perceptual limitations in our interaction with 2D knot diagrams of 3D knots and 3D projective images of 4D mathematical objects.

  2. European Pressurized water Reactor (EPR) SAR ATWS Accident Analyses by using 3D Code Internal Coupling Method

    SciTech Connect

    Gagner, Renata; Lafitte, Helene; Dormeau, Pascal; Stoudt, Roger H.

    2004-07-01

    Anticipated Transients Without Scram (ATWS) accident analyses make part of the Safety Analysis Report of the European Pressurized water Reactor (EPR), covering Risk Reduction Category A (Core Melt Prevention) events. This paper deals with three of the most penalizing RRC-A sequences of ATWS caused by mechanical blockage of the control/shutdown rods, regarding their consequences on the Reactor Coolant System (RCS) and core integrity. A new 3D code internal coupling calculation method has been introduced. (authors)

  3. High accuracy modeling for advanced nuclear reactor core designs using Monte Carlo based coupled calculations

    NASA Astrophysics Data System (ADS)

    Espel, Federico Puente

    The main objective of this PhD research is to develop a high accuracy modeling tool using a Monte Carlo based coupled system. The presented research comprises the development of models to include the thermal-hydraulic feedback to the Monte Carlo method and speed-up mechanisms to accelerate the Monte Carlo criticality calculation. Presently, deterministic codes based on the diffusion approximation of the Boltzmann transport equation, coupled with channel-based (or sub-channel based) thermal-hydraulic codes, carry out the three-dimensional (3-D) reactor core calculations of the Light Water Reactors (LWRs). These deterministic codes utilize nuclear homogenized data (normally over large spatial zones, consisting of fuel assembly or parts of fuel assembly, and in the best case, over small spatial zones, consisting of pin cell), which is functionalized in terms of thermal-hydraulic feedback parameters (in the form of off-line pre-generated cross-section libraries). High accuracy modeling is required for advanced nuclear reactor core designs that present increased geometry complexity and material heterogeneity. Such high-fidelity methods take advantage of the recent progress in computation technology and coupled neutron transport solutions with thermal-hydraulic feedback models on pin or even on sub-pin level (in terms of spatial scale). The continuous energy Monte Carlo method is well suited for solving such core environments with the detailed representation of the complicated 3-D problem. The major advantages of the Monte Carlo method over the deterministic methods are the continuous energy treatment and the exact 3-D geometry modeling. However, the Monte Carlo method involves vast computational time. The interest in Monte Carlo methods has increased thanks to the improvements of the capabilities of high performance computers. Coupled Monte-Carlo calculations can serve as reference solutions for verifying high-fidelity coupled deterministic neutron transport methods

  4. Investigation of Asymmetries in Inductively Coupled Plasma Etching Reactors Using a 3-Dimensional Hybrid Model

    NASA Astrophysics Data System (ADS)

    Kushner, Mark J.; Grapperhaus, Michael J.

    1996-10-01

    Inductively Coupled Plasma (ICP) reactors have the potential for scaling to large area substrates while maintaining azimuthal symmetry or side-to-side uniformity across the wafer. Asymmetric etch properties in these devices have been attributed to transmission line properties of the coil, internal structures (such as wafer clamps) and non-uniform gas injection or pumping. To investigate the origins of asymmetric etch properties, a 3-dimensional hybrid model has been developed. The hybrid model contains electromagnetic, electric circuit, electron energy equation, and fluid modules. Continuity and momentum equations are solved in the fluid module along with Poisson's equation. We will discuss results for ion and radical flux uniformity to the substrate while varying the transmission line characteristics of the coil, symmetry of gas inlets/pumping, and internal structures. Comparisons will be made to expermental measurements of etch rates. ^*Work supported by SRC, NSF, ARPA/AFOSR and LAM Research.

  5. Gas Core Reactor Numerical Simulation Using a Coupled MHD-MCNP Model

    NASA Technical Reports Server (NTRS)

    Kazeminezhad, F.; Anghaie, S.

    2008-01-01

    Analysis is provided in this report of using two head-on magnetohydrodynamic (MHD) shocks to achieve supercritical nuclear fission in an axially elongated cylinder filled with UF4 gas as an energy source for deep space missions. The motivation for each aspect of the design is explained and supported by theory and numerical simulations. A subsequent report will provide detail on relevant experimental work to validate the concept. Here the focus is on the theory of and simulations for the proposed gas core reactor conceptual design from the onset of shock generations to the supercritical state achieved when the shocks collide. The MHD model is coupled to a standard nuclear code (MCNP) to observe the neutron flux and fission power attributed to the supercritical state brought about by the shock collisions. Throughout the modeling, realistic parameters are used for the initial ambient gaseous state and currents to ensure a resulting supercritical state upon shock collisions.

  6. Interface requirements for coupling a containment code to a reactor system thermal hydraulic codes

    SciTech Connect

    Baratta, A.J.

    1997-07-01

    To perform a complete analysis of a reactor transient, not only the primary system response but the containment response must also be accounted for. Such transients and accidents as a loss of coolant accident in both pressurized water and boiling water reactors and inadvertent operation of safety relief valves all challenge the containment and may influence flows because of containment feedback. More recently, the advanced reactor designs put forth by General Electric and Westinghouse in the US and by Framatome and Seimens in Europe rely on the containment to act as the ultimate heat sink. Techniques used by analysts and engineers to analyze the interaction of the containment and the primary system were usually iterative in nature. Codes such as RELAP or RETRAN were used to analyze the primary system response and CONTAIN or CONTEMPT the containment response. The analysis was performed by first running the system code and representing the containment as a fixed pressure boundary condition. The flows were usually from the primary system to the containment initially and generally under choked conditions. Once the mass flows and timing are determined from the system codes, these conditions were input into the containment code. The resulting pressures and temperatures were then calculated and the containment performance analyzed. The disadvantage of this approach becomes evident when one performs an analysis of a rapid depressurization or a long term accident sequence in which feedback from the containment can occur. For example, in a BWR main steam line break transient, the containment heats up and becomes a source of energy for the primary system. Recent advances in programming and computer technology are available to provide an alternative approach. The author and other researchers have developed linkage codes capable of transferring data between codes at each time step allowing discrete codes to be coupled together.

  7. Lunar electric power systems utilizing the SP-100 reactor coupled to dynamic conversion systems

    NASA Astrophysics Data System (ADS)

    Harty, Richard B.; Durand, Richard E.

    1993-03-01

    An integration study was performed by Rocketdyne under contract to NASA-LeRC. The study was concerned with coupling an SP-0100 reactor to either a Brayton or Stirling power conversion system. The application was for a surface power system to supply power requirements to a lunar base. A power level of 550 kWe was selected based on the NASA Space Exploration Initiative 90-day study. Reliability studies were initially performed to determine optimum power conversion redundancy. This study resulted in selecting three operating engines and one stand-by unit. Integration design studies indicated that either the Brayton or Stirling power conversion systems could be integrated with the PS-100 reactor. The Stirling system had an integration advantage because of smaller piping size and fewer components. The Stirling engine, however, is more complex and heavier than the Brayton rotating unit, which tends to off-set the Stirling integration advantage. From a performance consideration, the Brayton had a 9 percent mass advantage, and the Stirling had a 50 percent radiator advantage.

  8. Lunar electric power systems utilizing the SP-100 reactor coupled to dynamic conversion systems. Final report

    SciTech Connect

    Harty, R.B.; Durand, R.E.

    1993-03-01

    An integration study was performed by Rocketdyne under contract to NASA-LeRC. The study was concerned with coupling an SP-0100 reactor to either a Brayton or Stirling power conversion system. The application was for a surface power system to supply power requirements to a lunar base. A power level of 550 kWe was selected based on the NASA Space Exploration Initiative 90-day study. Reliability studies were initially performed to determine optimum power conversion redundancy. This study resulted in selecting three operating engines and one stand-by unit. Integration design studies indicated that either the Brayton or Stirling power conversion systems could be integrated with the PS-100 reactor. The Stirling system had an integration advantage because of smaller piping size and fewer components. The Stirling engine, however, is more complex and heavier than the Brayton rotating unit, which tends to off-set the Stirling integration advantage. From a performance consideration, the Brayton had a 9 percent mass advantage, and the Stirling had a 50 percent radiator advantage.

  9. Lunar electric power systems utilizing the SP-100 reactor coupled to dynamic conversion systems

    NASA Technical Reports Server (NTRS)

    Harty, Richard B.; Durand, Richard E.

    1993-01-01

    An integration study was performed by Rocketdyne under contract to NASA-LeRC. The study was concerned with coupling an SP-0100 reactor to either a Brayton or Stirling power conversion system. The application was for a surface power system to supply power requirements to a lunar base. A power level of 550 kWe was selected based on the NASA Space Exploration Initiative 90-day study. Reliability studies were initially performed to determine optimum power conversion redundancy. This study resulted in selecting three operating engines and one stand-by unit. Integration design studies indicated that either the Brayton or Stirling power conversion systems could be integrated with the PS-100 reactor. The Stirling system had an integration advantage because of smaller piping size and fewer components. The Stirling engine, however, is more complex and heavier than the Brayton rotating unit, which tends to off-set the Stirling integration advantage. From a performance consideration, the Brayton had a 9 percent mass advantage, and the Stirling had a 50 percent radiator advantage.

  10. Coupled radiation transport/thermal analysis of the radiation shield for a space nuclear reactor

    NASA Astrophysics Data System (ADS)

    Barattino, W. J.

    1985-07-01

    A coupled radiation transport-heat transfer-stress analysis of the radiation shield for an SP-100 reactor was performed using a numerical code developed at the University of New Mexico and Sandia National Laboratory. For a fast reactor operating at 1.66 MW sub th, the energy deposited and resulting temperature distribution was determined for a shield consisting of tungsten and lithium hydride pressed into a stainless steel honeycomb matrix. While temperature feedback was shown to have a minor effect on energy deposition, the shielding configuration was found to have a major influence in meeting thermal requirements of the lithium hydride. It was shown that a shield optimized for radiation protection will fail because of melting. However, with minor modifications in the shield layering and material selection, the thermal integrity of the shield can be preserved. A shield design of graphite, depleted lithium hydride, tungsten, and natural lithium hydride was shown to satisfy neutron and gamma fluence requirements, maximum temperature limits, and minimize cracking in the LiH portion of the shield.

  11. A knot or not a knot? SETting the record 'straight' on proteins.

    PubMed

    Taylor, William R; Xiao, Bing; Gamblin, Steven J; Lin, Kuang

    2003-02-01

    A novel knot found in the SET domain is examined in the light of five recent crystal structures and their descriptions in the literature. Using the algorithm of Taylor it was established that the backbone chain does not form a true knot. However, only two crosslinks corresponding to hydrogen-bonds were needed to form a knotted structure. Such loosely knotted structures formed by hydrogen-bonded crosslinks were assessed as lying between covalent crosslinks (such as disulphide bonds) and threaded-loops which are formed by close (unbonded) contacts between different parts of the chain. The term pseudo-knot was introduced (from the RNA field) to distinguish hydrogen-bonded 'knots'. PMID:12798035

  12. Spontaneous knotting of self-trapped waves

    PubMed Central

    Desyatnikov, Anton S.; Buccoliero, Daniel; Dennis, Mark R.; Kivshar, Yuri S.

    2012-01-01

    We describe theory and simulations of a spinning optical soliton whose propagation spontaneously excites knotted and linked optical vortices. The nonlinear phase of the self-trapped light beam breaks the wave front into a sequence of optical vortex loops around the soliton, which, through the soliton's orbital angular momentum and spatial twist, tangle on propagation to form links and knots. We anticipate similar spontaneous knot topology to be a universal feature of waves whose phase front is twisted and nonlinearly modulated, including superfluids and trapped matter waves. PMID:23105969

  13. Molecular knots in biology and chemistry.

    PubMed

    Lim, Nicole C H; Jackson, Sophie E

    2015-09-01

    Knots and entanglements are ubiquitous. Beyond their aesthetic appeal, these fascinating topological entities can be either useful or cumbersome. In recent decades, the importance and prevalence of molecular knots have been increasingly recognised by scientists from different disciplines. In this review, we provide an overview on the various molecular knots found in naturally occurring biological systems (DNA, RNA and proteins), and those created by synthetic chemists. We discuss the current knowledge in these fields, including recent developments in experimental and, in some cases, computational studies which are beginning to shed light into the complex interplay between the structure, formation and properties of these topologically intricate molecules. PMID:26291690

  14. Molecular knots in biology and chemistry

    NASA Astrophysics Data System (ADS)

    Lim, Nicole C. H.; Jackson, Sophie E.

    2015-09-01

    Knots and entanglements are ubiquitous. Beyond their aesthetic appeal, these fascinating topological entities can be either useful or cumbersome. In recent decades, the importance and prevalence of molecular knots have been increasingly recognised by scientists from different disciplines. In this review, we provide an overview on the various molecular knots found in naturally occurring biological systems (DNA, RNA and proteins), and those created by synthetic chemists. We discuss the current knowledge in these fields, including recent developments in experimental and, in some cases, computational studies which are beginning to shed light into the complex interplay between the structure, formation and properties of these topologically intricate molecules.

  15. Spontaneous knotting of self-trapped waves.

    PubMed

    Desyatnikov, Anton S; Buccoliero, Daniel; Dennis, Mark R; Kivshar, Yuri S

    2012-01-01

    We describe theory and simulations of a spinning optical soliton whose propagation spontaneously excites knotted and linked optical vortices. The nonlinear phase of the self-trapped light beam breaks the wave front into a sequence of optical vortex loops around the soliton, which, through the soliton's orbital angular momentum and spatial twist, tangle on propagation to form links and knots. We anticipate similar spontaneous knot topology to be a universal feature of waves whose phase front is twisted and nonlinearly modulated, including superfluids and trapped matter waves. PMID:23105969

  16. Energy functions for knots: Beginning to predict physical behavior

    SciTech Connect

    Simon, J.

    1996-12-31

    Several definitions have been proposed for the {open_quotes}energy{close_quotes} of a knot. The intuitive goal is to define a number u(K) that somehow measures how {open_quotes}tangled{close_quotes} or {open_quotes}crumpled{close_quotes} a knot K is. Typically, one starts with the idea that a small piece of the knot somehow repels other pieces, and then adds up the contributions from all the pieces. From a purely mathematical standpoint, one may hope to define new knot-type invariants, e.g by considering the minimum of u(K) as K ranges over all the knots of a given knot-type. We also are motivated by the desire to understand and predict how knot-type affects the behavior of physically real knots, in particular DNA loops in gel electrophoresis or random knotting experiments. Despite the physical naivete of recently studied knot energies, there now is enough laboratory data on relative gel velocity, along with computer calculations of idealized knot energies, to justify the assertion that knot energies can predict relative knot behavior in physical systems. The relationships between random knot frequencies and either gel velocities or knot energies is less clear at this time. 50 refs., 8 figs., 2 tabs.

  17. Methane coupling by membrane reactor. Quarterly report, June 25--September 24, 1996

    SciTech Connect

    Ma, Y.H.

    1996-12-28

    To prevent the deep oxidation of methane catalyzed by the direct contact between methane and the dense membrane material (SrFeCo{sub 0.5}O{sub 3{minus}x}), BaCe{sub 0.6}Sm{sub 0.4}O{sub 3} perovskite was coated on the inner surface of the dense membrane tube by the sol-gel technique. Different pretreatment methods were tested to compare their effects on the coated film. The morphology of the coated membrane was studied by SEM. The BaCe{sub 0.6}Sm{sub 0.4}O{sub 3}-coated membrane which was pretreated with a basic solution before coating was more evenly covered by the coating material. The oxygen permanence through the modified membrane tube were measured at different temperatures. The oxygen permanence were found to be about 70% lower than those of the unmodified tubes. The catalytic runs were carried out with La/MgO catalyst packed inside the membrane tube. The C{sub 2} yields obtained using the dense membrane reactor were less than 4%. This may have resulted from the fact that the methane fed to the tube side was still exposed to the uncoated area of the dense membrane surface due to the incomplete coverage of the coating material (BaCe{sub 0.6}Sm{sub 0.4}O{sub 3}). A hybrid dense membrane reactor, in which the oxygen was supplied by co-feeding oxygen with methane to the tube side and feeding air to the shell side, was used for the oxidative coupling of methane. Again, the inner surface of the membrane tube was coated with BaCe{sub 0.6}Sm{sub 0.4}O{sub 3} by the sol-gel technique, and the La/MgO catalyst was packed inside the membrane tube. The oxygen permanence through the membrane tube was found to be about ten times higher than that under non-reaction conditions. C{sub 2} yields up to 12% were obtained using the coated dense membrane reactor. These yields are higher than those obtained in an uncoated dense membrane reactor setup with methane and oxygen co-fed into the tube side, where the same catalyst was packed.

  18. Fluidized bed coupled rotary reactor for nanoparticles coating via atomic layer deposition

    SciTech Connect

    Duan, Chen-Long; Liu, Xiao; Chen, Rong E-mail: bshan@mail.hust.edu.cn; Shan, Bin E-mail: bshan@mail.hust.edu.cn

    2015-07-15

    A fluidized bed coupled rotary reactor has been designed for coating on nanoparticles (NPs) via atomic layer deposition. It consists of five major parts: reaction chamber, dosing and fluidizing section, pumping section, rotary manipulator components, as well as a double-layer cartridge for the storage of particles. In the deposition procedure, continuous fluidization of particles enlarges and homogenizes the void fraction in the particle bed, while rotation enhances the gas-solid interactions to stabilize fluidization. The particle cartridge presented here enables both the fluidization and rotation acting on the particle bed, demonstrated by the analysis of pressure drop. Moreover, enlarged interstitials and intense gas–solid contact under sufficient fluidizing velocity and proper rotation speed facilitate the precursor delivery throughout the particle bed and consequently provide a fast coating process. The cartridge can ensure precursors flowing through the particle bed exclusively to achieve high utilization without static exposure operation. By optimizing superficial gas velocities and rotation speeds, minimum pulse time for complete coating has been shortened in experiment, and in situ mass spectrometry showed the precursor usage can reach 90%. Inductively coupled plasma-optical emission spectroscopy results suggested a saturated growth of nanoscale Al{sub 2}O{sub 3} films on spherical SiO{sub 2} NPs. Finally, the uniformity and composition of the shells were characterized by high angle annular dark field-transmission electron microscopy and energy dispersive X-ray spectroscopy.

  19. Fluidized bed coupled rotary reactor for nanoparticles coating via atomic layer deposition.

    PubMed

    Duan, Chen-Long; Liu, Xiao; Shan, Bin; Chen, Rong

    2015-07-01

    A fluidized bed coupled rotary reactor has been designed for coating on nanoparticles (NPs) via atomic layer deposition. It consists of five major parts: reaction chamber, dosing and fluidizing section, pumping section, rotary manipulator components, as well as a double-layer cartridge for the storage of particles. In the deposition procedure, continuous fluidization of particles enlarges and homogenizes the void fraction in the particle bed, while rotation enhances the gas-solid interactions to stabilize fluidization. The particle cartridge presented here enables both the fluidization and rotation acting on the particle bed, demonstrated by the analysis of pressure drop. Moreover, enlarged interstitials and intense gas-solid contact under sufficient fluidizing velocity and proper rotation speed facilitate the precursor delivery throughout the particle bed and consequently provide a fast coating process. The cartridge can ensure precursors flowing through the particle bed exclusively to achieve high utilization without static exposure operation. By optimizing superficial gas velocities and rotation speeds, minimum pulse time for complete coating has been shortened in experiment, and in situ mass spectrometry showed the precursor usage can reach 90%. Inductively coupled plasma-optical emission spectroscopy results suggested a saturated growth of nanoscale Al2O3 films on spherical SiO2 NPs. Finally, the uniformity and composition of the shells were characterized by high angle annular dark field-transmission electron microscopy and energy dispersive X-ray spectroscopy. PMID:26233411

  20. Fluidized bed coupled rotary reactor for nanoparticles coating via atomic layer deposition

    NASA Astrophysics Data System (ADS)

    Duan, Chen-Long; Liu, Xiao; Shan, Bin; Chen, Rong

    2015-07-01

    A fluidized bed coupled rotary reactor has been designed for coating on nanoparticles (NPs) via atomic layer deposition. It consists of five major parts: reaction chamber, dosing and fluidizing section, pumping section, rotary manipulator components, as well as a double-layer cartridge for the storage of particles. In the deposition procedure, continuous fluidization of particles enlarges and homogenizes the void fraction in the particle bed, while rotation enhances the gas-solid interactions to stabilize fluidization. The particle cartridge presented here enables both the fluidization and rotation acting on the particle bed, demonstrated by the analysis of pressure drop. Moreover, enlarged interstitials and intense gas-solid contact under sufficient fluidizing velocity and proper rotation speed facilitate the precursor delivery throughout the particle bed and consequently provide a fast coating process. The cartridge can ensure precursors flowing through the particle bed exclusively to achieve high utilization without static exposure operation. By optimizing superficial gas velocities and rotation speeds, minimum pulse time for complete coating has been shortened in experiment, and in situ mass spectrometry showed the precursor usage can reach 90%. Inductively coupled plasma-optical emission spectroscopy results suggested a saturated growth of nanoscale Al2O3 films on spherical SiO2 NPs. Finally, the uniformity and composition of the shells were characterized by high angle annular dark field-transmission electron microscopy and energy dispersive X-ray spectroscopy.

  1. Cotranslational folding of deeply knotted proteins

    NASA Astrophysics Data System (ADS)

    Chwastyk, Mateusz; Cieplak, Marek

    2015-09-01

    Proper folding of deeply knotted proteins has a very low success rate even in structure-based models which favor formation of the native contacts but have no topological bias. By employing a structure-based model, we demonstrate that cotranslational folding on a model ribosome may enhance the odds to form trefoil knots for protein YibK without any need to introduce any non-native contacts. The ribosome is represented by a repulsive wall that keeps elongating the protein. On-ribosome folding proceeds through a a slipknot conformation. We elucidate the mechanics and energetics of its formation. We show that the knotting probability in on-ribosome folding is a function of temperature and that there is an optimal temperature for the process. Our model often leads to the establishment of the native contacts without formation of the knot.

  2. Cotranslational folding of deeply knotted proteins.

    PubMed

    Chwastyk, Mateusz; Cieplak, Marek

    2015-09-01

    Proper folding of deeply knotted proteins has a very low success rate even in structure-based models which favor formation of the native contacts but have no topological bias. By employing a structure-based model, we demonstrate that cotranslational folding on a model ribosome may enhance the odds to form trefoil knots for protein YibK without any need to introduce any non-native contacts. The ribosome is represented by a repulsive wall that keeps elongating the protein. On-ribosome folding proceeds through a a slipknot conformation. We elucidate the mechanics and energetics of its formation. We show that the knotting probability in on-ribosome folding is a function of temperature and that there is an optimal temperature for the process. Our model often leads to the establishment of the native contacts without formation of the knot. PMID:26292194

  3. Vortex knot cascade in polynomial skein relations

    NASA Astrophysics Data System (ADS)

    Ricca, Renzo L.

    2016-06-01

    The process of vortex cascade through continuous reduction of topological complexity by stepwise unlinking, that has been observed experimentally in the production of vortex knots (Kleckner & Irvine, 2013), is shown to be reproduced in the branching of the skein relations of knot polynomials (Liu & Ricca, 2015) used to identify topological complexity of vortex systems. This observation can be usefully exploited for predictions of energy-complexity estimates for fluid flows.

  4. Wastewater treatment from biodiesel production via a coupled photo-Fenton-aerobic sequential batch reactor (SBR) system.

    PubMed

    Ramírez, Ximena María Vargas; Mejía, Gina Maria Hincapié; López, Kelly Viviana Patiño; Vásquez, Gloria Restrepo; Sepúlveda, Juan Miguel Marín

    2012-01-01

    A coupled system of the photo-Fenton advanced oxidation technique and an aerobic sequential batch reactor (SBR) was used to treat wastewater from biodiesel production using either palm or castor oil. The photo-Fenton reaction and biological process were evaluated individually and were effective at treating the wastewater; nevertheless, each process required longer degradation times for the wastewater pollutants compared with the coupled system. The proposed coupled photo-Fenton/aerobic SBR system obtained a 90% reduction of the chemical oxygen demand (COD) in half of the time required for the biological system individually. PMID:22766873

  5. 3D neutronic codes coupled with thermal-hydraulic system codes for PWR, and BWR and VVER reactors

    SciTech Connect

    Langenbuch, S.; Velkov, K.; Lizorkin, M.

    1997-07-01

    This paper describes the objectives of code development for coupling 3D neutronics codes with thermal-hydraulic system codes. The present status of coupling ATHLET with three 3D neutronics codes for VVER- and LWR-reactors is presented. After describing the basic features of the 3D neutronic codes BIPR-8 from Kurchatov-Institute, DYN3D from Research Center Rossendorf and QUABOX/CUBBOX from GRS, first applications of coupled codes for different transient and accident scenarios are presented. The need of further investigations is discussed.

  6. Absence of knots in known RNA structures.

    PubMed

    Micheletti, Cristian; Di Stefano, Marco; Orland, Henri

    2015-02-17

    The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also, abound in viral DNA packaged inside bacteriophages. RNA molecules, however, have not yet been systematically screened for the occurrence of physical knots. We have accordingly undertaken the systematic profiling of the several thousand RNA structures present in the Protein Data Bank (PDB). The search identified no more than three deeply knotted RNA molecules. These entries are rRNAs of about 3,000 nt solved by cryo-EM. Their genuine knotted state is, however, doubtful based on the detailed structural comparison with homologs of higher resolution, which are all unknotted. Compared with the case of proteins and viral DNA, the observed incidence of knots in available RNA structures is, therefore, practically negligible. This fact suggests that either evolutionary selection or thermodynamic and kinetic folding mechanisms act toward minimizing the entanglement of RNA to an extent that is unparalleled by other types of biomolecules. A possible general strategy for designing synthetic RNA sequences capable of self-tying in a twist-knot fold is finally proposed. PMID:25646433

  7. Torus Knots and the Topological Vertex

    NASA Astrophysics Data System (ADS)

    Jockers, Hans; Klemm, Albrecht; Soroush, Masoud

    2014-08-01

    We propose a class of toric Lagrangian A-branes on the resolved conifold that is suitable to describe torus knots on S 3. The key role is played by the transformation, which generates a general torus knot from the unknot. Applying the topological vertex to the proposed A-branes, we rederive the colored HOMFLY polynomials for torus knots, in agreement with the Rosso and Jones formula. We show that our A-model construction is mirror symmetric to the B-model analysis of Brini, Eynard and Mariño. Compared to the recent proposal by Aganagic and Vafa for knots on S 3, we demonstrate that the disk amplitude of the A-brane associated with any knot is sufficient to reconstruct the entire B-model spectral curve. Finally, the construction of toric Lagrangian A-branes is generalized to other local toric Calabi-Yau geometries, which paves the road to study knots in other three-manifolds such as lens spaces.

  8. Prediction of the optimal set of contacts to fold the smallest knotted protein

    NASA Astrophysics Data System (ADS)

    Dabrowski-Tumanski, P.; Jarmolinska, A. I.; Sulkowska, J. I.

    2015-09-01

    Knotted protein chains represent a new motif in protein folds. They have been linked to various diseases, and recent extensive analysis of the Protein Data Bank shows that they constitute 1.5% of all deposited protein structures. Despite thorough theoretical and experimental investigations, the role of knots in proteins still remains elusive. Nonetheless, it is believed that knots play an important role in mechanical and thermal stability of proteins. Here, we perform a comprehensive analysis of native, shadow-specific and non-native interactions which describe free energy landscape of the smallest knotted protein (PDB id 2efv). We show that the addition of shadow-specific contacts in the loop region greatly enhances folding kinetics, while the addition of shadow-specific contacts along the C-terminal region (H3 or H4) results in a new folding route with slower kinetics. By means of direct coupling analysis (DCA) we predict non-native contacts which also can accelerate kinetics. Next, we show that the length of the C-terminal knot tail is responsible for the shape of the free energy barrier, while the influence of the elongation of the N-terminus is not significant. Finally, we develop a concept of a minimal contact map sufficient for 2efv protein to fold and analyze properties of this protein using this map.

  9. Origin of metastable knots in single flexible chains.

    PubMed

    Dai, Liang; Renner, C Benjamin; Doyle, Patrick S

    2015-01-23

    Recent theoretical progress has explained the physics of knotting of semiflexible polymers, yet knotting of flexible polymers is relatively unexplored. We herein develop a new theory for the size distribution of knots on a flexible polymer and the existence of metastable knots. We show the free energy of a flexible molecule in a tube can be mapped to quantitatively reproduce the free energy distribution of a knot on a flexible chain. The size distribution of knots on flexible chains is expected to be universal and might be observed at a macroscopic scale, such as a string of hard balls. PMID:25659023

  10. Comparing models of Red Knot population dynamics

    USGS Publications Warehouse

    McGowan, Conor

    2015-01-01

    Predictive population modeling contributes to our basic scientific understanding of population dynamics, but can also inform management decisions by evaluating alternative actions in virtual environments. Quantitative models mathematically reflect scientific hypotheses about how a system functions. In Delaware Bay, mid-Atlantic Coast, USA, to more effectively manage horseshoe crab (Limulus polyphemus) harvests and protect Red Knot (Calidris canutus rufa) populations, models are used to compare harvest actions and predict the impacts on crab and knot populations. Management has been chiefly driven by the core hypothesis that horseshoe crab egg abundance governs the survival and reproduction of migrating Red Knots that stopover in the Bay during spring migration. However, recently, hypotheses proposing that knot dynamics are governed by cyclical lemming dynamics garnered some support in data analyses. In this paper, I present alternative models of Red Knot population dynamics to reflect alternative hypotheses. Using 2 models with different lemming population cycle lengths and 2 models with different horseshoe crab effects, I project the knot population into the future under environmental stochasticity and parametric uncertainty with each model. I then compare each model's predictions to 10 yr of population monitoring from Delaware Bay. Using Bayes' theorem and model weight updating, models can accrue weight or support for one or another hypothesis of population dynamics. With 4 models of Red Knot population dynamics and only 10 yr of data, no hypothesis clearly predicted population count data better than another. The collapsed lemming cycle model performed best, accruing ~35% of the model weight, followed closely by the horseshoe crab egg abundance model, which accrued ~30% of the weight. The models that predicted no decline or stable populations (i.e. the 4-yr lemming cycle model and the weak horseshoe crab effect model) were the most weakly supported.

  11. Self-powered denitration of landfill leachate through ammonia/nitrate coupled redox fuel cell reactor.

    PubMed

    Zhang, Huimin; Xu, Wei; Feng, Daolun; Liu, Zhanmeng; Wu, Zucheng

    2016-03-01

    In order to explore the feasibility of energy-free denitrifying N-rich wastewater, a self-powered device was uniquely assembled, in which ammonia/nitrate coupled redox fuel cell (CRFC) reactor was served as removing nitrogen and harvesting electric energy simultaneously. Ammonia is oxidized at anodic compartment and nitrate is reduced at cathodic compartment spontaneously by electrocatalysis. In 7.14 mM ammonia+0.2M KOH anolyte and 4.29 mM KNO3+0.1M H2SO4 catholyte, the nitrate removal efficiency was 46.9% after 18 h. Meanwhile, a maximum power density of 170 mW m(-2) was achieved when applying Pd/C cathode. When NH4Cl/nitrate and ammonia/nitrite CRFCs were tested, 26.2% N-NH4Cl and 91.4% N-NO2(-) were removed respectively. Nitrogen removal efficiency for real leachate at the same initial NH3-N concentration is 22.9% and nitrification of ammonia in leachate can be used as nitrate source. This work demonstrated a new way for N-rich wastewater remediation with electricity generation. PMID:26720140

  12. Modeling of the simulated countercurrent moving-bed chromatographic reactor used for the oxidative coupling of methane

    SciTech Connect

    Tonkovich, A.L.Y.; Carr, R.W.

    1994-09-01

    The oxidative coupling reaction of methane (OCM) is a potential industrial reaction for the efficient production of ethylene. Replacement of current technologies requires significant product yield improvements. An experimental novel reactor design, the modified simulated countercurrent moving-bed chromatographic reactor (SCMCR), has reported improved ethane and ethylene product yields over other reported values. An understanding of the reactor operation is aided by concurrent mathematical modeling. The model mimics the exact experimental reactor configuration. Four sections are used; each section contains a reaction column and two separation columns connected in series. The feed is switched from section to section at discrete intervals. Reaction occurs in the first column and is followed by product and reactant separation in the ensuing section columns. Langmuir adsorption isotherms are used. The model does not incorporate the realistic and complex kinetics rising, from the OCM, rather a simplified reaction term is used to qualitatively gain insight into the operation of the modified SCMCR. A unimolecular reaction network is used in the model. The rate constants are set to permit a small fractional conversion, 5% per pass, at the concentrations during the first cycle. Similarly to the experimental reactor, the model adds a make-up feed (defined as percentage of the original feed, where excess methane is fed during the first cycle of the experimental reactor) to augment lost reactants.

  13. Cynod: A Neutronics Code for Pebble Bed Modular Reactor Coupled Transient Analysis

    SciTech Connect

    Hikaru Hiruta; Abderrafi M. Ougouag; Hans D. Gougar; Javier Ortensi

    2008-09-01

    The Pebble Bed Reactor (PBR) is one of the two concepts currently considered for development into the Next Generation Nuclear Plant (NGNP). This interest is due, in particular, to the concept’s inherent safety characteristics. In order to verify and confirm the design safety characteristics of the PBR computational tools must be developed that treat the range of phenomena that are expected to be important for this type of reactors. This paper presents a recently developed 2D R-Z cylindrical nodal kinetics code and shows some of its capabilities by applying it to a set of known and relevant benchmarks. The new code has been coupled to the thermal hydraulics code THERMIX/KONVEK[1] for application to the simulation of very fast transients in PBRs. The new code, CYNOD, has been written starting with a fixed source solver extracted from the nodal cylindrical geometry solver contained within the PEBBED code. The fixed source solver was then incorporated into a kinetic solver.. The new code inherits the spatial solver characteristics of the nodal solver within PEBBED. Thus, the time-dependent neutron diffusion equation expressed analytically in each node of the R-Z cylindrical geometry sub-domain (or node) is transformed into one-dimensional equations by means of the usual transverse integration procedure. The one-dimensional diffusion equations in each of the directions are then solved using the analytic Green’s function method. The resulting equations for the entire domain are then re-cast in the form of the Direct Coarse Mesh Finite Difference (D-CMFD) for convenience of solution. The implicit Euler method is used for the time variable discretization. In order to correctly treat the cusping effect for nodes that contain a partially inserted control rod a method is used that takes advantage of the Green’s function solution available in the intrinsic method. In this corrected treatment, the nodes are re-homogenized using axial flux shapes reconstructed based on the

  14. The inner knot of the Crab nebula

    NASA Astrophysics Data System (ADS)

    Lyutikov, Maxim; Komissarov, Serguei S.; Porth, Oliver

    2016-02-01

    We model the inner knot of the Crab nebula as a synchrotron emission coming from the non-spherical MHD termination shock of relativistic pulsar wind. The post-shock flow is mildly relativistic; as a result the Doppler beaming has a strong impact on the shock appearance. The model can reproduce the knot location, size, elongation, brightness distribution, luminosity and polarization provided the effective magnetization of the section of the pulsar wind producing the knot is low, σ ≤ 1. In the striped wind model, this implies that the striped zone is rather wide, with the magnetic inclination angle of the Crab pulsar ≥45°; this agrees with the previous model-dependent estimate based on the gamma-ray emission of the pulsar. We conclude that the tiny knot is indeed a bright spot on the surface of a quasi-stationary magnetic relativistic shock and that this shock is a site of efficient particle acceleration. On the other hand, the deduced low magnetization of the knot plasma implies that this is an unlikely site for the Crab's gamma-ray flares, if they are related to the fast relativistic magnetic reconnection events.

  15. Optimal tissue tension for secure laparoscopic knots.

    PubMed

    Raut, Vikram N; Takaori, Kyoichi; Uemoto, Shinji

    2011-02-01

    Security and strength of a knot are main concerns of the surgeon since last 4000 years. The advancement of endoscopic and minimally invasive surgery in last few decades had a significant influence on a knot tying. The most difficult methods of a knot tying are performed during endoscopic procedures, in which the surgeon execute instrumentation from outside the body without palpation of organs and three-dimensional vision. In addition, laparoscopic instruments due to friction in transmission mechanism have very poor force feedback. This results into difficulty in applying the appropriate grasping force to the tissue, resulting in slippage or damage to the tissue. Our hypothesis highlights the need of tissue approximation at the 'optimum tissue tension' sufficient to resist the slippage of suture/clip without strangulation. The purpose of suture is to maintain an approximation of the tissue until healing progresses to the point where artificial support is no longer necessary for the wound to resist normal stress. When the approximation is too tight, tension in tissue leads to diminished blood supply resulting into the necrosis. Various tissues need different blood supply and different tissue pressure for optimum healings. Proposed hypothesis helps to improve the feedback of current knot pushers or clip applicators used in laparoscopic surgery using optimum tissue tension. Tissue approximation at an optimal tissue tension translates into the secure laparoscopic knot/clip application resulting in prevention of wound dehiscence, anastomosis leak, and secondary haemorrhages. PMID:21071154

  16. Dynamic Modeling and Control of Nuclear Reactors Coupled to Closed-Loop Brayton Cycle Systems using SIMULINK™

    NASA Astrophysics Data System (ADS)

    Wright, Steven A.; Sanchez, Travis

    2005-02-01

    The operation of space reactors for both in-space and planetary operations will require unprecedented levels of autonomy and control. Development of these autonomous control systems will require dynamic system models, effective control methodologies, and autonomous control logic. This paper briefly describes the results of reactor, power-conversion, and control models that are implemented in SIMULINK™ (Simulink, 2004). SIMULINK™ is a development environment packaged with MatLab™ (MatLab, 2004) that allows the creation of dynamic state flow models. Simulation modules for liquid metal, gas cooled reactors, and electrically heated systems have been developed, as have modules for dynamic power-conversion components such as, ducting, heat exchangers, turbines, compressors, permanent magnet alternators, and load resistors. Various control modules for the reactor and the power-conversion shaft speed have also been developed and simulated. The modules are compiled into libraries and can be easily connected in different ways to explore the operational space of a number of potential reactor, power-conversion system configurations, and control approaches. The modularity and variability of these SIMULINK™ models provides a way to simulate a variety of complete power generation systems. To date, both Liquid Metal Reactors (LMR), Gas Cooled Reactors (GCR), and electric heaters that are coupled to gas-dynamics systems and thermoelectric systems have been simulated and are used to understand the behavior of these systems. Current efforts are focused on improving the fidelity of the existing SIMULINK™ modules, extending them to include isotopic heaters, heat pipes, Stirling engines, and on developing state flow logic to provide intelligent autonomy. The simulation code is called RPC-SIM (Reactor Power and Control-Simulator).

  17. Simulations of electrophoretic collisions of DNA knots with gel obstacles

    NASA Astrophysics Data System (ADS)

    Weber, C.; DeLos Rios, P.; Dietler, G.; Stasiak, A.

    2006-04-01

    Gel electrophoresis can be used to separate nicked circular DNA molecules of equal length but forming different knot types. At low electric fields, complex knots drift faster than simpler knots. However, at high electric field the opposite is the case and simpler knots migrate faster than more complex knots. Using Monte Carlo simulations we investigate the reasons of this reversal of relative order of electrophoretic mobility of DNA molecules forming different knot types. We observe that at high electric fields the simulated knotted molecules tend to hang over the gel fibres and require passing over a substantial energy barrier to slip over the impeding gel fibre. At low electric field the interactions of drifting molecules with the gel fibres are weak and there are no significant energy barriers that oppose the detachment of knotted molecules from transverse gel fibres.

  18. Estimation of Electron Temperature and Frequency Components in a Dual Frequency Capacitively-Coupled Plasma Processing Reactor

    NASA Astrophysics Data System (ADS)

    Ito, Toru; Mo, Yun; Masahiro, Horigome

    2008-10-01

    The measurement of electron temperature in RF plasma sources with Langmuir probes is difficult because of the influence of rf noise. We attempted to estimate the electron temperature in a capacitively-coupled plasma processing reactor with a Surface Wave Probe [1] which employs microwaves. We also estimated the frequency spectrum with the sensitive PAP [1, 2]. We measured the harmonics which appeared in the bulk plasma for various experimental conditions in the dual-frequency [60 MHz and 2MHz] capacitively-coupled plasma processing reactor. We estimated RF power spectra for several experimental conditions like RF power [500-2000W], gas pressure [3-20Pa], and gas species [Ar, CF4]. The measurement results suggest the existence of energy transport among several frequency spectrum. [1ex] [1] K. Nakamura, M. Ohata, and H. Sugai: J. Vac. Sci. Technol. A 21, 325 (2003). [0pt] [2] T. Shirakawa and H. Sugai : Jpn. J. Appl. Phys. 32, 5129 (1993).

  19. Polymer theta-point as a knot delocalization transition.

    PubMed

    Orlandini, E; Stella, A L; Vanderzande, C

    2003-09-01

    We study numerically the tightness of prime flat knots in a model of self-attracting polymers with excluded volume. We find that these knots are localized in the high temperature swollen regime, but become delocalized in the low temperature globular phase. Precisely at the collapse transition, the knots are weakly localized. Some of our results can be interpreted in terms of the theory of polymer networks, which allows one to conjecture exact exponents for the knot length probability distributions. PMID:14524795

  20. Evaluation of Nodal Reactor Physics Methods for Quasi-Static and Time-Dependent Coupled Neutronic Thermal - Analysis of Pressurized Water Reactor Transients

    NASA Astrophysics Data System (ADS)

    Feltus, Madeline Anne

    1990-01-01

    This thesis examines coupled time-dependent thermal -hydraulic (T/H) and neutronics solution methods for Pressurized Water Reactor (PWR) transient analysis. The degree of equivalence is evaluated between the typical quasi-static approach and a newly-developed iterative tandem method. Four specific PWR transients that exhibit a wide range of Reactor Coolant System (RCS) T/H response were investigated: (1) a Station Blackout Anticipated Transient Without Scram (ATWS), (2) a Loss of Feedwater ATWS, (3) a Total Loss of RCS Flow with Scram, and (4) a Main Steam Line Break (MSLB). Rather than using simplified RCS and core models, the theory and method in this thesis were applied practically by using realistic models for an actual four-loop Westinghouse PWR plant. The time-dependent STAR kinetics code, based on the QUANDRY Analytic Nodal Method, and the RETRAN and MCPWR T/H systems codes were used to develop a new, fully coupled, tandem STAR/MCPWRQ methodology that runs tandemly on an enhanced 386/387 IBM PC architecture. MCPWRQ uses externally calculated power input rather than point kinetics power level results. The tandem method was compared to quasi -static STAR and time-dependent STAR 2-D and 3-D kinetics results. The new STAR/MCPWRQ method uses RETRAN time-dependent T/H and point kinetics power input as a first estimate. STAR and MCPWRQ are used tandemly to couple STAR 3-D, time-dependent core power results with the MCPWRQ RCS T/H phenomena. This thesis shows that: (a) quasi-static and point kinetics methods are not able to describe severe PWR transient phenomena adequately; and (b) fully coupled, 3-D, time -dependent, tandem (or possibly parallel) analysis methods should be used for PWR reactor transients instead. By tandemly coupling the RCS response in terms of updated core inlet conditions with 3-D time-dependent core kinetics response, the core power response and T/H conditions are forced to be self-consistent during the entire transient. The transient analyses

  1. Nonlinear electrodynamics is skilled with knots

    NASA Astrophysics Data System (ADS)

    Goulart, E.

    2016-07-01

    The aim of this letter is threefold: First is to show that nonlinear generalizations of electrodynamics support various types of knotted solutions in vacuum. The solutions are universal in the sense that they do not depend on the specific Lagrangian density, at least if the latter gives rise to a well-posed theory. Second, is to describe the interaction between probe waves and knotted background configurations. We show that the qualitative behaviour of this interaction may be described in terms of Robinson congruences, which appear explicitly in the causal structure of the theory. Finally, we argue that optical arrangements endowed with intense background fields could be the natural place to look for the knots experimentally.

  2. Test Results from a Direct Drive Gas Reactor Simulator Coupled to a Brayton Power Conversion Unit

    NASA Technical Reports Server (NTRS)

    Hervol, David S.; Briggs, Maxwell H.; Owen, Albert K.; Bragg-Sitton, Shannon M.; Godfroy, Thomas J.

    2010-01-01

    Component level testing of power conversion units proposed for use in fission surface power systems has typically been done using relatively simple electric heaters for thermal input. These heaters do not adequately represent the geometry or response of proposed reactors. As testing of fission surface power systems transitions from the component level to the system level it becomes necessary to more accurately replicate these reactors using reactor simulators. The Direct Drive Gas-Brayton Power Conversion Unit test activity at the NASA Glenn Research Center integrates a reactor simulator with an existing Brayton test rig. The response of the reactor simulator to a change in Brayton shaft speed is shown as well as the response of the Brayton to an insertion of reactivity, corresponding to a drum reconfiguration. The lessons learned from these tests can be used to improve the design of future reactor simulators which can be used in system level fission surface power tests.

  3. Are there p-adic knot invariants?

    NASA Astrophysics Data System (ADS)

    Morozov, A. Yu.

    2016-04-01

    We suggest using the Hall-Littlewood version of the Rosso-Jones formula to define the germs of p-adic HOMFLY-PT polynomials for torus knots [ m, n] as coefficients of superpolynomials in a q-expansion. In this form, they have at least the [ m, n] ↔ [ n, m] topological invariance. This opens a new possibility to interpret superpolynomials as p-adic deformations of HOMFLY polynomials and poses a question of generalizing to other knot families, which is a substantial problem for several branches of modern theory.

  4. On the geometry of stiff knots

    NASA Astrophysics Data System (ADS)

    Pierre-Louis, O.

    2009-09-01

    We analyse the geometry of a thin knotted string with bending rigidity. Two types of geometric properties are investigated. First, following the approach of von der Mosel [H. von der Mosel, Asymptotic Anal. 18, 49 (1998)], we derive upper bounds for the multiplicity of crossings and braids. Then, using a general inequality for the length of 3D curves derived by Chakerian [G.D. Chakerian, Proc. of the American Math. Soc. 15, 886 (1964)], we analyze the size and confinement of a knot

  5. The Miller׳s knot as an alternative to the surgical knotting? Characterization of the mechanical behavior.

    PubMed

    Ortillés, A; Rodríguez, J; Calvo, B

    2014-10-01

    Several types of materials and surgical suture patterns are used in conventional surgery. Their combination with an appropriate knot is the basis for correct tissue apposition and healing. Knot security is essential to prevent loosening or slipping before the suture line is completely closed. Nevertheless, the knot itself is the weakest link in any surgical handling. The aim of this study is to determine and compare the mechanical behavior of four surgical knot types (square knot, surgeon׳s knot, square slipknot and Miller׳s knot) performed with three different suture materials (absorbable monofilament glyconate, non-absorbable monofilament polyamide and absorbable braided polyglycolic acid) in a non-biological experimental in vitro model (a tube of synthetic material with non-linear mechanical behavior). The mechanical properties of each suture material are also compared. Ten samples were mechanically tested for each suture and knot using a uniaxial tensile test until complete sample rupture. The failure Cauchy stress and stretch were calculated. The Cauchy stress at 5%, 10% and 15% strain and standard deviation were compared for each suture and knot type. The results demonstrated that all the suture materials had statistically significant differences in their non-linear mechanical behavior. Absorbable monofilament glyconate was the most compliant suture with the greatest tensile strength, while absorbable braided polyglycolic acid was the stiffest. Regardless of the suture type used, the Miller׳s knot had the greatest failure Cauchy stress and stretch, while the square, surgeon׳s and square slipknot had the lowest. In all cases, the Miller׳s knot was more compliant and had greater tensile strength than the other knots. The square knot, surgeon׳s knot, and square slipknot had statistically significant similarities in their mechanical behavior. Therefore, the Miller׳s knot could be classified as the gold standard and an alternative to the surgical knotting

  6. REACTOR

    DOEpatents

    Szilard, L.

    1963-09-10

    A breeder reactor is described, including a mass of fissionable material that is less than critical with respect to unmoderated neutrons and greater than critical with respect to neutrons of average energies substantially greater than thermal, a coolant selected from sodium or sodium--potassium alloys, a control liquid selected from lead or lead--bismuth alloys, and means for varying the quantity of control liquid in the reactor. (AEC)

  7. REACTOR

    DOEpatents

    Christy, R.F.

    1961-07-25

    A means is described for co-relating the essential physical requirements of a fission chain reaction in order that practical, compact, and easily controllable reactors can be built. These objects are obtained by employing a composition of fissionsble isotope and moderator in fluid form in which the amount of fissionsble isotcpe present governs the reaction. The size of the reactor is no longer a critical factor, the new criterion being the concentration of the fissionable isotope.

  8. Knotted proteins: A tangled tale of Structural Biology

    PubMed Central

    Faísca, Patrícia F.N.

    2015-01-01

    Knotted proteins have their native structures arranged in the form of an open knot. In the last ten years researchers have been making significant efforts to reveal their folding mechanism and understand which functional advantage(s) knots convey to their carriers. Molecular simulations have been playing a fundamental role in this endeavor, and early computational predictions about the knotting mechanism have just been confirmed in wet lab experiments. Here we review a collection of simulation results that allow outlining the current status of the field of knotted proteins, and discuss directions for future research. PMID:26380658

  9. A trefoil knotted polymer produced through ring expansion.

    PubMed

    Cao, Peng-Fei; Mangadlao, Joey; Advincula, Rigoberto

    2015-04-20

    A synthetic strategy is reported for the production of a trefoil knotted polymer from a copper(I)-templated helical knot precursor through ring expansion. The expected changes in the properties of the knotted polymer compared to a linear analogue, for example, reduced hydrodynamic radius and lower intrinsic viscosity, together with an atomic force microscopy (AFM) image of individual molecular knots, confirmed the formation of the resulting trefoil knotted polymer. The strategies employed here could be utilized to enrich the variety of available polymers with new architectures. PMID:25728998

  10. Use of RELAP5-3D for Dynamic Analysis of a Closed-Loop Brayton Cycle Coupled To a Nuclear Reactor

    SciTech Connect

    McCann, Larry D.

    2007-01-30

    This paper describes results of a dynamic system model for a pair of closed Brayton-cycle (CBC) loops running in parallel that are connected to a nuclear gas reactor. The model assumes direct coupling between the reactor and the Brayton-cycle loops. The RELAP5-3D (version 2.4.1) computer program was used to perform the analysis. Few reactors have ever been coupled to closed Brayton-cycle systems. As such their behavior under dynamically varying loads, startup and shut down conditions, and requirements for safe and autonomous operation are largely unknown. The model described in this paper represents the reactor, turbine, compressor, recuperator, heat rejection system and alternator. The initial results of the model indicate stable operation of the reactor-driven Brayton-cycle system. However, for analysts with mostly pressurized water reactor experience, the Brayton cycle loops coupled to a gas-cooled reactor also indicate some counter-intuitive behavior for the complete coupled system. This model has provided crucial information in evaluating the reactor design and would have been further developed for use in developing procedures for safe start up, shut down, safe-standby, and other autonomous operating modes had the plant development cycle been completed.

  11. Use of RELAP5-3D for Dynamic Analysis of a Closed-Loop Brayton Cycle Coupled To a Nuclear Reactor

    NASA Astrophysics Data System (ADS)

    McCann, Larry D.

    2007-01-01

    This paper describes results of a dynamic system model for a pair of closed Brayton-cycle (CBC) loops running in parallel that are connected to a nuclear gas reactor. The model assumes direct coupling between the reactor and the Brayton-cycle loops. The RELAP5-3D (version 2.4.1) computer program was used to perform the analysis. Few reactors have ever been coupled to closed Brayton-cycle systems. As such their behavior under dynamically varying loads, startup and shut down conditions, and requirements for safe and autonomous operation are largely unknown. The model described in this paper represents the reactor, turbine, compressor, recuperator, heat rejection system and alternator. The initial results of the model indicate stable operation of the reactor-driven Brayton-cycle system. However, for analysts with mostly pressurized water reactor experience, the Brayton cycle loops coupled to a gas-cooled reactor also indicate some counter-intuitive behavior for the complete coupled system. This model has provided crucial information in evaluating the reactor design and would have been further developed for use in developing procedures for safe start up, shut down, safe-standby, and other autonomous operating modes had the plant development cycle been completed.

  12. A preliminary design of a knot undulator.

    PubMed

    Xi, Fuchun; Shi, Tan; Fan, Qingyan; Prestemon, Soren; Wan, Weishi; An, Zhenghua; Qiao, S

    2013-01-01

    The magnetic field configuration of the previously proposed knot undulator [Qiao et al. (2009). Rev. Sci. Instrum. 80, 085108] is realised in the design of a hybridized elliptically polarized undulator, which is presented. Although the details of the field distribution are not the same as those in the theoretical proposal, it is demonstrated that the practical knot undulator could work perfectly. In order to understand the minor discrepancies of the two, mathematical formulae of the synchrotron radiation are derived based on the Fourier transform of the magnetic field. From the results of calculations by simulation program, the discrepancies could be well interpreted by the corresponding formulae. The results show the importance of optimization of the end sections of the knot undulator to suppress the on-axis heat load. Furthermore, a study of the impact of the undulator on beam dynamics of the storage ring was conducted using the Shanghai Synchrotron Radiation Facility as an example and the results show that the knot undulator has little effect on the beam. PMID:23254667

  13. High velocity knot in the Helix nebula

    SciTech Connect

    Meaburn, J.; Walsh, J.R.

    1980-01-01

    A high velocity (about 66 km/s) split feature about 15 arcseconds in extent has been detected in forbidden O II emission over a dark knot in the loop of the Helix nebula. This velocity splitting is much greater than the 20 km/s large scale splitting observed previously, and several mechanisms are proposed to account for this feature.

  14. Spontaneous Intravesical Knotting of Urethral Catheter

    PubMed Central

    2011-01-01

    Infant feeding tubes (IFT) have been universally used as urethral catheters in neonates and children for several decades. Though generally a safe procedure, it may cause significant morbidity if the catheter spontaneously knots inside the bladder. We report this complication in three children including a neonate. PMID:22953288

  15. Untying vortex knots in fluids and superfluids

    NASA Astrophysics Data System (ADS)

    Kleckner, Dustin; Scheeler, Martin; Kedia, Hridesh; Irvine, William T. M.

    Recent work has demonstrated that vortex knots appear to always untie in fluids and superfluids. Should we expect the same behavior from these two very different systems? I will discuss this unknotting behavior, both quantitatively - through helicity - and qualitatively through the geometry and topology of the vortex lines as they evolve.

  16. Black hole physics: More similar than knot

    NASA Astrophysics Data System (ADS)

    Gómez, José L.

    2016-08-01

    The detection of a discrete knot of particle emission from the active galaxy M81* reveals that black hole accretion is self-similar with regard to mass, producing the same knotty jets irrespective of black hole mass and accretion rate.

  17. Nuclear-coupled thermal-hydraulic stability analysis of boiling water reactors

    NASA Astrophysics Data System (ADS)

    Karve, Atul A.

    We have studied the nuclear-coupled thermal-hydraulic stability of boiling water reactors (BWRs) using a model we developed from: the space-time modal neutron kinetics equations based on spatial omega-modes, the equations for two-phase flow in parallel boiling channels, the fuel rod heat conduction equations, and a simple model for the recirculation loop. The model is represented as a dynamical system comprised of time-dependent nonlinear ordinary differential equations, and it is studied using stability analysis, modern bifurcation theory, and numerical simulations. We first determine the stability boundary (SB) in the most relevant parameter plane, the inlet-subcooling-number/external-pressure-drop plane, for a fixed control rod induced external reactivity equal to the 100% rod line value and then transform the SB to the practical power-flow map. Using this SB, we show that the normal operating point at 100% power is very stable, stability of points on the 100% rod line decreases as the flow rate is reduced, and that points are least stable in the low-flow/high-power region. We also determine the SB when the modal kinetics is replaced by simple point reactor kinetics and show that the first harmonic mode has no significant effect on the SB. Later we carry out the relevant numerical simulations where we first show that the Hopf bifurcation, that occurs as a parameter is varied across the SB is subcritical, and that, in the important low-flow/high-power region, growing oscillations can result following small finite perturbations of stable steady-states on the 100% rod line. Hence, a point on the 100% rod line in the low-flow/high-power region, although stable, may nevertheless be a point at which a BWR should not be operated. Numerical simulations are then done to calculate the decay ratios (DRs) and frequencies of oscillations for various points on the 100% rod line. It is determined that the NRC requirement of DR < 0.75-0.8 is not rigorously satisfied in the low

  18. REACTOR

    DOEpatents

    Roman, W.G.

    1961-06-27

    A pressurized water reactor in which automatic control is achieved by varying the average density of the liquid moderator-cooiant is patented. Density is controlled by the temperature and power level of the reactor ftself. This control can be effected by the use of either plate, pellet, or tubular fuel elements. The fuel elements are disposed between upper and lower coolant plenum chambers and are designed to permit unrestricted coolant flow. The control chamber has an inlet opening communicating with the lower coolant plenum chamber and a restricted vapor vent communicating with the upper coolant plenum chamber. Thus, a variation in temperature of the fuel elements will cause a variation in the average moderator density in the chamber which directly affects the power level of the reactor.

  19. Coupling of kinetic Monte Carlo simulations of surface reactions to transport in a fluid for heterogeneous catalytic reactor modeling

    SciTech Connect

    Schaefer, C.; Jansen, A. P. J.

    2013-02-07

    We have developed a method to couple kinetic Monte Carlo simulations of surface reactions at a molecular scale to transport equations at a macroscopic scale. This method is applicable to steady state reactors. We use a finite difference upwinding scheme and a gap-tooth scheme to efficiently use a limited amount of kinetic Monte Carlo simulations. In general the stochastic kinetic Monte Carlo results do not obey mass conservation so that unphysical accumulation of mass could occur in the reactor. We have developed a method to perform mass balance corrections that is based on a stoichiometry matrix and a least-squares problem that is reduced to a non-singular set of linear equations that is applicable to any surface catalyzed reaction. The implementation of these methods is validated by comparing numerical results of a reactor simulation with a unimolecular reaction to an analytical solution. Furthermore, the method is applied to two reaction mechanisms. The first is the ZGB model for CO oxidation in which inevitable poisoning of the catalyst limits the performance of the reactor. The second is a model for the oxidation of NO on a Pt(111) surface, which becomes active due to lateral interaction at high coverages of oxygen. This reaction model is based on ab initio density functional theory calculations from literature.

  20. Coupling of kinetic Monte Carlo simulations of surface reactions to transport in a fluid for heterogeneous catalytic reactor modeling.

    PubMed

    Schaefer, C; Jansen, A P J

    2013-02-01

    We have developed a method to couple kinetic Monte Carlo simulations of surface reactions at a molecular scale to transport equations at a macroscopic scale. This method is applicable to steady state reactors. We use a finite difference upwinding scheme and a gap-tooth scheme to efficiently use a limited amount of kinetic Monte Carlo simulations. In general the stochastic kinetic Monte Carlo results do not obey mass conservation so that unphysical accumulation of mass could occur in the reactor. We have developed a method to perform mass balance corrections that is based on a stoichiometry matrix and a least-squares problem that is reduced to a non-singular set of linear equations that is applicable to any surface catalyzed reaction. The implementation of these methods is validated by comparing numerical results of a reactor simulation with a unimolecular reaction to an analytical solution. Furthermore, the method is applied to two reaction mechanisms. The first is the ZGB model for CO oxidation in which inevitable poisoning of the catalyst limits the performance of the reactor. The second is a model for the oxidation of NO on a Pt(111) surface, which becomes active due to lateral interaction at high coverages of oxygen. This reaction model is based on ab initio density functional theory calculations from literature. PMID:23406093

  1. Coupled thermohydraulic-neutronic instabilities in boiling water nuclear reactors: A review of the state of the art

    SciTech Connect

    March-Leuba, J. ); Rey, J.M. )

    1992-01-01

    This paper provides a review of the current state of the art on the topic of coupled neutronic-thermohydraulic instabilities in boiling water nuclear reactors (BWRs). The topic of BWR instabilities is of great current relevance since it affects the operation of a large number of commercial nuclear reactors. The recent trends towards introduction of high efficiency fuels that permit reactor operation at higher power densities with increased void reactivity feedback and decreased response times, has resulted in a decrease of the stability margin in the low-flow, high-power region of the operating map. This trend has resulted in a number of unexpected'' instability events. For instance, United States plants have experienced two instability events recently, one of them resulted in an automatic reactor scram; in Spain, two BWR plants have experienced unstable limit cycle oscillations that required operator action to suppress. Similar events have been experienced in other European countries. In recent years, BWR instabilities have been one of the more exciting topics of work in the area of transient thermohydraulics. As a result, significant advances in understanding the physics behind these events have occurred, and a new and improved'' state of the art has emerged recently.

  2. Coupled thermohydraulic-neutronic instabilities in boiling water nuclear reactors: A review of the state of the art

    SciTech Connect

    March-Leuba, J.; Rey, J.M.

    1992-05-01

    This paper provides a review of the current state of the art on the topic of coupled neutronic-thermohydraulic instabilities in boiling water nuclear reactors (BWRs). The topic of BWR instabilities is of great current relevance since it affects the operation of a large number of commercial nuclear reactors. The recent trends towards introduction of high efficiency fuels that permit reactor operation at higher power densities with increased void reactivity feedback and decreased response times, has resulted in a decrease of the stability margin in the low-flow, high-power region of the operating map. This trend has resulted in a number of ``unexpected`` instability events. For instance, United States plants have experienced two instability events recently, one of them resulted in an automatic reactor scram; in Spain, two BWR plants have experienced unstable limit cycle oscillations that required operator action to suppress. Similar events have been experienced in other European countries. In recent years, BWR instabilities have been one of the more exciting topics of work in the area of transient thermohydraulics. As a result, significant advances in understanding the physics behind these events have occurred, and a ``new and improved`` state of the art has emerged recently.

  3. Coupling of kinetic Monte Carlo simulations of surface reactions to transport in a fluid for heterogeneous catalytic reactor modeling

    NASA Astrophysics Data System (ADS)

    Schaefer, C.; Jansen, A. P. J.

    2013-02-01

    We have developed a method to couple kinetic Monte Carlo simulations of surface reactions at a molecular scale to transport equations at a macroscopic scale. This method is applicable to steady state reactors. We use a finite difference upwinding scheme and a gap-tooth scheme to efficiently use a limited amount of kinetic Monte Carlo simulations. In general the stochastic kinetic Monte Carlo results do not obey mass conservation so that unphysical accumulation of mass could occur in the reactor. We have developed a method to perform mass balance corrections that is based on a stoichiometry matrix and a least-squares problem that is reduced to a non-singular set of linear equations that is applicable to any surface catalyzed reaction. The implementation of these methods is validated by comparing numerical results of a reactor simulation with a unimolecular reaction to an analytical solution. Furthermore, the method is applied to two reaction mechanisms. The first is the ZGB model for CO oxidation in which inevitable poisoning of the catalyst limits the performance of the reactor. The second is a model for the oxidation of NO on a Pt(111) surface, which becomes active due to lateral interaction at high coverages of oxygen. This reaction model is based on ab initio density functional theory calculations from literature.

  4. REACTORS

    DOEpatents

    Spitzer, L. Jr.

    1961-10-01

    Thermonuclear reactors, methods, and apparatus are described for controlling and confining high temperature plasma. Main axial confining coils in combination with helical windings provide a rotational transform that avoids the necessity of a figure-eight shaped reactor tube. The helical windings provide a multipolar helical magnetic field transverse to the axis of the main axial confining coils so as to improve the effectiveness of the confining field by counteracting the tendency of the more central lines of force in the stellarator tube to exchange positions with the magnetic lines of force nearer the walls of the tube. (AEC)

  5. Coupled high fidelity thermal hydraulics and neutronics for reactor safety simulations

    SciTech Connect

    Vincent A. Mousseau; Hongbin Zhang; Haihua Zhao

    2008-09-01

    This work is a continuation of previous work on the importance of accuracy in the simulation of nuclear reactor safety transients. This work is qualitative in nature and future work will be more quantitative. The focus of this work will be on a simplified single phase nuclear reactor primary. The transient of interest investigates the importance of accuracy related to passive (inherent) safety systems. The transient run here will be an Unprotected Loss of Flow (ULOF) transient. Here the coolant pump is turned off and the un’SCRAM’ed reactor transitions from forced to free convection (Natural circulation). Results will be presented that show the difference that the first order in time truncation physics makes on the transient. The purpose of this document is to illuminate a possible problem in traditional reactor simulation approaches. Detailed studies need to be done on each simulation code for each transient analyzed to determine if the first order truncation physics plays an important role.

  6. A model for stationary and dynamic impression of undercooled boiling in coupled thermohydraulic and neutron physics calculations of nuclear reactors

    NASA Astrophysics Data System (ADS)

    Mueller, Roland Guenther

    1987-06-01

    In order to account for subcooled boiling in calculations of neutron physics and thermal hydraulics of light water reactors (where vapor bubbles strongly influence the nuclear chain reaction), a dynamic model is derived from the time-dependent conservation equations. It contains methods for the time-dependent determination of evaporation and condensation heat flow and for the heat transfer coefficient in subcooled boiling. It enables the complete two-phase flow region to be treated consistently. The calculation model was verified using measured data of experiments covering a wide range of thermodynamic boundary conditions. In all cases very good agreement is reached. The results from the coupling of the new calculation model with a neutron kinetics program proves its suitability for the steady-state and transient calculation of reactor cores.

  7. The effect of dielectric top lids on materials processing in a low frequency inductively coupled plasma (LF-ICP) reactor

    NASA Astrophysics Data System (ADS)

    Lim, J. W. M.; Chan, C. S.; Xu, L.; Xu, S.

    2014-08-01

    The advent of the plasma revolution began in the 1970's with the exploitation of plasma sources for anisotropic etching and processing of materials. In recent years, plasma processing has gained popularity, with research institutions adopting projects in the field and industries implementing dry processing in their production lines. The advantages of utilizing plasma sources would be uniform processing over a large exposed surface area, and the reduction of toxic emissions. This leads to reduced costs borne by manufacturers which could be passed down as consumer savings, and a reduction in negative environmental impacts. Yet, one constraint that plagues the industry would be the control of contaminants in a plasma reactor which becomes evident when reactions are conducted in a clean vacuum environment. In this work, amorphous silicon (a-Si) thin films were grown on glass substrates in a low frequency inductively coupled plasma (LF-ICP) reactor with a top lid made of quartz. Even though the chamber was kept at high vacuum ( 10-4 Pa), it was evident through secondary ion mass spectroscopy (SIMS) and Fourier-transform infra-red spectroscopy (FTIR) that oxygen contaminants were present. With the aid of optical emission spectroscopy (OES) the contaminant species were identified. The design of the LF-ICP reactor was then modified to incorporate an Alumina (Al2O3) lid. Results indicate that there were reduced amounts of contaminants present in the reactor, and that an added benefit of increased power transfer to the plasma, improving deposition rate of thin films was realized. The results of this study is conclusive in showing that Al2O3 is a good alternative as a top-lid of an LF-ICP reactor, and offers industries a solution in improving quality and rate of growth of thin films.

  8. Catalytic Chan–Lam coupling using a ‘tube-in-tube’ reactor to deliver molecular oxygen as an oxidant

    PubMed Central

    Mallia, Carl J; Burton, Paul M; Smith, Alexander M R; Walter, Gary C

    2016-01-01

    Summary A flow system to perform Chan–Lam coupling reactions of various amines and arylboronic acids has been realised employing molecular oxygen as an oxidant for the re-oxidation of the copper catalyst enabling a catalytic process. A tube-in-tube gas reactor has been used to simplify the delivery of the oxygen accelerating the optimisation phase and allowing easy access to elevated pressures. A small exemplification library of heteroaromatic products has been prepared and the process has been shown to be robust over extended reaction times. PMID:27559412

  9. Catalytic Chan-Lam coupling using a 'tube-in-tube' reactor to deliver molecular oxygen as an oxidant.

    PubMed

    Mallia, Carl J; Burton, Paul M; Smith, Alexander M R; Walter, Gary C; Baxendale, Ian R

    2016-01-01

    A flow system to perform Chan-Lam coupling reactions of various amines and arylboronic acids has been realised employing molecular oxygen as an oxidant for the re-oxidation of the copper catalyst enabling a catalytic process. A tube-in-tube gas reactor has been used to simplify the delivery of the oxygen accelerating the optimisation phase and allowing easy access to elevated pressures. A small exemplification library of heteroaromatic products has been prepared and the process has been shown to be robust over extended reaction times. PMID:27559412

  10. A side-by-side comparison of two systems of sequencing coupled reactors for anaerobic digestion of the organic fraction of municipal solid waste.

    PubMed

    Poggi-Varaldo, Héctor M; Alzate-Gaviria, Liliana M; Pérez-Hernández, Antonino; Nevarez-Morillón, Virginia G; Rinderknecht-Seijas, Noemí

    2005-06-01

    The objective of this work was to compare the performance of two laboratory-scale, mesophilic systems aiming at the anaerobic digestion of the organic fraction of municipal solid wastes (OFMSW). The first system consisted of two coupled reactors packed with OFMSW (PBR1.1-PBR1.2) and the second system consisted of an upflow anaerobic sludge bed reactor (UASB) coupled to a packed reactor (UASB2.1-PBR2.2). For the start-up phase, both reactors PBR 1.1 and the UASB 2.1 (also called leading reactors) were inoculated with a mixture of non-anaerobic inocula and worked with leachate and effluent full recirculation, respectively. Once a full methanogenic regime was achieved in the leading reactors, their effluents were fed to the fresh-packed reactors PBR1.2 and PBR2.2, respectively. The leading PBR 1.1 reached its full methanogenic regime after 118 days (Tm, time to achieve methanogenesis) whereas the other leading UASB 2.1 reactor reached its full methanogenesis regime after only 34 days. After coupling the leading reactors to the corresponding packed reactors, it was found that both coupled anaerobic systems showed similar performances regarding the degradation of the OFMSW. Removal efficiencies of volatile solids and cellulose and the methane pseudo-yield were 85.95%, 80.88% and 0.109 NL CH4 g(-1) VS(fed) in the PBR-PBR system; and 88.75%, 82.61% and 0.115 NL CH4 g(-1) VS(fed0 in the UASB-PBR system [NL, normalized litre (273 degrees K, 1 ata basis)]. Yet, the second system UASB-PBR system showed a faster overall start-up. PMID:15988946

  11. REACTOR

    DOEpatents

    Spitzer, L. Jr.

    1962-01-01

    The system conteraplates ohmically heating a gas to high temperatures such as are useful in thermonuclear reactors of the stellarator class. To this end the gas is ionized and an electric current is applied to the ionized gas ohmically to heat the gas while the ionized gas is confined to a central portion of a reaction chamber. Additionally, means are provided for pumping impurities from the gas and for further heating the gas. (AEC)

  12. COUPLING

    DOEpatents

    Hawke, B.C.

    1963-02-26

    This patent relates to a releasable coupling connecting a control rod to a control rod drive. This remotely operable coupling mechanism can connect two elements which are laterally and angviarly misaligned, and provides a means for sensing the locked condition of the elements. The coupling utilizes a spherical bayonet joint which is locked against rotation by a ball detent lock. (AEC)

  13. Parity and cobordism of free knots

    SciTech Connect

    Manturov, Vassily O

    2012-02-28

    A simple invariant is constructed which obstructs a free knot to be truncated. In particular, this invariant provides an obstruction to the truncatedness of curves immersed in two-dimensional surfaces. A curve on an oriented two-dimensional surface S{sub g} is referred to as truncated (null-cobordant) if there exists a three-dimensional manifold M with boundary S{sub g} and a smooth proper map of a two-disc to M such that the image of the boundary of the disc coincides with the curve. The problem of truncatedness for free knots is solved in this paper using the notion of parity recently introduced by the author. Bibliography: 12 titles.

  14. Towards effective topological field theory for knots

    NASA Astrophysics Data System (ADS)

    Mironov, A.; Morozov, A.

    2015-10-01

    Construction of (colored) knot polynomials for double-fat graphs is further generalized to the case when "fingers" and "propagators" are substituting R-matrices in arbitrary closed braids with m-strands. Original version of [25] corresponds to the case m = 2, and our generalization sheds additional light on the structure of those mysterious formulas. Explicit expressions are now combined from Racah matrices of the type R ⊗ R ⊗ R bar ⟶ R bar and mixing matrices in the sectors R⊗3 ⟶ Q. Further extension is provided by composition rules, allowing to glue two blocks, connected by an m-strand braid (they generalize the product formula for ordinary composite knots with m = 1).

  15. Cometary Knots Around A Dying Star

    NASA Technical Reports Server (NTRS)

    1994-01-01

    These gigantic, tadpole-shaped objects are probably the result of a dying star's last gasps. Dubbed 'cometary knots' because their glowing heads and gossamer tails resemble comets, the gaseous objects probably were formed during a star's final stages of life. Hubble astronomer C. Robert O'Dell and graduate student Kerry P. Handron of Rice University in Houston, Texas discovered thousands of these knots with the Hubble Space Telescope while exploring the Helix nebula, the closest planetary nebula to Earth at 450 light-years away in the constellation Aquarius. Although ground-based telescopes have revealed such objects, astronomers have never seen so many of them. The most visible knots all lie along the inner edge of the doomed star's ring, trillions of miles away from the star's nucleus. Although these gaseous knots appear small, they're actually huge. Each gaseous head is at least twice the size of our solar system; each tail stretches for 100 billion miles, about 1,000 times the distance between the Earth and the Sun. Astronomers theorize that the doomed star spews hot, lower-density gas from its surface, which collides with cooler, higher-density gas that had been ejected 10,000 years before. The crash fragments the smooth cloud surrounding the star into smaller, denser finger-like droplets, like dripping paint. This image was taken in August, 1994 with Hubble's Wide Field Planetary Camera 2. The red light depicts nitrogen emission ([NII] 6584A); green, hydrogen (H-alpha, 6563A); and blue, oxygen (5007A).

  16. Monopoles and knots in skyrme theory.

    PubMed

    Cho, Y M

    2001-12-17

    We show that the Skyrme theory is actually a theory of monopoles which allows a new type of soliton, the topological knot made of the monopole-antimonopole pair, which is different from the well-known skyrmion. Furthermore, we derive a generalized Skyrme action from the Yang-Mills action of QCD, which we propose to be an effective action of QCD in the infrared limit. We discuss the physical implications of our results. PMID:11736568

  17. Magnetohydrodynamic solitons and radio knots in jets

    NASA Technical Reports Server (NTRS)

    Fiedler, R.

    1986-01-01

    Weakly nonlinear surface waves are examined in the context of the beam model for jetlike radio sources. By introducing a finite scale length, viz. the beam radius, geometrical dispersion can act to balance nonlinear wave growth and thereby produce solitons, localized wave packets of stable waveform. A method for obtaining a soliton equation from the MHD equations is presented and then applied to radio knots in jets.

  18. 2D fluid model analysis for the effect of 3D gas flow on a capacitively coupled plasma deposition reactor

    NASA Astrophysics Data System (ADS)

    Kim, Ho Jun; Lee, Hae June

    2016-06-01

    The wide applicability of capacitively coupled plasma (CCP) deposition has increased the interest in developing comprehensive numerical models, but CCP imposes a tremendous computational cost when conducting a transient analysis in a three-dimensional (3D) model which reflects the real geometry of reactors. In particular, the detailed flow features of reactive gases induced by 3D geometric effects need to be considered for the precise calculation of radical distribution of reactive species. Thus, an alternative inclusive method for the numerical simulation of CCP deposition is proposed to simulate a two-dimensional (2D) CCP model based on the 3D gas flow results by simulating flow, temperature, and species fields in a 3D space at first without calculating the plasma chemistry. A numerical study of a cylindrical showerhead-electrode CCP reactor was conducted for particular cases of SiH4/NH3/N2/He gas mixture to deposit a hydrogenated silicon nitride (SiN x H y ) film. The proposed methodology produces numerical results for a 300 mm wafer deposition reactor which agree very well with the deposition rate profile measured experimentally along the wafer radius.

  19. Allosteric initiation and regulation of catalysis with a molecular knot.

    PubMed

    Marcos, Vanesa; Stephens, Alexander J; Jaramillo-Garcia, Javier; Nussbaumer, Alina L; Woltering, Steffen L; Valero, Alberto; Lemonnier, Jean-François; Vitorica-Yrezabal, Iñigo J; Leigh, David A

    2016-06-24

    Molecular knots occur in DNA, proteins, and other macromolecules. However, the benefits that can potentially arise from tying molecules in knots are, for the most part, unclear. Here, we report on a synthetic molecular pentafoil knot that allosterically initiates or regulates catalyzed chemical reactions by controlling the in situ generation of a carbocation formed through the knot-promoted cleavage of a carbon-halogen bond. The knot architecture is crucial to this function because it restricts the conformations that the molecular chain can adopt and prevents the formation of catalytically inactive species upon metal ion binding. Unknotted analogs are not catalytically active. Our results suggest that knotting molecules may be a useful strategy for reducing the degrees of freedom of flexible chains, enabling them to adopt what are otherwise thermodynamically inaccessible functional conformations. PMID:27339983

  20. Stretching Response of Knotted and Unknotted Polymer Chains

    NASA Astrophysics Data System (ADS)

    Caraglio, Michele; Micheletti, Cristian; Orlandini, Enzo

    2015-10-01

    Recent theoretical and experimental advances have clarified the major effects of knotting on the properties of stretched chains. Yet, how knotted chains respond to weak mechanical stretching and how this behavior differs from the unknotted case are still open questions and we address them here by profiling the complete stretching response of chains of hundreds of monomers and different topology. We find that the ratio of the knotted and unknotted chain extensions varies nonmonotonically with the applied force. This surprising feature is shown to be a signature of the crossover between the well-known high-force stretching regime and the previously uncharacterized low-force one. The observed differences of knotted and unknotted chain response increases with knot complexity and are sufficiently marked that they could be harnessed in single-molecule contexts to infer the presence and complexity of physical knots in micron-long biomolecules.

  1. Collaboration on Modeling of Ion Bernstein Wave Antenna Array and Coupling to Plasma on Tokamak Fusion Text Reactor. Final report

    SciTech Connect

    Intrator, T.

    2000-06-01

    This proposal was peer reviewed and funded as a Collaboration on ''Low Phase Speed Radio Frequency Current Drive Experiments at the Tokamak Fusion Test Reactor''. The original plans we had were to carry out the collaboration proposal by including a post doctoral scientist stationed at PPPL. In response to a 60+% funding cut, all expenses were radically pruned. The post doctoral position was eliminated, and the Principal Investigator (T. Intrator) carried out the brunt of the collaboration. Visits to TFTR enabled T. Intrator to set up access to the TFTR computing network, database, and get familiar with the new antennas that were being installed in TFTR during an up to air. One unfortunate result of the budget squeeze that TFTR felt for its last year of operation was that the experiments that we specifically got funded to perform were not granted run time on TFTR., On the other hand we carried out some modeling of the electric field structure around the four strap direct launch Ion Bernstein Wave (IBW) antenna that was operated on TFTR. This turned out to be a useful exercise and shed some light on the operational characteristics of the IBW antenna and its coupling to the plasma. Because of this turn of events, the project was renamed ''Modeling of Ion Bernstein Wave Antenna Array and Coupling to Plasma on Tokamak Fusion Test Reactor''.

  2. Application of Gamma code coupled with turbomachinery models for high temperature gas-cooled reactors

    SciTech Connect

    Chang Oh

    2008-02-01

    The very high-temperature gas-cooled reactor (VHTR) is envisioned as a single- or dual-purpose reactor for electricity and hydrogen generation. The concept has average coolant temperatures above 9000C and operational fuel temperatures above 12500C. The concept provides the potential for increased energy conversion efficiency and for high-temperature process heat application in addition to power generation. While all the High Temperature Gas Cooled Reactor (HTGR) concepts have sufficiently high temperature to support process heat applications, such as coal gasification, desalination or cogenerative processes, the VHTR’s higher temperatures allow broader applications, including thermochemical hydrogen production. However, the very high temperatures of this reactor concept can be detrimental to safety if a loss-ofcoolant accident (LOCA) occurs. Following the loss of coolant through the break and coolant depressurization, air will enter the core through the break by molecular diffusion and ultimately by natural convection, leading to oxidation of the in-core graphite structure and fuel. The oxidation will accelerate heatup of the reactor core and the release of a toxic gas, CO, and fission products. Thus, without any effective countermeasures, a pipe break may lead to significant fuel damage and fission product release. Prior to the start of this Korean/United States collaboration, no computer codes were available that had been sufficiently developed and validated to reliably simulate a LOCA in the VHTR. Therefore, we have worked for the past three years on developing and validating advanced computational methods for simulating LOCAs in a VHTR. GAMMA code is being developed to implement turbomachinery models in the power conversion unit (PCU) and ultimately models associated with the hydrogen plant. Some preliminary results will be described in this paper.

  3. GDNF Gene Delivery via a 2-(Dimethylamino)ethyl Methacrylate Based Cyclized Knot Polymer for Neuronal Cell Applications

    PubMed Central

    2013-01-01

    Nonviral genetic therapeutic intervention strategies for neurological disorders hold great promise, but a lack of vector efficacy, coupled with vector toxicity, continue to hinder progress. Here we report the application of a newly developed class of polymer, distinctly different from conventional branched polymers, as a transfection agent for the delivery of glial cell line derived neurotrophic factor (GDNF) encoding gene. This new 2-(dimethylamino)ethyl methacrylate (DMAEMA) based cyclized knot polymer was studied for neuronal cell transfection applications, in comparison to branched polyethyleneimine (PEI). While showing a similar transfection profile over multiple cell types, the cyclized knot polymer showed far lower toxicity. In addition, transfection of Neu7 astrocytes with the GDNF encoding gene was able to cause neurite outgrowth when cocultured with dorsal root ganglia (DRGs). The cyclized knot polymer assessed here (PD-E 8%PEG), synthesized via a simple one-pot reaction, was shown to have great potential for neuronal gene therapy applications. PMID:23391146

  4. Knotting and unknotting of a protein in single molecule experiments.

    PubMed

    Ziegler, Fabian; Lim, Nicole C H; Mandal, Soumit Sankar; Pelz, Benjamin; Ng, Wei-Ping; Schlierf, Michael; Jackson, Sophie E; Rief, Matthias

    2016-07-01

    Spontaneous folding of a polypeptide chain into a knotted structure remains one of the most puzzling and fascinating features of protein folding. The folding of knotted proteins is on the timescale of minutes and thus hard to reproduce with atomistic simulations that have been able to reproduce features of ultrafast folding in great detail. Furthermore, it is generally not possible to control the topology of the unfolded state. Single-molecule force spectroscopy is an ideal tool for overcoming this problem: by variation of pulling directions, we controlled the knotting topology of the unfolded state of the 52-knotted protein ubiquitin C-terminal hydrolase isoenzyme L1 (UCH-L1) and have therefore been able to quantify the influence of knotting on its folding rate. Here, we provide direct evidence that a threading event associated with formation of either a 31 or 52 knot, or a step closely associated with it, significantly slows down the folding of UCH-L1. The results of the optical tweezers experiments highlight the complex nature of the folding pathway, many additional intermediate structures being detected that cannot be resolved by intrinsic fluorescence. Mechanical stretching of knotted proteins is also of importance for understanding the possible implications of knots in proteins for cellular degradation. Compared with a simple 31 knot, we measure a significantly larger size for the 52 knot in the unfolded state that can be further tightened with higher forces. Our results highlight the potential difficulties in degrading a 52 knot compared with a 31 knot. PMID:27339135

  5. Safety Related Investigations of the VVER-1000 Reactor Type by the Coupled Code System TRACE/PARCS

    NASA Astrophysics Data System (ADS)

    Jaeger, Wadim; Espinoza, Victor Hugo Sánchez; Lischke, Wolfgang

    This study was performed at the Institute of Reactor Safety at the Forschungszentrum Karlsruhe. It is embedded in the ongoing investigations of the international code assessment and maintenance program (CAMP) for qualification and validation of system codes like TRACE(1) and PARCS(2). The chosen reactor type used to validate these two codes was the Russian designed VVER-1000 because the OECD/NEA VVER-1000 Coolant Transient Benchmark Phase 2(3) includes detailed information of the Bulgarian nuclear power plant (NPP) Kozloduy unit 6. The post-test investigations of a coolant mixing experiment have shown that the predicted parameters (coolant temperature, pressure drop, etc.) are in good agreement with the measured data. The coolant mixing pattern, especially in the downcomer, has been also reproduced quiet well by TRACE. The coupled code system TRACE/PARCS which was applied on a postulated main steam line break (MSLB) provided good results compared to reference values and the ones of other participants of the benchmark. The results show that the developed three-dimensional nodalization of the reactor pressure vessel (RPV) is appropriate to describe the coolant mixing phenomena in the downcomer and the lower plenum of a VVER-1000 reactor. This phenomenon is a key issue for investigations of MSLB transient where the thermal hydraulics and the core neutronics are strongly linked. The simulation of the RPV and core behavior for postulated transients using the validated 3D TRACE RPV model, taking into account boundary conditions at vessel in- and outlet, indicates that the results are physically sound and in good agreement to other participant's results.

  6. A comparison of ultrasonic suture welding and traditional knot tying.

    PubMed

    Richmond, J C

    2001-01-01

    The slippage of knots and the technical challenge of tying them securely are potential impediments to certain arthroscopic procedures. Ultrasonic energy delivered at 70 kHz can be used to weld No. 2 polypropylene suture. This method was compared with a traditional knot (surgeon's knot with four alternating half hitches) tied with an open technique to determine whether welding of sutures is comparable, in mechanical properties, to hand-tied knots. Both loops were fashioned around a 0.25-inch mandrel and then tested. The load to reach 3-mm elongation (point of likely biologic failure of a repair) was significantly greater for welded sutures than for knots. The elongation at ultimate failure was significantly less for welded sutures than for knots. The number of cycles to failure and the creep after initial displacement were similar for both welded and knotted suture loops. The ultimate load to failure was significantly greater for the knotted than for the welded suture. The welding of suture for the repair of musculoskeletal soft tissue presents an attractive alternative to traditional knot tying, particularly for arthroscopic applications. PMID:11394598

  7. Escape of a knot from a DNA molecule in flow

    NASA Astrophysics Data System (ADS)

    Renner, Benjamin; Doyle, Patrick

    2014-03-01

    Macroscale knots are an everyday occurrence when trying to unravel an unorganized flexible string (e.g. an iPhone cord taken out of your pocket). In nature, knots are found in proteins and viral capsid DNA, and the properties imbued by their topologies are thought to have biological significance. Unlike their macroscale counterparts, thermal fluctuations greatly influence the dynamics of polymer knots. Here, we use Brownian Dynamics simulations to study knot diffusion along a linear polymer chain. The model is parameterized to dsDNA, a model polymer used in previous simulation and experimental studies of knot dynamics. We have used this model to study the process of knot escape and transport along a dsDNA strand extended by an elongational flow. For a range of knot topologies and flow strengths, we show scalings that result in collapse of the data onto a master curve. We show a topologically mediated mode of transport coincides with observed differences in rates of knot transport, and we provide a simple mechanistic explanation for its effect. We anticipate these results will build on the growing body of fundamental studies of knotted polymers and inform future experimental study. This work is supported by the Singapore-MIT Alliance for Research and Technology (SMART) and National Science Foundation (NSF) grant CBET-0852235.

  8. Fractions of Particular Knots in Gaussian Random Polygons

    NASA Astrophysics Data System (ADS)

    Tsurusaki, Kyoichi; Deguchi, Tetsuo

    1995-05-01

    Fractions of knotted polygons in Gaussian random polygonare numerically studied. Three dimensional random polygons with N stepsare prepared by closed N-step Gaussian random walks. LetPK(N) denote the probability that an N-step Gaussian polygon has aknot type K. For prime knots (31, 41, 51, 52) andcomposite knots (31 #31, 31 #41, 31 #31 #31),PK(N)'s are evaluated in the range 30≤N≤2400. We confirm thata scaling formula gives nice fitting curves for the numerical dataplots of PK(N) versus N for the different knot types.

  9. Reactor

    DOEpatents

    Evans, Robert M.

    1976-10-05

    1. A neutronic reactor having a moderator, coolant tubes traversing the moderator from an inlet end to an outlet end, bodies of material fissionable by neutrons of thermal energy disposed within the coolant tubes, and means for circulating water through said coolant tubes characterized by the improved construction wherein the coolant tubes are constructed of aluminum having an outer diameter of 1.729 inches and a wall thickness of 0.059 inch, and the means for circulating a liquid coolant through the tubes includes a source of water at a pressure of approximately 350 pounds per square inch connected to the inlet end of the tubes, and said construction including a pressure reducing orifice disposed at the inlet ends of the tubes reducing the pressure of the water by approximately 150 pounds per square inch.

  10. Towards a better knot: Using mechanics methods to evaluate three knot-tying techniques in laparo-endoscopic single-site surgery

    PubMed Central

    Xu, An An; Zhu, Jiang Fan; Su, Yuantao

    2015-01-01

    INTRODUCTION: Knot tying is difficult but important for laparo-endoscopic single-site surgery (LESS). There are several techniques for LESS knot-tying. However, objective assessment of these skills has not yet been established. The aim of this study was to assess three different knot-tying techniques in LESS using mechanical methods. MATERIALS AND METHODS: The subject tied 24 knots, eight knots with each of the three techniques in an inanimate box laparoscopic trainer while the movements of their instruments were evaluated using a LESS mechanical evaluation platform. The operations were assessed on the basis of the time, average load of the dominant hand. Then, forces caused the knots to rupture were measured using a material testing system and used to compare the knots's strength. RESULTS: The intracorporeal one-hand knot-tying technique presented significantly better time and average load scores than the extracorporeal knot-tying technique (P < 0.01), and the intracorporeal side winding technique was more time and average load consuming in comparison to other techniques during the performance of knot-tying (P < 0.01). The intracorporeal one-handed knot-tying knots can tolerate better distraction forces compared with the intracorporeal side winding knot-tying knots and the extracorporeal knot-tying knots (P < 0.05). CONCLUSIONS: The intracorporeal one-hand knot-tying technique and knots showed better results than the intracorporeal “side winding” technique and the extracorporeal knot-tying technique in terms of the time, average load taken and the force caused the knot to rupture. PMID:26622113

  11. Coupled full core neutron transport/CFD simulations of pressurized water reactors

    SciTech Connect

    Kochunas, B.; Stimpson, S.; Collins, B.; Downar, T.; Brewster, R.; Baglietto, E.; Yan, J.

    2012-07-01

    Recently as part of the CASL project, a capability to perform 3D whole-core coupled neutron transport and computational fluid dynamics (CFD) calculations was demonstrated. This work uses the 2D/1D transport code DeCART and the commercial CFD code STAR-CCM+. It builds on previous CASL work demonstrating coupling for smaller spatial domains. The coupling methodology is described along with the problem simulated and results are presented for fresh hot full power conditions. An additional comparison is made to an equivalent model that uses lower order T/H feedback to assess the importance and cost of high fidelity feedback to the neutronics problem. A simulation of a quarter core Combustion Engineering (CE) PWR core was performed with the coupled codes using a Fixed Point Gauss-Seidel iteration technique. The total approximate calculation requirements are nearly 10,000 CPU hours and 1 TB of memory. The problem took 6 coupled iterations to converge. The CFD coupled model and low order T/H feedback model compared well for global solution parameters, with a difference in the critical boron concentration and average outlet temperature of 14 ppm B and 0.94 deg. C, respectively. Differences in the power distribution were more significant with maximum relative differences in the core-wide pin peaking factor (Fq) of 5.37% and average relative differences in flat flux region power of 11.54%. Future work will focus on analyzing problems more relevant to CASL using models with less approximations. (authors)

  12. Optical knots and contact geometry II. From Ranada dyons to transverse and cosmetic knots

    NASA Astrophysics Data System (ADS)

    Kholodenko, Arkady L.

    2016-08-01

    Some time ago Ranada (1989) obtained new nontrivial solutions of the Maxwellian gauge fields without sources. These were reinterpreted in Kholodenko (2015) [10] (part I) as particle-like (monopoles, dyons, etc.). They were obtained by the method of Abelian reduction of the non-Abelian Yang-Mills functional. The developed method uses instanton-type calculations normally employed for the non-Abelian gauge fields. By invoking the electric-magnetic duality it then becomes possible to replace all known charges/masses by the particle-like solutions of the source-free Abelian gauge fields. To employ these results in high energy physics, it is essential to extend Ranada's results by carefully analyzing and classifying all dynamically generated knotted/linked structures in gauge fields, including those discovered by Ranada. This task is completed in this work. The study is facilitated by the recent progress made in solving the Moffatt conjecture. Its essence is stated as follows: in steady incompressible Euler-type fluids the streamlines could have knots/links of all types. By employing the correspondence between the ideal hydrodynamics and electrodynamics discussed in part I and by superimposing it with the already mentioned method of Abelian reduction, it is demonstrated that in the absence of boundaries only the iterated torus knots and links could be dynamically generated. Obtained results allow to develop further particle-knot/link correspondence studied in Kholodenko (2015) [13].

  13. High-order Spatio-temporal Schemes for Coupled, Multi-physics Reactor Simulations

    SciTech Connect

    Mr. Vijay S. Mahadevan; Dr. Jean C. Ragusa

    2008-09-01

    This report summarizes the work done in the summer of 08 by the Ph.D. student Vijay Mahadevan. The main focus of the work was to coupled 3-D neutron difusion to 3-D heat conduction in parallel with accuracy greater than or equal to 2nd order in space and time. Results show that the goal was attained.

  14. COUPLING

    DOEpatents

    Frisch, E.; Johnson, C.G.

    1962-05-15

    A detachable coupling arrangement is described which provides for varying the length of the handle of a tool used in relatively narrow channels. The arrangement consists of mating the key and keyhole formations in the cooperating handle sections. (AEC)

  15. Structural recognition and nomenclature standardization in forensic knot analysis.

    PubMed

    Chisnall, Robert Charles

    2016-07-01

    The analysis of knots during civil and criminal investigations is characterized by two fundamental challenges: the precise recognition of all structural nuances and the application of accurate, universally recognized terms. These challenges are exacerbated by inconsistencies, contradictions and regional terminology, which occur in common practice and in mainstream books as well as within forensic science. Some knots bear multiple or value-laden names, even misnomers, and some terms have manifold applications. This can lead to ambiguity and confusion. Additionally, many topological concepts and terms are applicable to practical knot-tying, despite the differences between real-world and theoretical knots, but the esoterica of topology are inaccessible to anyone unfamiliar with that branch of mathematics. To highlight these challenges some examples of knots encountered in case work are presented. Significantly, an overview of a few previously ignored issues is examined and several new concepts are introduced. An emphasis is placed on identifying structural variations, standardized nomenclature is outlined, and recommended terminology is derived from fields such as forensic science, chemistry, archaeology, topology and the textile industry. Greater precision in knot identifications, characterizations and descriptions can assist investigators in linking specific tying practises to potential suspects, analysing the manner in which knotted evidence was tied, and understanding how knots and ligatures perform in given scenarios. PMID:27320402

  16. Root-knot nematode resistant rootstocks for grafted watermelon

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rootstock lines of wild watermelon (Citrullus lanatus var. citroides) with resistance to root-knot nematodes (RKN) were developed by our team at the U.S. Vegetable Laboratory. Rootstock lines RKVL 301, RKVL 316, and RKVL 318 (RKVL = Root Knot Vegetable Laboratory) were compared to wild tinda (Praec...

  17. The Verbal Facilitation Effect in Learning to Tie Nautical Knots

    ERIC Educational Resources Information Center

    Huff, Markus; Schwan, Stephan

    2012-01-01

    Motor skills are often demonstrated with a combination of verbal information and video demonstration. In this study, participants learned to tie nautical knots with a video clip demonstrating the motor task preceded by a descriptive or a metaphorical, picture-like verbalization. In a control condition participants learned the knots with a video…

  18. Knot security: how many throws does it really take?

    PubMed

    Tidwell, John E; Kish, Vincent L; Samora, Julie B; Prud'homme, Joseph

    2012-04-01

    The purpose of this study was to determine the minimum number of throws needed for knot security for square knots using 5 common suture materials and 3 common sizes by in vitro single load to failure biomechanical testing. The hypothesis was that each suture combination studied would share a common minimum of at least 5 throws to guarantee security. Five suture materials (FiberWire [Arthrex, Inc, Naples, Florida], Monosof, Surgipro, Maxon, and Polysorb [Covidien, Mansfield, Massachusetts]) with varying suture sizes (#5, #2, 0, 2-0, and 4-0) were tied in vitro, varying the number of square knot throws (3, 4, 5, and 6). Twenty knots for each combination were statically loaded to failure in tension; whether the knot failed by fracture or slippage and the tensile strength at knot failure was determined. For the tested materials, at least 5 flat square throws should be used to confer knot security based on a binomial proportion score 95% confidence interval (CI) 0.84 to 1.0 or at least 4 throws for a 95% CI of 0.76 to 0.99. FiberWire requires 6 flat square throws per knot for security at either 95% CI level. Unless a surgeon has specific knowledge of experimental evidence that fewer throws are necessary for a specific application, the default should be a minimum of 4 throws, with 5 conferring additional security in most situations, and FiberWire requiring 6 throws. PMID:22495855

  19. Knot invariants as nondegenerate quantum geometries

    SciTech Connect

    Bruegmann, B.; Gambini, R.; Pullin, J. Instituto de Fisica, Facultad de Ciencias, Tristan Narvaja 1674, Montevideo Department of Physics, University of Utah, Salt Lake City, Utah 84112 )

    1992-01-27

    The loop-space representation based on Ashtekar's new variables has allowed for the first time the construction of quantum states of the gravitational field. However, all states known up to the present were associated with spacetime metrics that were everywhere degenerate. In this Letter we present a new exact solution of the constraint equations of quantum gravity that is the first quantum state of the gravitational field known to be associated with a not-everywhere-degenerate metric. The state is associated with the second coefficient of the Alexander-Conway polynomial of knot theory.

  20. Ventriculoperitoneal Shunt Peritoneal Catheter Knot Formation

    PubMed Central

    Ul-Haq, Anwar; Al-Otaibi, Faisal; Alshanafey, Saud; Sabbagh, Mohamed Diya; Al Shail, Essam

    2013-01-01

    The ventriculoperitoneal (VP) shunt is a common procedure in pediatric neurosurgery that carries a risk of complications at cranial and abdominal sites. We report on the case of a child with shunt infection and malfunction. The peritoneal catheter was tethered within the abdominal cavity, precluding its removal. Subsequently, laparoscopic exploration identified a knot at the distal end of the peritoneal catheter around the omentum. A new VP shunt was inserted after the infection was healed. This type of complication occurs rarely, so there are a limited number of case reports in the literature. This report is complemented by a literature review. PMID:24109528

  1. Single and Coupled Electrochemical Processes and Reactors for the Abatement of Organic Water Pollutants: A Critical Review.

    PubMed

    Martínez-Huitle, Carlos A; Rodrigo, Manuel A; Sirés, Ignasi; Scialdone, Onofrio

    2015-12-23

    Traditional physicochemical and biological techniques, as well as advanced oxidation processes (AOPs), are often inadequate, ineffective, or expensive for industrial water reclamation. Within this context, the electrochemical technologies have found a niche where they can become dominant in the near future, especially for the abatement of biorefractory substances. In this critical review, some of the most promising electrochemical tools for the treatment of wastewater contaminated by organic pollutants are discussed in detail with the following goals: (1) to present the fundamental aspects of the selected processes; (2) to discuss the effect of both the main operating parameters and the reactor design on their performance; (3) to critically evaluate their advantages and disadvantages; and (4) to forecast the prospect of their utilization on an applicable scale by identifying the key points to be further investigated. The review is focused on the direct electrochemical oxidation, the indirect electrochemical oxidation mediated by electrogenerated active chlorine, and the coupling between anodic and cathodic processes. The last part of the review is devoted to the critical assessment of the reactors that can be used to put these technologies into practice. PMID:26654466

  2. Coupled radiation transport/thermal analysis of the radiation shield for a space nuclear reactor. Doctoral thesis

    SciTech Connect

    Barattino, W.J.

    1985-07-01

    A coupled radiation transport-heat transfer-stress analysis of the radiation shield for an SP-100 reactor was performed using a numerical code developed at the University of New Mexico and Sandia National Laboratory. For a fast reactor operating at 1.66 MW/sub th/, the energy deposited and resulting temperature distribution was determined for a shield consisting of tungsten and lithium hydride pressed into a stainless steel honeycomb matrix. While temperature feedback was shown to have a minor effect on energy deposition, the shielding configuration was found to have a major influence in meeting thermal requirements of the lithium hydride. It was shown that a shield optimized for radiation protection will fail because of melting. However, with minor modifications in the shield layering and material selection, the thermal integrity of the shield can be preserved. A shield design of graphite, depleted lithium hydride, tungsten, and natural lithium hydride was shown to satisfy neutron and gamma fluence requirements, maximum temperature limits, and minimize cracking in the LiH portion of the shield.

  3. A coupled radiation transport-thermal analysis of the radiation shield for an SP-100 type reactor

    NASA Astrophysics Data System (ADS)

    Barattino, William J.; El-Genk, Mohamed S.; McDaniel, Patrick J.

    A coupled radiation transport-thermal analysis of the radiation shield for an SP-100 reactor was performed using finite element codes developed at the University of New Mexico and Sandia National Laboratories. For a fast reactor operating at 1.66 MWt, the energy deposited and resulting temperature distribution were determined for a shield consisting of tungsten and lithium hydride pressed into a stainless steel honeycomb matrix. While temperature feedback was shown to have a minor effect on energy deposition, the shielding configuration was found to have a major influence in meeting thermal requirements of the lithium hydride. It was shown that a shield optimized only for radiation protection will fail because of LiH melting. However, with minor modifications in the shield layering and material selection, the thermal integrity of the shield can be preserved. A shield design of graphite, depleted lithium hydride, tungsten, and natural lithium hydride was shown to satisfy neutron and gamma fluence requirements, and maximum temperature limits, and to minimize cracking in the LiH portion of the shield.

  4. Influence of a knot on the strength of a polymer strand.

    PubMed

    Saitta, A M; Soper, P D; Wasserman, E; Klein, M L

    1999-05-01

    Many experiments have been done to determine the relative strengths of different knots, and these show that the break in a knotted rope almost invariably occurs at the point just outside the 'entrance' to the knot. The influence of knots on the properties of polymers has become of great interest, in part because of their effect on mechanical properties. Knot theory applied to the topology of macromolecules indicates that the simple trefoil or 'overhand' knot is likely to be present in any long polymer strand. Fragments of DNA have been observed to contain such knots in experiments and computer simulations. Here we use ab initio computational methods to investigate the effect of a trefoil knot on the breaking strength of a polymer strand. We find that the knot weakens the strand significantly, and that, like a knotted rope, it breaks under tension at the entrance to the knot. PMID:10331387

  5. UNEXPECTED IONIZATION STRUCTURE IN ETA CARINAE'S ''WEIGELT KNOTS''

    SciTech Connect

    Remmen, Grant N.; Davidson, Kris; Mehner, Andrea

    2013-08-10

    The Weigelt knots, dense slow-moving ejecta near {eta} Carinae, are mysterious in structure as well as in origin. Using spatially dithered spectrograms obtained with the Hubble Space Telescope/Space Telescope Imaging Spectrograph (HST/STIS), we have partially resolved the ionization zones of one knot. Contrary to simple models, higher ionization levels occur on the outer side, i.e., farther from the star. They cannot represent a bow shock, and no satisfying explanation is yet available-though we sketch one qualitative possibility. STIS spectrograms provide far more reliable spatial measurements of the Weigelt knots than HST images do, and this technique can also be applied to the knots' proper motion problem. Our spatial measurement accuracy is about 10 mas, corresponding to a projected linear scale of the order of 30 AU, which is appreciably smaller than the size of each Weigelt knot.

  6. Design principles for rapid folding of knotted DNA nanostructures.

    PubMed

    Kočar, Vid; Schreck, John S; Čeru, Slavko; Gradišar, Helena; Bašić, Nino; Pisanski, Tomaž; Doye, Jonathan P K; Jerala, Roman

    2016-01-01

    Knots are some of the most remarkable topological features in nature. Self-assembly of knotted polymers without breaking or forming covalent bonds is challenging, as the chain needs to be threaded through previously formed loops in an exactly defined order. Here we describe principles to guide the folding of highly knotted single-chain DNA nanostructures as demonstrated on a nano-sized square pyramid. Folding of knots is encoded by the arrangement of modules of different stability based on derived topological and kinetic rules. Among DNA designs composed of the same modules and encoding the same topology, only the one with the folding pathway designed according to the 'free-end' rule folds efficiently into the target structure. Besides high folding yield on slow annealing, this design also folds rapidly on temperature quenching and dilution from chemical denaturant. This strategy could be used to design folding of other knotted programmable polymers such as RNA or proteins. PMID:26887681

  7. Knot Solitons in Spinor Bose-Einstein Condensates

    NASA Astrophysics Data System (ADS)

    Hall, David; Ray, Michael; Tiurev, Konstantin; Ruokokoski, Emmi; Gheorghe, Andrei Horia; Möttönen, Mikko

    2016-05-01

    Knots are familiar entities that appear at a captivating nexus of art, technology, mathematics and science. Following a lengthy period of theoretical investigation and development, they have recently attracted great experimental interest in classical contexts ranging from knotted DNA and nanostructures to vortex knots in fluids. We demonstrate here the controlled creation and detection of knot solitons in the quantum-mechanical order parameter of a spinor Bose-Einstein condensate. Images of the superfluid reveal the circular shape of the soliton core and its associated linked rings. Our observations of the knot soliton establish an experimental foundation for future studies of their stability, dynamics and applications within quantum systems. Supported in part by NSF Grant PHY-1205822.

  8. Design principles for rapid folding of knotted DNA nanostructures

    PubMed Central

    Kočar, Vid; Schreck, John S.; Čeru, Slavko; Gradišar, Helena; Bašić, Nino; Pisanski, Tomaž; Doye, Jonathan P. K.; Jerala, Roman

    2016-01-01

    Knots are some of the most remarkable topological features in nature. Self-assembly of knotted polymers without breaking or forming covalent bonds is challenging, as the chain needs to be threaded through previously formed loops in an exactly defined order. Here we describe principles to guide the folding of highly knotted single-chain DNA nanostructures as demonstrated on a nano-sized square pyramid. Folding of knots is encoded by the arrangement of modules of different stability based on derived topological and kinetic rules. Among DNA designs composed of the same modules and encoding the same topology, only the one with the folding pathway designed according to the ‘free-end' rule folds efficiently into the target structure. Besides high folding yield on slow annealing, this design also folds rapidly on temperature quenching and dilution from chemical denaturant. This strategy could be used to design folding of other knotted programmable polymers such as RNA or proteins. PMID:26887681

  9. Test Results From a Direct Drive Gas Reactor Simulator Coupled to a Brayton Power Conversion Unit

    NASA Technical Reports Server (NTRS)

    Hervol, David S.; Briggs, Maxwell H.; Owen, Albert K.; Bragg-Sitton, Shannon M.

    2009-01-01

    The Brayton Power Conversion Unit (BPCU) located at NASA Glenn Research Center (GRC) in Cleveland, OH is a closed cycle system incorporating a turboaltemator, recuperator, and gas cooler connected by gas ducts to an external gas heater. For this series of tests, the BPCU was modified by replacing the gas heater with the Direct Drive Gas heater or DOG. The DOG uses electric resistance heaters to simulate a fast spectrum nuclear reactor similar to those proposed for space power applications. The combined system thermal transient behavior was the focus of these tests. The BPCU was operated at various steady state points. At each point it was subjected to transient changes involving shaft rotational speed or DOG electrical input. This paper outlines the changes made to the test unit and describes the testing that took place along with the test results.

  10. The genomes of root-knot nematodes.

    PubMed

    Bird, David McK; Williamson, Valerie M; Abad, Pierre; McCarter, James; Danchin, Etienne G J; Castagnone-Sereno, Philippe; Opperman, Charles H

    2009-01-01

    Plant-parasitic nematodes are the most destructive group of plant pathogens worldwide and are extremely challenging to control. The recent completion of two root-knot nematode genomes opens the way for a comparative genomics approach to elucidate the success of these parasites. Sequencing revealed that Meloidogyne hapla, a diploid that reproduces by facultative, meiotic parthenogenesis, encodes approximately 14,200 genes in a compact, 54 Mpb genome. Indeed, this is the smallest metazoan genome completed to date. By contrast, the 86 Mbp Meloidogyne incognita genome encodes approximately 19,200 genes. This species reproduces by obligate mitotic parthenogenesis and exhibits a complex pattern of aneuploidy. The genome includes triplicated regions and contains allelic pairs with exceptionally high degrees of sequence divergence, presumably reflecting adaptations to the strictly asexual reproductive mode. Both root-knot nematode genomes have compacted gene families compared with the free-living nematode Caenorhabditis elegans, and both encode large suites of enzymes that uniquely target the host plant. Acquisition of these genes, apparently via horizontal gene transfer, and their subsequent expansion and diversification point to the evolutionary history of these parasites. It also suggests new routes to their control. PMID:19400640

  11. Determining the microwave coupling and operational efficiencies of a microwave plasma assisted chemical vapor deposition reactor under high pressure diamond synthesis operating conditions

    SciTech Connect

    Nad, Shreya; Gu, Yajun; Asmussen, Jes

    2015-07-15

    The microwave coupling efficiency of the 2.45 GHz, microwave plasma assisted diamond synthesis process is investigated by experimentally measuring the performance of a specific single mode excited, internally tuned microwave plasma reactor. Plasma reactor coupling efficiencies (η) > 90% are achieved over the entire 100–260 Torr pressure range and 1.5–2.4 kW input power diamond synthesis regime. When operating at a specific experimental operating condition, small additional internal tuning adjustments can be made to achieve η > 98%. When the plasma reactor has low empty cavity losses, i.e., the empty cavity quality factor is >1500, then overall microwave discharge coupling efficiencies (η{sub coup}) of >94% can be achieved. A large, safe, and efficient experimental operating regime is identified. Both substrate hot spots and the formation of microwave plasmoids are eliminated when operating within this regime. This investigation suggests that both the reactor design and the reactor process operation must be considered when attempting to lower diamond synthesis electrical energy costs while still enabling a very versatile and flexible operation performance.

  12. Determining the microwave coupling and operational efficiencies of a microwave plasma assisted chemical vapor deposition reactor under high pressure diamond synthesis operating conditions.

    PubMed

    Nad, Shreya; Gu, Yajun; Asmussen, Jes

    2015-07-01

    The microwave coupling efficiency of the 2.45 GHz, microwave plasma assisted diamond synthesis process is investigated by experimentally measuring the performance of a specific single mode excited, internally tuned microwave plasma reactor. Plasma reactor coupling efficiencies (η) > 90% are achieved over the entire 100-260 Torr pressure range and 1.5-2.4 kW input power diamond synthesis regime. When operating at a specific experimental operating condition, small additional internal tuning adjustments can be made to achieve η > 98%. When the plasma reactor has low empty cavity losses, i.e., the empty cavity quality factor is >1500, then overall microwave discharge coupling efficiencies (η(coup)) of >94% can be achieved. A large, safe, and efficient experimental operating regime is identified. Both substrate hot spots and the formation of microwave plasmoids are eliminated when operating within this regime. This investigation suggests that both the reactor design and the reactor process operation must be considered when attempting to lower diamond synthesis electrical energy costs while still enabling a very versatile and flexible operation performance. PMID:26233399

  13. Determining the microwave coupling and operational efficiencies of a microwave plasma assisted chemical vapor deposition reactor under high pressure diamond synthesis operating conditions

    NASA Astrophysics Data System (ADS)

    Nad, Shreya; Gu, Yajun; Asmussen, Jes

    2015-07-01

    The microwave coupling efficiency of the 2.45 GHz, microwave plasma assisted diamond synthesis process is investigated by experimentally measuring the performance of a specific single mode excited, internally tuned microwave plasma reactor. Plasma reactor coupling efficiencies (η) > 90% are achieved over the entire 100-260 Torr pressure range and 1.5-2.4 kW input power diamond synthesis regime. When operating at a specific experimental operating condition, small additional internal tuning adjustments can be made to achieve η > 98%. When the plasma reactor has low empty cavity losses, i.e., the empty cavity quality factor is >1500, then overall microwave discharge coupling efficiencies (ηcoup) of >94% can be achieved. A large, safe, and efficient experimental operating regime is identified. Both substrate hot spots and the formation of microwave plasmoids are eliminated when operating within this regime. This investigation suggests that both the reactor design and the reactor process operation must be considered when attempting to lower diamond synthesis electrical energy costs while still enabling a very versatile and flexible operation performance.

  14. Test of an anaerobic prototype reactor coupled with a filtration unit for production of VFAs.

    PubMed

    Poughon, Laurent; Creuly, Catherine; Farges, Bérangère; Dussap, Claude-Gilles; Schiettecatte, Wim; Jovetic, Srdjan; De Wever, Heleen

    2013-10-01

    The artificial ecosystem MELiSSA, supported by the European Space Agency is a closed loop system consisting of 5 compartments in which food, water and oxygen are produced out of organic waste. The first compartment is conceived as a thermophilic anaerobic membrane bioreactor liquefying organic waste into VFAs, ammonium and CO2 without methane. A 20 L reactor was assembled to demonstrate the selected design and process at prototype scale. We characterized system performance from start-up to steady state and evaluated process efficiencies with special attention drawn to the mass balances. An overall efficiency for organic matter biodegradation of 50% was achieved. The dry matter content was stabilized around 40-50 g L(-1) and VFA production around 5-6 g L(-1). The results were consistent for the considered substrate mixture and can also be considered relevant in a broader context, as a first processing step to produce building blocks for synthesis of primary energy vectors. PMID:23333084

  15. Code Development in Coupled PARCS/RELAP5 for Supercritical Water Reactor

    DOE PAGESBeta

    Hu, Po; Wilson, Paul

    2014-01-01

    The new capability is added to the existing coupled code package PARCS/RELAP5, in order to analyze SCWR design under supercritical pressure with the separated water coolant and moderator channels. This expansion is carried out on both codes. In PARCS, modification is focused on extending the water property tables to supercritical pressure, modifying the variable mapping input file and related code module for processing thermal-hydraulic information from separated coolant/moderator channels, and modifying neutronics feedback module to deal with the separated coolant/moderator channels. In RELAP5, modification is focused on incorporating more accurate water properties near SCWR operation/transient pressure and temperature in themore » code. Confirming tests of the modifications is presented and the major analyzing results from the extended codes package are summarized.« less

  16. Controlling the Motion of Knotted Polymers through Nanopores

    NASA Astrophysics Data System (ADS)

    Narsimhan, Vivek; Renner, C. Benjamin; Doyle, Patrick

    Nanopore sequencing is a technique where DNA moves through a pore and base-pair information is read along the chain as an electric signal. One hurdle facing this technique is that DNA passes too quickly through the pore, rendering the signal to be too noisy. In this talk, we discuss one strategy to control the speed by which polymers move through pores. By tying a knot on a polymer chain, we find that we can jam the polymer at the pore's entrance and halt translocation completely. This idea by itself may not seem useful, but by cycling the field on and off at the relaxation time scale of the knot, we can control the swelling dynamics of the knot at the pore's entrance, and hence ratchet the polymer through the pore. This talk focuses on two parts. First, we will discuss the dynamics of a knot jamming at the pore entrance and determine what sets the critical tension to halt translocation. We will determine how knot topology affects these results and discuss what regimes lead to large fluctuations in the translocation speed. We will then discuss the dynamics of a knot under a time-dependent, periodic force. Lastly, we develop a model to describe the knot's swelling dynamics during relaxation, and use this to explain some of the trends observed in our simulations. Now at Liquiglide.

  17. On the groundstate energy spectrum of magnetic knots and links

    NASA Astrophysics Data System (ADS)

    Ricca, Renzo L.; Maggioni, Francesca

    2014-05-01

    By using analytical results for the constrained minimum energy of magnetic knots we determine the influence of internal twist on the minimum magnetic energy levels of knots and links, and by using ropelength data from the RIDGERUNNER tightening algorithm (Ashton et al 2011 Exp. Math. 20 57-90) we obtain the groundstate energy spectra of the first 250 prime knots and 130 prime links. The two spectra are found to follow an almost identical logarithmic law. By assuming that the number of knot types grows exponentially with the topological crossing number, we show that this generic behavior can be justified by a general relationship between ropelength and crossing number, which is in good agreement with former analytical estimates (Buck and Simon 1999 Topol. Appl. 91 245-57, Diao 2003 J. Knot Theory Ramifications 12 1-16). Moreover, by considering the ropelength averaged over a given knot family, we establish a new connection between the averaged ropelength and the topological crossing number of magnetic knots.

  18. Development of knotting during the collapse transition of polymers.

    PubMed

    Mansfield, Marc L

    2007-12-28

    A dynamic Monte Carlo simulation of the collapse transition of polymer chains is presented. The chains are represented as self-avoiding walks on the simple cubic lattice with a nearest-neighbor contact potential to model the effect of solvent quality. The knot state of the chains is determined using the knot group procedure presented in the accompanying paper. The equilibrium knot spectrum and the equilibrium rms radius of gyration as functions of the chain length and the contact potential are reported. The collapse transition was studied following quenches from good-to poor-solvent conditions. Our results confirm the prediction that the newly formed globule is not yet at equilibrium, since it has not yet achieved its equilibrium knot spectrum. For our model system, the relaxation of the knot spectrum is about an order of magnitude slower than that of the radius of gyration. The collapse transition is also studied for a model in which both ends of the chain remain in good-solvent conditions. Over the time scale of these simulations, knot formation is frustrated in this inhomogeneous model, verifying that the mechanism of knotting is the tunneling of chain ends in and out of the globule. PMID:18163701

  19. Multimedia article. The keys to the new laparoscopic world Thumbs up! knot and Tornado knot.

    PubMed

    Uchida, K; Haruta, N; Okajima, M; Matsuda, M; Yamamoto, M

    2005-06-01

    Most laparoscopic surgeons feel some anxiety when performing intracorporeal knotting with conventional techniques [1, 2]. Two factors contribute to this anxiety. The first is the necessity of recognizing three dimensions on a two-dimensional monitor. The conventional intracorporeal knotting techniques make loops by twisting the thread with a second pair of forceps. This necessitates cooperative movement of both hands, with the added difficulties of depth perception. Regular touch confirmations reduce problems with depth perception. However, touch confirmation is more complicated in laparoscopic surgery than in laparotomy. The second problem is that tied loops can come loose and escape the instruments, especially with hard thread. This is not only stressful but also increases operation time. PMID:15868264

  20. EJECTA KNOT FLICKERING, MASS ABLATION, AND FRAGMENTATION IN CASSIOPEIA A

    SciTech Connect

    Fesen, Robert A.; Zastrow, Jordan A.; Hammell, Molly C.; Shull, J. Michael; Silvia, Devin W.

    2011-08-01

    Ejecta knot flickering, ablation tails, and fragmentation are expected signatures associated with the gradual dissolution of high-velocity supernova (SN) ejecta caused by their passage through an inhomogeneous circumstellar medium or interstellar medium (ISM). Such phenomena mark the initial stages of the gradual merger of SN ejecta with and the enrichment of the surrounding ISM. Here we report on an investigation of this process through changes in the optical flux and morphology of several high-velocity ejecta knots located in the outskirts of the young core-collapse SN remnant Cassiopeia A using Hubble Space Telescope images. Examination of WFPC2 F675W and combined ACS F625W + F775W images taken between 1999 June and 2004 December of several dozen debris fragments in the remnant's northeast ejecta stream and along the remnant's eastern limb reveal substantial emission variations ('flickering') over timescales as short as nine months. Such widespread and rapid variability indicates knot scale lengths {approx_equal} 10{sup 15} cm and a highly inhomogeneous surrounding medium. We also identify a small percentage of ejecta knots located all around the remnant's outer periphery which show trailing emissions typically 0.''2-0.''7 in length aligned along the knot's direction of motion suggestive of knot ablation tails. We discuss the nature of these trailing emissions as they pertain to ablation cooling, knot disruption, and fragmentation, and draw comparisons to the emission 'strings' seen in {eta} Car. Finally, we identify several tight clusters of small ejecta knots which resemble models of shock-induced fragmentation of larger SN ejecta knots caused by a high-velocity interaction with a lower density ambient medium.

  1. Hybrid adsorptive membrane reactor

    DOEpatents

    Tsotsis, Theodore T.; Sahimi, Muhammad; Fayyaz-Najafi, Babak; Harale, Aadesh; Park, Byoung-Gi; Liu, Paul K. T.

    2011-03-01

    A hybrid adsorbent-membrane reactor in which the chemical reaction, membrane separation, and product adsorption are coupled. Also disclosed are a dual-reactor apparatus and a process using the reactor or the apparatus.

  2. Hybrid adsorptive membrane reactor

    NASA Technical Reports Server (NTRS)

    Tsotsis, Theodore T. (Inventor); Sahimi, Muhammad (Inventor); Fayyaz-Najafi, Babak (Inventor); Harale, Aadesh (Inventor); Park, Byoung-Gi (Inventor); Liu, Paul K. T. (Inventor)

    2011-01-01

    A hybrid adsorbent-membrane reactor in which the chemical reaction, membrane separation, and product adsorption are coupled. Also disclosed are a dual-reactor apparatus and a process using the reactor or the apparatus.

  3. Ileosigmoid knotting in early pregnancy: A case report

    PubMed Central

    Maunganidze, Aspect Jacob Vengani; Mungazi, Simbarashe Gift; Siamuchembu, Maphios; Mlotshwa, Makhosini

    2016-01-01

    Ileosigmoid knotting refers to the wrapping of the ileum around the base of the sigmoid colon, or vice versa thus forming a knot. It is a rare cause of intestinal obstruction, more so in pregnancy. We herein report a case of a primigravid woman who presented with an acute abdomen at 13weeks of gestation. The patient underwent emergency surgery. Laparotomy showed ileosigmoid knotting with gangrenous loops of both small bowel and sigmoid colon. The gangrenous bowel was resected. Primary anastomosis of small bowel and a Hartman’s procedure was performed. PMID:27082994

  4. Particle on a Torus Knot: A Hamiltonian Analysis

    NASA Astrophysics Data System (ADS)

    Das, Praloy; Ghosh, Subir

    2016-08-01

    We have studied the dynamics and symmetries of a particle constrained to move in a torus knot. The Hamiltonian system turns out to be Second Class in Dirac's formulation and the Dirac brackets yield novel noncommutative structures. The equations of motion are obtained for a path in general where the knot is present in the particle orbit but it is not restricted to a particular torus. We also study the motion when it is restricted to a specific torus. The rotational symmetries are studied as well. We have also considered the behavior of small fluctuations of the particle motion about a fixed torus knot.

  5. Pore translocation of polymer chains with physical knots

    NASA Astrophysics Data System (ADS)

    Suma, Antonio; Rosa, Angelo; Micheletti, Cristian

    The driven traslocation of knotted chains through narrow pores has important implications for single-molecule manipulation contexts. Its complex phenomenology is, however, still largely unexplored, both as a function of knot complexity and the magnitude of the driving, translocating force. We accordingly report on a systematic theoretical and computational investigation of both aspects. In particular we consider the case of flexible chains accommodating a large repertoire of knots that are driven through pores too narrow to allow for their passage. We show that the observed rich translocation phenomenology can be rationalised in a transparent mechanical framework that can further be used for predictive purposes.

  6. Two Adhesive Sites Can Enhance the Knotting Probability of DNA

    PubMed Central

    2015-01-01

    Self-entanglement, or knotting, is entropically favored in long polymers. Relatively short polymers such as proteins can knot as well, but in this case the entanglement is mainly driven by fine-tuned, sequence-specific interactions. The relation between the sequence of a long polymer and its topological state is here investigated by means of a coarse-grained model of DNA. We demonstrate that the introduction of two adhesive regions along the sequence of a self-avoiding chain substantially increases the probability of forming a knot. PMID:26136125

  7. Knots in the cath lab, an embarrassing complication of radial angiography

    PubMed Central

    Gupta, Prabha Nini; Praveen, G K; Ahmed, Sajan Z; Kumar, B Krishna; V S, Sajith

    2013-01-01

    Most case reports or series describe knots in the venous system such as knots of Swan-Ganz catheters, pacing wires or thermodilution catheters. Knots during radial angiography are relatively rare. Here we describe a simple method of unravelling a radial knot via the femoral route, together with a review of the literature on knots in the catherisation laboratory and the techniques to deal with them.

  8. Review of ion energy and angular distributions in capacitively coupled RF plasma reactors

    SciTech Connect

    Kawamura, E.; Lieberman, M.A.; Birdsall, C.K.; Vahedi, V.

    1995-12-31

    The authors present a historical review and discussion of previous works on ion energy and angular distributions (IED and IAD) arriving at the target in the collisionless regime. This regime is of great interest to experimentalists and modelers studying the new generation of high density sources in which the sheath is much thinner than in the conventional RIE systems. The purpose of the review is to asses what has been done so far, and to clarify some issues about sheaths in high density systems. Having determined the important parameters, the authors show some particle-in-cell simulation results of a dually excited capacitively coupled plasma in which the sheath ions roughly see the scaling as in high density sources. The results show that when {tau}{sub ion}/{tau}{sub rf} < 1, the oscillating voltage and width of the rf sheath significantly affect the IEDs, where {tau}{sub ion} is the ion transit-time and {tau}{sub rf} is rf period.

  9. Knotted Strings and Leptonic Flavor Structure

    NASA Astrophysics Data System (ADS)

    Kephart, T. W.; Leser, P.; Päs, H.

    2012-12-01

    We propose a third idea for the explanation of the leptonic flavor structure in addition to the prominent approaches based on flavor symmetry and anarchy. Typical flavor patterns can be modeled by using mass spectra obtained from the discrete lengths spectrum of tight knots and links. We assume that a string theory model exists in which this idea can be incorporated via the Majorana mass structure of a type I seesaw model. It is shown by a scan over the parameter space that such a model is able to provide an excellent fit to current neutrino data and that it predicts a normal neutrino mass hierarchy as well as a small mixing angle θ13. Startlingly, such scenarios could be related to the dimensionality of spacetime via an anthropic argument.

  10. Torus Knot Polynomials and Susy Wilson Loops

    NASA Astrophysics Data System (ADS)

    Giasemidis, Georgios; Tierz, Miguel

    2014-12-01

    We give, using an explicit expression obtained in (Jones V, Ann Math 126:335, 1987), a basic hypergeometric representation of the HOMFLY polynomial of ( n, m) torus knots, and present a number of equivalent expressions, all related by Heine's transformations. Using this result, the symmetry and the leading polynomial at large N are explicit. We show the latter to be the Wilson loop of 2d Yang-Mills theory on the plane. In addition, after taking one winding to infinity, it becomes the Wilson loop in the zero instanton sector of the 2d Yang-Mills theory, which is known to give averages of Wilson loops in = 4 SYM theory. We also give, using matrix models, an interpretation of the HOMFLY polynomial and the corresponding Jones-Rosso representation in terms of q-harmonic oscillators.

  11. New knotted solutions of Maxwell's equations

    NASA Astrophysics Data System (ADS)

    Hoyos, Carlos; Sircar, Nilanjan; Sonnenschein, Jacob

    2015-06-01

    In this paper we have further developed the study of topologically non-trivial solutions of vacuum electrodynamics. We have discovered a novel method of generating such solutions by applying conformal transformations with complex parameters on known solutions expressed in terms of Bateman's variables. This has enabled us to obtain a wide class of solutions from the basic configuration, such as constant electromagnetic fields and plane-waves. We have introduced a covariant formulation of Bateman's construction and discussed the conserved charges associated with the conformal group as well as a set of four types of conserved helicities. We have also given a formulation in terms of quaternions. This led to a simple map between the electromagnetic knotted and linked solutions into flat connections of SU(2) gauge theory. We have computed the corresponding Chern-Simons charge in a class of solutions and the charge takes integer values.

  12. Ejecta Knot Evolution in Cas A

    NASA Astrophysics Data System (ADS)

    Rutherford, John; Figueroa-Feliciano, E.; Dewey, D.; Trowbridge, S.; Bastien, F.; Sato, K.

    2011-01-01

    Supernova remnants are remarkable laboratories for studying, among other phenomena, explosive nucleosynthesis and plasma dynamics. Time-dependent signatures of such processes can further inform our understanding, and may be found in widely spaced epochs of observation from high spatial and spectral resolution instruments. We investigated the spectral evolution in the X-ray band of the bright ejecta knots in Cassiopeia A over the last decade. Both dispersed and non-dispersed spectra from the Chandra HETG and ACIS instruments were used for this study, helping to better constrain signs of evolution. We present our findings of how such physical properties as the temperature, elemental abundances, velocity, and non-equilibrium ionization age changed over ten years of the several hundred year old remnant's lifetime, along with a careful analysis of the confounding background contamination and model parameter correlations.

  13. Detection of some stable species during the oxidation of methane by coupling a jet-stirred reactor (JSR) to cw-CRDS

    PubMed Central

    Bahrini, Chiheb; Herbinet, Olivier; Glaude, Pierre-Alexandre; Schoemaecker, Coralie; Fittschen, Christa; Battin-Leclerc, Frédérique

    2013-01-01

    We present the coupling of a jet-stirred reactor to detection by cw-CRDS in the near infrared and first results obtained during the oxidation of methane. The mixture is rapidly expanded from the jet-stirred reactor into a 80 cm-long cw-CRDS cell maintained at a the pressure around 1.33 kPa, thus freezing the reaction and decreasing pressure broadening of the absorption lines. Some stable species (CH4, H2O and CH2O) have been quantified through their well structured spectra around 1506 nm, while H2O2 and HO2 radicals could not be detected. PMID:23710075

  14. Detection of some stable species during the oxidation of methane by coupling a jet-stirred reactor (JSR) to cw-CRDS

    NASA Astrophysics Data System (ADS)

    Bahrini, Chiheb; Herbinet, Olivier; Glaude, Pierre-Alexandre; Schoemaecker, Coralie; Fittschen, Christa; Battin-Leclerc, Frédérique

    2012-05-01

    We present the coupling of a jet-stirred reactor to detection by cw-CRDS in the near infrared and first results obtained during the oxidation of methane. The mixture is rapidly expanded from the jet-stirred reactor into a 80 cm-long cw-CRDS cell maintained at a the pressure around 1.33 kPa, thus freezing the reaction and decreasing pressure broadening of the absorption lines. Some stable species (CH4, H2O and CH2O) have been quantified through their well structured spectra around 1506 nm, while H2O2 and HO2 radicals could not be detected.

  15. Detection of some stable species during the oxidation of methane by coupling a jet-stirred reactor (JSR) to cw-CRDS.

    PubMed

    Bahrini, Chiheb; Herbinet, Olivier; Glaude, Pierre-Alexandre; Schoemaecker, Coralie; Fittschen, Christa; Battin-Leclerc, Frédérique

    2012-05-01

    We present the coupling of a jet-stirred reactor to detection by cw-CRDS in the near infrared and first results obtained during the oxidation of methane. The mixture is rapidly expanded from the jet-stirred reactor into a 80 cm-long cw-CRDS cell maintained at a the pressure around 1.33 kPa, thus freezing the reaction and decreasing pressure broadening of the absorption lines. Some stable species (CH4, H2O and CH2O) have been quantified through their well structured spectra around 1506 nm, while H2O2 and HO2 radicals could not be detected. PMID:23710075

  16. A UASB reactor coupled to a hybrid aerobic MBR as innovative plant configuration to enhance the removal of organic micropollutants.

    PubMed

    Alvarino, T; Suárez, S; Garrido, M; Lema, J M; Omil, F

    2016-02-01

    An innovative plant configuration based in an UASB reactor coupled to a hybrid aerobic membrane bioreactor designed for sustainable treatment of municipal wastewater at ambient temperatures and low hydraulic retention time was studied in terms of organic micropollutants (OMPs) removal. OMPs removal mechanisms, as well as the potential influence of biomass activity and physical conformation were assessed. Throughout all periods of operation (150 days) high organic matter removals were maintained (>95%) and, regarding OMPs removal, this innovative system has shown to be more efficient than conventional technologies for those OMPs which are prone to be biotransformed under anaerobic conditions. For instance, sulfamethoxazole and trimethoprim have both shown to be biodegradable under anaerobic conditions with similar efficiencies (removal efficiencies above 84%). OMPs main removal mechanism was found to be biotransformation, except in the case of musk fragrances which showed medium sorption onto sludge. OMPs removal was strongly dependent on the efficiency of the primary metabolism (organic matter degradation and nitrification) and the type of biomass. PMID:26386770

  17. Investigation of ion energy and angular distributions at the wafer edge in rf capacitively coupled reactors using CFD-ACE+

    NASA Astrophysics Data System (ADS)

    Bhoj, Ananth; Roy, Abhra; Jain, Kunal; Xiong, Zhongmin

    2015-09-01

    Dual frequency capacitively coupled reactors are now commonly used in microelectronics fabrication. The extent of possible independent control of ion fluxes and ion energy and angular distribution (IEADs) by varying HF and LF signals is currently a topic of great interest. In this study, we report on investigations of IEADs in single and dual frequency CCPs, including the wafer edge refinement using CFD-ACE+. The current algorithms in CFD-ACE+ allow the determination of total power at the electrode or in the discharge. To account for the presence of two or more rf sources connected to a powered electrode, the existing numerical algorithms for power targeting were enhanced to track current at the electrode as a function of time, vary voltage and determine power as a function of frequency. The Monte Carlo transport module for heavy species in CFD-ACE+ was recently enhanced to compute IEADs in rf discharges. Results for the effect of varying power and pressure on IEADs were compared to semi-analytical models and data reported in Gahan et al.. The validated model was applied to investigate the effect of details of HF and LF signals on IEADs in Argon discharges.

  18. ICECO-CEL: a coupled Eulerian-Lagrangian code for analyzing primary system response in fast reactors

    SciTech Connect

    Wang, C.Y.

    1981-02-01

    This report describes a coupled Eulerian-Lagrangian code, ICECO-CEL, for analyzing the response of the primary system during hypothetical core disruptive accidents. The implicit Eulerian method is used to calculate the fluid motion so that large fluid distortion, two-dimensional sliding interface, flow around corners, flow through coolant passageways, and out-flow boundary conditions can be treated. The explicit Lagrangian formulation is employed to compute the response of the containment vessel and other elastic-plastic solids inside the reactor containment. Large displacements, as well as geometrical and material nonlinearities are considered in the analysis. Marker particles are utilized to define the free surface or the material interface and to visualize the fluid motion. The basic equations and numerical techniques used in the Eulerian hydrodynamics and Lagrangian structural dynamics are described. Treatment of the above-core hydrodynamics, sodium spillage, fluid cavitation, free-surface boundary conditions and heat transfer are also presented. Examples are given to illustrate the capabilities of the computer code. Comparisons of the code predictions with available experimental data are also made.

  19. Life cycle assessment of hydrogen production from S-I thermochemical process coupled to a high temperature gas reactor

    SciTech Connect

    Giraldi, M. R.; Francois, J. L.; Castro-Uriegas, D.

    2012-07-01

    The purpose of this paper is to quantify the greenhouse gas (GHG) emissions associated to the hydrogen produced by the sulfur-iodine thermochemical process, coupled to a high temperature nuclear reactor, and to compare the results with other life cycle analysis (LCA) studies on hydrogen production technologies, both conventional and emerging. The LCA tool was used to quantify the impacts associated with climate change. The product system was defined by the following steps: (i) extraction and manufacturing of raw materials (upstream flows), (U) external energy supplied to the system, (iii) nuclear power plant, and (iv) hydrogen production plant. Particular attention was focused to those processes where there was limited information from literature about inventory data, as the TRISO fuel manufacture, and the production of iodine. The results show that the electric power, supplied to the hydrogen plant, is a sensitive parameter for GHG emissions. When the nuclear power plant supplied the electrical power, low GHG emissions were obtained. These results improve those reported by conventional hydrogen production methods, such as steam reforming. (authors)

  20. Knots cascade detected by a monotonically decreasing sequence of values.

    PubMed

    Liu, Xin; Ricca, Renzo L

    2016-01-01

    Due to reconnection or recombination of neighboring strands superfluid vortex knots and DNA plasmid torus knots and links are found to undergo an almost identical cascade process, that tend to reduce topological complexity by stepwise unlinking. Here, by using the HOMFLYPT polynomial recently introduced for fluid knots, we prove that under the assumption that topological complexity decreases by stepwise unlinking this cascade process follows a path detected by a unique, monotonically decreasing sequence of numerical values. This result holds true for any sequence of standardly embedded torus knots T(2, 2n + 1) and torus links T(2, 2n). By this result we demonstrate that the computation of this adapted HOMFLYPT polynomial provides a powerful tool to measure topological complexity of various physical systems. PMID:27052386

  1. Knots cascade detected by a monotonically decreasing sequence of values

    PubMed Central

    Liu, Xin; Ricca, Renzo L.

    2016-01-01

    Due to reconnection or recombination of neighboring strands superfluid vortex knots and DNA plasmid torus knots and links are found to undergo an almost identical cascade process, that tend to reduce topological complexity by stepwise unlinking. Here, by using the HOMFLYPT polynomial recently introduced for fluid knots, we prove that under the assumption that topological complexity decreases by stepwise unlinking this cascade process follows a path detected by a unique, monotonically decreasing sequence of numerical values. This result holds true for any sequence of standardly embedded torus knots T(2, 2n + 1) and torus links T(2, 2n). By this result we demonstrate that the computation of this adapted HOMFLYPT polynomial provides a powerful tool to measure topological complexity of various physical systems. PMID:27052386

  2. Knots cascade detected by a monotonically decreasing sequence of values

    NASA Astrophysics Data System (ADS)

    Liu, Xin; Ricca, Renzo L.

    2016-04-01

    Due to reconnection or recombination of neighboring strands superfluid vortex knots and DNA plasmid torus knots and links are found to undergo an almost identical cascade process, that tend to reduce topological complexity by stepwise unlinking. Here, by using the HOMFLYPT polynomial recently introduced for fluid knots, we prove that under the assumption that topological complexity decreases by stepwise unlinking this cascade process follows a path detected by a unique, monotonically decreasing sequence of numerical values. This result holds true for any sequence of standardly embedded torus knots T(2, 2n + 1) and torus links T(2, 2n). By this result we demonstrate that the computation of this adapted HOMFLYPT polynomial provides a powerful tool to measure topological complexity of various physical systems.

  3. Untangling the mechanics versus topology of overhand knots

    NASA Astrophysics Data System (ADS)

    Reis, Pedro; Jawed, Mohammad; Dieleman, Peter; Audoly, Basile

    2015-03-01

    We study the interplay between mechanics and topology of overhand knots in slender elastic rods. We perform precision desktop experiments of overhand knots with increasing values for the crossing number (our measure of topology) and characterize their mechanical response through tension-displacement tests. The tensile force required to tighten the knot is governed by an intricate balance between topology, bending, friction, and contact forces. Digital imaging is employed to characterize the configuration of the contact braid as a function of crossing number. A robust scaling law is found for the pulling force in terms of the geometric and topological parameters of the knot. A reduced theory is developed, which predictively rationalizes the process.

  4. The folding of knotted proteins: insights from lattice simulations.

    PubMed

    Faísca, Patrícia F N; Travasso, Rui D M; Charters, Tiago; Nunes, Ana; Cieplak, Marek

    2010-01-01

    We carry out systematic Monte Carlo simulations of Gō lattice proteins to investigate and compare the folding processes of two model proteins whose native structures differ from each other due to the presence of a trefoil knot located near the terminus of one of the protein chains. We show that the folding time of the knotted fold is larger than that of the unknotted protein and that this difference in folding time is particularly striking in the temperature region below the optimal folding temperature. Both proteins display similar folding transition temperatures, which is indicative of similar thermal stabilities. By using the folding probability reaction coordinate as an estimator of folding progression we have found out that the formation of the knot is mainly a late folding event in our shallow knot system. PMID:20130340

  5. The folding of knotted proteins: insights from lattice simulations

    NASA Astrophysics Data System (ADS)

    Faísca, Patrícia F. N.; Travasso, Rui D. M.; Charters, Tiago; Nunes, Ana; Cieplak, Marek

    2010-03-01

    We carry out systematic Monte Carlo simulations of Gō lattice proteins to investigate and compare the folding processes of two model proteins whose native structures differ from each other due to the presence of a trefoil knot located near the terminus of one of the protein chains. We show that the folding time of the knotted fold is larger than that of the unknotted protein and that this difference in folding time is particularly striking in the temperature region below the optimal folding temperature. Both proteins display similar folding transition temperatures, which is indicative of similar thermal stabilities. By using the folding probability reaction coordinate as an estimator of folding progression we have found out that the formation of the knot is mainly a late folding event in our shallow knot system.

  6. Pd-Ag Membrane Coupled to a Two-Zone Fluidized Bed Reactor (TZFBR) for Propane Dehydrogenation on a Pt-Sn/MgAl2O4 Catalyst.

    PubMed

    Medrano, José-Antonio; Julián, Ignacio; Herguido, Javier; Menéndez, Miguel

    2013-01-01

    Several reactor configurations have been tested for catalytic propane dehydrogenation employing Pt-Sn/MgAl2O4 as a catalyst. Pd-Ag alloy membranes coupled to the multifunctional Two-Zone Fluidized Bed Reactor (TZFBR) provide an improvement in propane conversion by hydrogen removal from the reaction bed through the inorganic membrane in addition to in situ catalyst regeneration. Twofold process intensification is thereby achieved when compared to the use of traditional fluidized bed reactors (FBR), where coke formation and thermodynamic equilibrium represent important process limitations. Experiments were carried out at 500-575 °C and with catalyst mass to molar flow of fed propane ratios between 15.1 and 35.2 g min mmol-1, employing three different reactor configurations: FBR, TZFBR and TZFBR + Membrane (TZFBR + MB). The results in the FBR showed catalyst deactivation, which was faster at high temperatures. In contrast, by employing the TZFBR with the optimum regenerative agent flow (diluted oxygen), the process activity was sustained throughout the time on stream. The TZFBR + MB showed promising results in catalytic propane dehydrogenation, displacing the reaction towards higher propylene production and giving the best results among the different reactor configurations studied. Furthermore, the results obtained in this study were better than those reported on conventional reactors. PMID:24958620

  7. Pd-Ag Membrane Coupled to a Two-Zone Fluidized Bed Reactor (TZFBR) for Propane Dehydrogenation on a Pt-Sn/MgAl2O4 Catalyst

    PubMed Central

    Medrano, José-Antonio; Julián, Ignacio; Herguido, Javier; Menéndez, Miguel

    2013-01-01

    Several reactor configurations have been tested for catalytic propane dehydrogenation employing Pt-Sn/MgAl2O4 as a catalyst. Pd-Ag alloy membranes coupled to the multifunctional Two-Zone Fluidized Bed Reactor (TZFBR) provide an improvement in propane conversion by hydrogen removal from the reaction bed through the inorganic membrane in addition to in situ catalyst regeneration. Twofold process intensification is thereby achieved when compared to the use of traditional fluidized bed reactors (FBR), where coke formation and thermodynamic equilibrium represent important process limitations. Experiments were carried out at 500–575 °C and with catalyst mass to molar flow of fed propane ratios between 15.1 and 35.2 g min mmol−1, employing three different reactor configurations: FBR, TZFBR and TZFBR + Membrane (TZFBR + MB). The results in the FBR showed catalyst deactivation, which was faster at high temperatures. In contrast, by employing the TZFBR with the optimum regenerative agent flow (diluted oxygen), the process activity was sustained throughout the time on stream. The TZFBR + MB showed promising results in catalytic propane dehydrogenation, displacing the reaction towards higher propylene production and giving the best results among the different reactor configurations studied. Furthermore, the results obtained in this study were better than those reported on conventional reactors. PMID:24958620

  8. Colored HOMFLY polynomials of knots presented as double fat diagrams

    NASA Astrophysics Data System (ADS)

    Mironov, A.; Morozov, A.; Morozov, An.; Ramadevi, P.; Singh, Vivek Kumar

    2015-07-01

    Many knots and links in S 3 can be drawn as gluing of three manifolds with one or more four-punctured S 2 boundaries. We call these knot diagrams as double fat graphs whose invariants involve only the knowledge of the fusion and the braiding matrices of four -strand braids. Incorporating the properties of four-point conformal blocks in WZNW models, we conjecture colored HOMFLY polynomials for these double fat graphs where the color can be rectangular or non-rectangular representation. With the recent work of Gu-Jockers, the fusion matrices for the non-rectangular [21] representation, the first which involves multiplicity is known. We verify our conjecture by comparing with the [21] colored HOMFLY of many knots, obtained as closure of three braids. The conjectured form is computationally very effective leading to writing [21]-colored HOMFLY polynomials for many pretzel type knots and non-pretzel type knots. In particular, we find class of pretzel mutants which are distinguished and another class of mutants which cannot be distinguished by [21] representation. The difference between the [21]-colored HOMFLY of two mutants seems to have a general form, with A-dependence completely defined by the old conjecture due to Morton and Cromwell. In particular, we check it for an entire multi-parametric family of mutant knots evaluated using evolution method.

  9. Probe knots and Hopf insulators with ultracold atoms

    NASA Astrophysics Data System (ADS)

    Deng, Dong-Ling; Wang, Sheng-Tao; Sun, Kai; Duan, Lu-Ming

    2015-05-01

    Knots and links are fascinating and intricate topological objects that have played a prominent role in physical and life sciences. Their influence spans from DNA and molecular chemistry to vortices in superfluid helium, defects in liquid crystals and cosmic strings in the early universe. Here, we show that knotted structures also exist in a peculiar class of three dimensional topological insulators--the Hopf insulators. In particular, we demonstrate that the spin textures of Hopf insulators in momentum space are twisted in a nontrivial way, which implies various knot and link structures. We further illustrate that the knots and nontrivial spin textures can be probed via standard time-of-flight images in cold atoms as preimage contours of spin orientations in stereographic coordinates. The extracted Hopf invariants, knots, and links are validated to be robust to typical experimental imperfections. Our work establishes the existence of knotted structures in cold atoms and may have potential applications in spintronics and quantum information processings. We thank X.-J. Liu and G. Ortiz for helpful discussions. S.T.W., D.L.D., and L.M.D. are supported by the NBRPC 2011CBA00300, the IARPA MUSIQC program, the ARO and the AFOSR MURI program. K.S. acknowledges support from NSF under Grant No. PHY1402971.

  10. Tensile strength of a surgeon’s or a square knot

    PubMed Central

    Muffly, Tyler M.; Boyce, Jamie; Kieweg, Sarah L.; Bonham, Aaron J.

    2014-01-01

    Objective To test the integrity of surgeon’s knots and flat square knots using four different suture materials. Study Design Chromic catgut, polyglactin 910, silk, and polydioxanone sutures were tied in the two types of knot configurations. For all sutures, a 0-gauge United States Pharmacopeia suture was used. Knots were tied by a single investigator (JB). Suture was soaked in 0.9 % sodium chloride for 60 seconds and subsequently transferred to a tensiometer where the tails were cut to 3 mm length. We compared the knots, measuring knot strength using a tensiometer until the sutures broke or untied. Results A total of 119 knots were tied. We found no difference in mean tension at failure between a surgeon’s knot (79.7 Newtons) and a flat square knot (82.9 Newtons). Using a Chi-square test, we did not find a statistically significant difference in the likelihood of knots coming untied between surgeon’s knots (29%) and flat square knots (38%). Conclusions Under laboratory conditions, surgeon’s knots and flat square knots did not differ in tension at failure or likelihood of untying. PMID:20816357

  11. Soliton stability in some knot soliton models

    SciTech Connect

    Adam, C.; Sanchez-Guillen, J.; Wereszczynski, A.

    2007-02-15

    We study the issue of stability of static solitonlike solutions in some nonlinear field theories which allow for knotted field configurations. Concretely, we investigate the Aratyn-Ferreira-Zimerman model [Phys. Lett. B 456, 162 (1999); Phys. Rev. Lett. 83, 1723 (1999)], based on a Lagrangian quartic in first derivatives with infinitely many conserved currents, for which infinitely many soliton solutions are known analytically. For this model we find that sectors with different (integer) topological charges (Hopf index) are not separated by an infinite energy barrier. Further, if variations which change the topological charge are allowed, then the static solutions are not even critical points of the energy functional. We also explain why soliton solutions can exist at all, in spite of these facts. In addition, we briefly discuss the Nicole model [J. Phys. G 4, 1363 (1978)], which is based on a sigma-model-type Lagrangian. For the Nicole model we find that different topological sectors are separated by an infinite energy barrier.

  12. Evolutionary origin of inhibitor cystine knot peptides.

    PubMed

    Zhu, Shunyi; Darbon, Herve; Dyason, Karin; Verdonck, Fons; Tytgat, Jan

    2003-09-01

    The inhibitor cystine knot (ICK) fold is an evolutionarily conserved structural motif shared by a large group of polypeptides with diverse sequences and bioactivities. Although found in different phyla (animal, plant, and fungus), ICK peptides appear to be most prominent in venoms of cone snail and spider. Recently, two scorpion toxins activating a calcium release channel have been found to adopt an ICK fold. We have isolated and identified both cDNA and genomic clones for this family of ICK peptides from the scorpion Opistophthalmus carinatus. The gene characterized by three well-delineated exons respectively coding for three structural and functional domains in the toxin precursors illustrates the correlation between exon and module as suggested by the "exon theory of genes." Based on the analysis of precursor organization and gene structure combined with the 3-D fold and functional data, our results highlight a common evolutionary origin for ICK peptides from animals. In contrast, ICK peptides from plant and fungus might be independently evolved from another ancestor. PMID:12958203

  13. Knots and Gamma Classes in Open Topological String Theory

    NASA Astrophysics Data System (ADS)

    Mahowald, Matthew

    This thesis explores some mathematical applications of string dualities in open topological string theory and presents some new techniques for studying and computing open Gromov-Witten invariants. First, we prove a mild generalization of the gamma class formula of [BCR13], and show that it applies in two novel examples: the quintic threefold Q with Lagrangian given by the real quintic QR Q, and for Lagrangians LK ? X = O P1 (--1, --1) obtained from the conormal bundles of (r, s) torus knots K ? S3 via the conifold transition. Disk enumeration on (Q, Q R ) was first considered in [PSW08], and disk enumeration for (X, LK) was studied in winding-1 in [DSV13]. The gamma class formula agrees with the results of [DSV13] and [PSW08], and we generalize the formula of [DSV13] to arbitrary winding. Next we study a relationship between mirror symmetry and knot contact homology described in [AENV14, AV12]. For knots K ? S 3 , large-N duality relates open Gromov-Witten theory on (X, L_K ) to SU (N) Chern-Simons theory on (S3, K). We use the conjecture of [AV12] to compute open Gromov-Witten invariants of (X, L K) through mirror symmetry in many examples, including several non-toric knots. We also find further evidence for this conjecture: for ( r, s) torus knots, we find a formula for the genus-0, 1-boundary-component, degree-d, winding-w open Gromov-Witten invariants of (X, LK ) using localization. This formula agrees with the results of the mirror symmetry calculation. Moreover, using this formula, we describe a method for obtaining the augmentation polynomial of a knot K from the open Gromov-Witten invariants of ( X, LK ). This method is shown to correctly recover the augmentation polynomial for the unknot and (3, 2) torus knot.

  14. To Knot or Not-That is the Question: A Nanofluidic Knot Factory based on Compression of Single DNA Molecules against Slit Barriers in Nanochannels

    NASA Astrophysics Data System (ADS)

    Amin, Susan; Khorshid, Ahmed; Zeng, Lili; Zimny, Philip; Reisner, Walter

    Knots can form during DNA packaging in chromosome and obstruct mapping of DNA in nanochannels. Studies have focused on theoretical and numerical studies of knots, but an efficient and fully controlled means of knotting has not yet been explored. Here, we introduce a knot factory on chip based on pneumatic compression of single T4 DNA against a slit barrier in a nanochannel. The DNA are compressed to a well-defined fraction of their initial equilibrium extension. The pressure is then released and the DNA molecules relax back to their equilibrium extension; knots are present along the relaxed DNA, visualized as sharply localized regions of high intensity. Via repeated compression and relaxation, we can measure the probabilities of forming single and multiple knot states and the distribution of knot sizes as a function of fractional compression and waiting time in the compressed state. We show that the total probability of knot formation increases with greater compression and waiting time.These findings are well described via a knot formation free energy derived from scaling arguments, suggesting that the enhanced knotting probability at high compression arises from avoiding the free energy cost due to self-exclusion interactions that would arise from contour stored in the knot.

  15. Fabrication and characterization of high order filter based on resonance in hybrid multi-knots microfiber structure

    NASA Astrophysics Data System (ADS)

    Nodehi, S.; Mohammed, W. S.; Ahmad, H.; Harun, S. W.

    2016-04-01

    This work proposes a novel design of a hybrid microfiber resonator which can be used as a band-pass and band-stop filter in various applications such as fiber lasers. The structure comprises of two microfiber knot resonators with different sizes which are surrounded by a semi-loop structure with one input and two output ports. Utilization of the Vernier effect in the proposed structure showed an enhancement of the free spectral range (FSR). The finesse has increased by a factor of three compared to a single knot providing a sharper roll-off. The filter bandwidth is adjustable as a result of the manipulation of the coupling length and rings' radii. The performance of the device is explained theoretically using transfer matrix analysis.

  16. Characterization of the red knot (Calidris canutus) mitochondrial control region.

    PubMed

    Buehler, Deborah M; Baker, Allan J

    2003-08-01

    We sequenced the complete mitochondrial control regions of 11 red knots (Calidris canutus). The control region is 1168 bp in length and is flanked by tRNA glutamate (glu) and the gene ND6 at its 5' end and tRNA phenylalanine (phe) and the gene 12S on its 3' end. The sequence possesses conserved sequence blocks F, E, D, C, CSB-1, and the bird similarity box (BSB), as expected for a mitochondrial copy. Flanking tRNA regions show correct secondary structure, and a relative rate test indicated no significant difference between substitution rates in the sequence we obtained versus the known mitochondrial sequence of turnstones (Charadriiformes: Scolopacidae). These characteristics indicate that the sequence is mitochondrial in origin. To confirm this, we sequenced the control region of a single individual using both purified mitochondrial DNA and genomic DNA. The sequences were identical using both methods. The sequence and methods presented in this paper may now serve as a reference for future studies using knot and other avian control regions. Furthermore, the discovery of five variable sites in 11 knots towards the 3' end of the control region, and the variability of this region in contrast to the more conserved central domain in the alignment between knots and other Charadriiformes, highlights the importance of this area as a source of variation for future studies in knots and other birds. PMID:12897864

  17. Equations on knot polynomials and 3d/5d duality

    SciTech Connect

    Mironov, A.; Morozov, A.

    2012-09-24

    We briefly review the current situation with various relations between knot/braid polynomials (Chern-Simons correlation functions), ordinary and extended, considered as functions of the representation and of the knot topology. These include linear skein relations, quadratic Plucker relations, as well as 'differential' and (quantum) A-polynomial structures. We pay a special attention to identity between the A-polynomial equations for knots and Baxter equations for quantum relativistic integrable systems, related through Seiberg-Witten theory to 5d super-Yang-Mills models and through the AGT relation to the q-Virasoro algebra. This identity is an important ingredient of emerging a 3d- 5d generalization of the AGT relation. The shape of the Baxter equation (including the values of coefficients) depend on the choice of the knot/braid. Thus, like the case of KP integrability, where (some, so far torus) knots parameterize particular points of the Universal Grassmannian, in this relation they parameterize particular points in the moduli space of many-body integrable systems of relativistic type.

  18. Validation of the U.S. NRC coupled code system TRITON/TRACE/PARCS with the special power excursion reactor test III (SPERT III)

    SciTech Connect

    Wang, R. C.; Xu, Y.; Downar, T.; Hudson, N.

    2012-07-01

    The Special Power Excursion Reactor Test III (SPERT III) was a series of reactivity insertion experiments conducted in the 1950's. This paper describes the validation of the U.S. NRC Coupled Code system TRITON/PARCS/TRACE to simulate reactivity insertion accidents (RIA) by using several of the SPERT III tests. The work here used the SPERT III E-core configuration tests in which the RIA was initiated by ejecting a control rod. The resulting super-prompt reactivity excursion and negative reactivity feedback produced the familiar bell shaped power increase and decrease. The energy deposition during such a power peak has important safety consequences and provides validation basis for core coupled multi-physics codes. The transients of five separate tests are used to benchmark the PARCS/TRACE coupled code. The models were thoroughly validated using the original experiment documentation. (authors)

  19. Topological zoo of free-standing knots in confined chiral nematic fluids.

    PubMed

    Seč, David; Copar, Simon; Zumer, Slobodan

    2014-01-01

    Knotted fields are an emerging research topic relevant to different areas of physics where topology plays a crucial role. Recent realization of knotted nematic disclinations stabilized by colloidal particles raised a challenge of free-standing knots. Here we demonstrate the creation of free-standing knotted and linked disclination loops in the cholesteric ordering fields, which are confined to spherical droplets with homeotropic surface anchoring. Our approach, using free energy minimization and topological theory, leads to the stabilization of knots via the interplay of the geometric frustration and intrinsic chirality. Selected configurations of the lowest complexity are characterized by knot or link types, disclination lengths and self-linking numbers. When cholesteric pitch becomes short on the confinement scale, the knotted structures change to practically unperturbed cholesteric structures with disclinations expelled close to the surface. The drops with knots could be controlled by optical beams and may be used for photonic elements. PMID:24419153

  20. Topological zoo of free-standing knots in confined chiral nematic fluids

    NASA Astrophysics Data System (ADS)

    Seč, David; Čopar, Simon; Žumer, Slobodan

    2014-01-01

    Knotted fields are an emerging research topic relevant to different areas of physics where topology plays a crucial role. Recent realization of knotted nematic disclinations stabilized by colloidal particles raised a challenge of free-standing knots. Here we demonstrate the creation of free-standing knotted and linked disclination loops in the cholesteric ordering fields, which are confined to spherical droplets with homeotropic surface anchoring. Our approach, using free energy minimization and topological theory, leads to the stabilization of knots via the interplay of the geometric frustration and intrinsic chirality. Selected configurations of the lowest complexity are characterized by knot or link types, disclination lengths and self-linking numbers. When cholesteric pitch becomes short on the confinement scale, the knotted structures change to practically unperturbed cholesteric structures with disclinations expelled close to the surface. The drops with knots could be controlled by optical beams and may be used for photonic elements.

  1. One-handed knot tying technique in single-incision laparoscopic surgery

    PubMed Central

    Thanakumar, John; John, Pravin Hector

    2011-01-01

    In an open surgery, two-handed as well as one-handed knot tying is commonplace. Knot tying in laparoscopic surgery traditionally involves the use of two instruments (for fashioning an intracorporeal knot) or passing of a ligature around a tubular structure, exteriorising it, fashioning a knot, and sliding it down with a knot-pusher (external slip knot). With increasing interest in expanding applications of single-incision laparoscopic surgery (SILS), surgeons are faced with new challenges. In SILS it is not usually possible to utilise two instruments for knot tying as they lie almost parallel. We describe a novel one-handed knot tying technique devised specifically for use in SILS. PMID:21197256

  2. One-handed knot tying technique in single-incision laparoscopic surgery.

    PubMed

    Thanakumar, John; John, Pravin Hector

    2011-01-01

    In an open surgery, two-handed as well as one-handed knot tying is commonplace. Knot tying in laparoscopic surgery traditionally involves the use of two instruments (for fashioning an intracorporeal knot) or passing of a ligature around a tubular structure, exteriorising it, fashioning a knot, and sliding it down with a knot-pusher (external slip knot). With increasing interest in expanding applications of single-incision laparoscopic surgery (SILS), surgeons are faced with new challenges. In SILS it is not usually possible to utilise two instruments for knot tying as they lie almost parallel. We describe a novel one-handed knot tying technique devised specifically for use in SILS. PMID:21197256

  3. Novel application of an established technique for removing a knotted ureteric stent.

    PubMed

    Tempest, Heidi; Turney, Ben; Kumar, Sunil

    2011-01-01

    This report describes a case whereby a ureteric stent became knotted during removal and lodged within the upper ureter. The authors describe a novel minimally invasive technique to remove the knotted ureteric stent using the holmium laser. PMID:22701009

  4. Innovative and Advanced Coupled Neutron Transport and Thermal Hydraulic Method (Tool) for the Design, Analysis and Optimization of VHTR/NGNP Prismatic Reactors

    SciTech Connect

    Rahnema, Farzad; Garimeela, Srinivas; Ougouag, Abderrafi; Zhang, Dingkang

    2013-11-29

    This project will develop a 3D, advanced coarse mesh transport method (COMET-Hex) for steady- state and transient analyses in advanced very high-temperature reactors (VHTRs). The project will lead to a coupled neutronics and thermal hydraulic (T/H) core simulation tool with fuel depletion capability. The computational tool will be developed in hexagonal geometry, based solely on transport theory without (spatial) homogenization in complicated 3D geometries. In addition to the hexagonal geometry extension, collaborators will concurrently develop three additional capabilities to increase the code’s versatility as an advanced and robust core simulator for VHTRs. First, the project team will develop and implement a depletion method within the core simulator. Second, the team will develop an elementary (proof-of-concept) 1D time-dependent transport method for efficient transient analyses. The third capability will be a thermal hydraulic method coupled to the neutronics transport module for VHTRs. Current advancements in reactor core design are pushing VHTRs toward greater core and fuel heterogeneity to pursue higher burn-ups, efficiently transmute used fuel, maximize energy production, and improve plant economics and safety. As a result, an accurate and efficient neutron transport, with capabilities to treat heterogeneous burnable poison effects, is highly desirable for predicting VHTR neutronics performance. This research project’s primary objective is to advance the state of the art for reactor analysis.

  5. Classification of knotted tori in 2-metastable dimension

    SciTech Connect

    Cencelj, Matija; Repovs, Dusan; Skopenkov, Mihail B

    2012-11-30

    This paper is devoted to the classical Knotting Problem: for a given manifold N and number m describe the set of isotopy classes of embeddings N{yields}S{sup m}. We study the specific case of knotted tori, that is, the embeddings S{sup p} Multiplication-Sign S{sup q}{yields}S{sup m}. The classification of knotted tori up to isotopy in the metastable dimension range m {>=} p + 3/2q + 2, p{<=}q, was given by Haefliger, Zeeman and A. Skopenkov. We consider the dimensions below the metastable range and give an explicit criterion for the finiteness of this set of isotopy classes in the 2-metastable dimension. Bibliography: 35 titles.

  6. Untangling Knots Via Reaction-Diffusion Dynamics of Vortex Strings.

    PubMed

    Maucher, Fabian; Sutcliffe, Paul

    2016-04-29

    We introduce and illustrate a new approach to the unknotting problem via the dynamics of vortex strings in a nonlinear partial differential equation of reaction-diffusion type. To untangle a given knot, a Biot-Savart construction is used to initialize the knot as a vortex string in the FitzHugh-Nagumo equation. Remarkably, we find that the subsequent evolution preserves the topology of the knot and can untangle an unknot into a circle. Illustrative test case examples are presented, including the untangling of a hard unknot known as the culprit. Our approach to the unknotting problem has two novel features, in that it applies field theory rather than particle mechanics and uses reaction-diffusion dynamics in place of energy minimization. PMID:27176541

  7. Untangling Knots Via Reaction-Diffusion Dynamics of Vortex Strings

    NASA Astrophysics Data System (ADS)

    Maucher, Fabian; Sutcliffe, Paul

    2016-04-01

    We introduce and illustrate a new approach to the unknotting problem via the dynamics of vortex strings in a nonlinear partial differential equation of reaction-diffusion type. To untangle a given knot, a Biot-Savart construction is used to initialize the knot as a vortex string in the FitzHugh-Nagumo equation. Remarkably, we find that the subsequent evolution preserves the topology of the knot and can untangle an unknot into a circle. Illustrative test case examples are presented, including the untangling of a hard unknot known as the culprit. Our approach to the unknotting problem has two novel features, in that it applies field theory rather than particle mechanics and uses reaction-diffusion dynamics in place of energy minimization.

  8. Sequence Controlled Self-Knotting Colloidal Patchy Polymers

    NASA Astrophysics Data System (ADS)

    Coluzza, Ivan; van Oostrum, Peter D. J.; Capone, Barbara; Reimhult, Erik; Dellago, Christoph

    2013-02-01

    Knotted chains are a promising class of polymers with many applications for materials science and drug delivery. Here we introduce an experimentally realizable model for the design of chains with controllable topological properties. Recently, we have developed a systematic methodology to construct self-assembling chains of simple particles, with final structures fully controlled by the sequence of particles along the chain. The individual particles forming the chain are colloids decorated with mutually interacting patches, which can be manufactured in the laboratory with current technology. Our methodology is applied to the design of sequences folding into self-knotting chains, in which the end monomers are by construction always close together in space. The knotted structure can then be externally locked simply by controlling the interaction between the end monomers, paving the way to applications in the design and synthesis of active materials and novel carriers for drugs delivery.

  9. Extraordinary line-emitting knots in the Crab Nebula

    NASA Technical Reports Server (NTRS)

    Macalpine, Gordon M.; Lawrence, Stephen S.; Brown, Beth A.; Uomoto, Alan; Woodgate, Bruce E.; Brown, Larry W.; Oliversen, Ronald J.; Lowenthal, James D.; Liu, Charles

    1994-01-01

    Extraordinary, semistellar, line-emitting knots are apparent in images of the Crab Nebula which were obtained with the Goddard Fabry-Perot imager at the Michigan-Dartmouth-MIT Observatory. The knots are most prominent for (O III) lambda 5007 emission through a 5.3 A (Full Width at Half Maximum (FWHM)) bandpass centered at 5015.3 A, with representative fluxes of roughly 10(exp -14) ergs/sq cm. They are aligned in arcs, seven to the north and four to the south, from the pulsar. The northern group appears to be in a bounded corridor through the filamentary structure. Measurements over a 2 year baseline yield proper motions of order 0.1 sec/yr, corresponding to transverse velocities of order 900 km/s for a distance of 1830 pc. The knots are characterized by remarkably strong (Ar III) emission, possibly indicating high argon abundances, high gas temperatures, or anomalous physical processes.

  10. Ferromagnetic Switching of Knotted Vector Fields in Liquid Crystal Colloids.

    PubMed

    Zhang, Qiaoxuan; Ackerman, Paul J; Liu, Qingkun; Smalyukh, Ivan I

    2015-08-28

    We experimentally realize polydomain and monodomain chiral ferromagnetic liquid crystal colloids that exhibit solitonic and knotted vector field configurations. Formed by dispersions of ferromagnetic nanoplatelets in chiral nematic liquid crystals, these colloidal ferromagnets exhibit spontaneous long-range alignment of magnetic dipole moments of individual platelets, giving rise to a continuum of the magnetization field M(r). Competing effects of surface confinement and chirality prompt spontaneous formation and enable the optical generation of localized twisted solitonic structures with double-twist tubes and torus knots of M(r), which exhibit a strong sensitivity to the direction of weak magnetic fields ∼1  mT. Numerical modeling, implemented through free energy minimization to arrive at a field-dependent three-dimensional M(r), shows a good agreement with experiments and provides insights into the torus knot topology of observed field configurations and the corresponding physical underpinnings. PMID:26371682

  11. Knots, Braids and Hedgehogs from the Eikonal Equation

    NASA Astrophysics Data System (ADS)

    Wereszczyński, A.

    The complex eikonal equation in the three space dimensions is considered. We show that apart from the recently found torus knots, this equation can also generate other topological configurations with a nontrivial value of the π2(S2) index: braided open strings as well as hedgehogs. In particular, cylindric strings, i.e. string solutions located on a cylinder with a constant radius are found. Moreover, solutions describing strings lying on an arbitrary surface topologically equivalent to cylinder are presented. We discuss them in the context of the eikonal knots. The physical importance of the results originates in the fact that the eikonal knots have been recently used to approximate the Faddeev-Niemi hopfions.

  12. Characterization of Root-Knot Nematode Resistance in Medicago truncatula

    PubMed Central

    Dhandaydham, Murali; Charles, Lauren; Zhu, Hongyan; Starr, James L.; Huguet, Thierry; Cook, Douglas R.; Prosperi, Jean-Marie; Opperman, Charles

    2008-01-01

    Root knot (Meloidogyne spp.) and cyst (Heterodera and Globodera spp.) nematodes infect all important crop species, and the annual economic loss due to these pathogens exceeds $90 billion. We screened the worldwide accession collection with the root-knot nematodes Meloidogyne incognita, M. arenaria and M. hapla, soybean cyst nematode (SCN-Heterodera glycines), sugar beet cyst nematode (SBCN-Heterodera schachtii) and clover cyst nematode (CLCN-Heterodera trifolii), revealing resistant and susceptible accessions. In the over 100 accessions evaluated, we observed a range of responses to the root-knot nematode species, and a non-host response was observed for SCN and SBCN infection. However, variation was observed with respect to infection by CLCN. While many cultivars including Jemalong A17 were resistant to H. trifolii, cultivar Paraggio was highly susceptible. Identification of M. truncatula as a host for root-knot nematodes and H. trifolii and the differential host response to both RKN and CLCN provide the opportunity to genetically and molecularly characterize genes involved in plant-nematode interaction. Accession DZA045, obtained from an Algerian population, was resistant to all three root-knot nematode species and was used for further studies. The mechanism of resistance in DZA045 appears different from Mi-mediated root-knot nematode resistance in tomato. Temporal analysis of nematode infection showed that there is no difference in nematode penetration between the resistant and susceptible accessions, and no hypersensitive response was observed in the resistant accession even several days after infection. However, less than 5% of the nematode population completed the life cycle as females in the resistant accession. The remainder emigrated from the roots, developed as males, or died inside the roots as undeveloped larvae. Genetic analyses carried out by crossing DZA045 with a susceptible French accession, F83005, suggest that one gene controls resistance in DZA

  13. A Comparative Study in Learning Curves of Two Different Intracorporeal Knot Tying Techniques

    PubMed Central

    Thiyagarajan, Manuneethimaran; Ravindrakumar, Chandru

    2016-01-01

    Objectives. In our study we are aiming to analyse the learning curves in our surgical trainees by using two standard methods of intracorporeal knot tying. Material and Method. Two randomized groups of trainees are trained with two different intracorporeal knot tying techniques (loop and winding) by single surgeon for eight sessions. In each session participants were allowed to make as many numbers of knots in thirty minutes. The duration for each set of knots and the number of knots for each session were calculated. At the end each session, participants were asked about their frustration level, difficulty in making knot, and dexterity. Results. In winding method the number of knots tied was increasing significantly in each session with less frustration and less difficulty level. Discussion. The suturing and knotting skill improved in every session in both groups. But group B (winding method) trainees made significantly higher number of knots and they took less time for each set of knots than group A (loop method). Although both knotting methods are standard methods, the learning curve is better in loop method. Conclusion. The winding method of knotting is simpler and easier to perform, especially for the surgeons who have limited laparoscopic experience. PMID:27022482

  14. KNOTS AND RANDOM WALKS IN VIBRATED GRANULAR CHAINS

    SciTech Connect

    E. BEN-NAIM; ET AL

    2000-08-01

    The authors study experimentally statistical properties of the opening times of knots in vertically vibrated granular chains. Our measurements are in good qualitative and quantitative agreement with a theoretical model involving three random walks interacting via hard core exclusion in one spatial dimension. In particular, the knot survival probability follows a universal scaling function which is independent of the chain length, with a corresponding diffusive characteristic time scale. Both the large-exit-time and the small-exit-time tails of the distribution are suppressed exponentially, and the corresponding decay coefficients are in excellent agreement with the theoretical values.

  15. Excitation of knotted vortex lines in matter waves

    NASA Astrophysics Data System (ADS)

    Maucher, F.; Gardiner, S. A.; Hughes, I. G.

    2016-06-01

    We study the creation of knotted ultracold matter waves in Bose–Einstein condensates via coherent two-photon Raman transitions with a Λ level configuration. The Raman transition allows an indirect transfer of atoms from the internal state | a> to the target state | b> via an excited state | e> , that would be otherwise dipole-forbidden. This setup enables us to imprint three-dimensional knotted vortex lines embedded in the probe field to the density in the target state. We elaborate on experimental feasibility as well as on subsequent dynamics of the matter wave.

  16. The life of vortex knots and the flow of helicity

    NASA Astrophysics Data System (ADS)

    Irvine, William

    What happens if you take a vortex loop - akin to a smoke ring in air - and tie it into a knot or a link? The knottiness (Helicity) of a fluid is a conserved quantity in many idealized situations (such as Euler fluids) offering the potential for fundamental insights into fluid flow. In real fluids, progress has been hindered by lack of accessible experimental systems. I will tell of how to make a vortex knot and link in water, in the wave function of a superfluid (on a computer) and of what happens thence, with an emphasis on universal aspects of the dynamics and the flow of helicity.

  17. In situ response of bay productivity to nutrient loading from a small tributary: The Delaware Bay-Murderkill Estuary tidally-coupled biogeochemical reactor

    NASA Astrophysics Data System (ADS)

    Voynova, Yoana G.; Lebaron, Karine C.; Barnes, Rebecca T.; Ullman, William J.

    2015-07-01

    A small, turbid and nutrient-rich tributary, the Murderkill Estuary, and a large estuarine ecosystem, the Delaware Bay, are tightly linked and form an efficient, tidally-coupled biogeochemical reactor during the summer. Nitrate loading from the Murderkill Estuary generates an instantaneous increase in biological oxygen production in the adjacent Delaware Bay. We are able to capture this primary production response with continuous hourly measurements of dissolved oxygen, chlorophyll, and nitrate. The nitrate influxes from the Murderkill support primary production rates in the Delaware Bay margins that are twice as high as the average production rates measured in the central Bay regions. This elevates chlorophyll in the Bay margins in the summer and fuels metabolism. Tidal transport of the newly produced autochthonous chlorophyll particles from the Bay into the Estuary could also provide a source of labile material to the marshes surrounding the Murderkill, thus perhaps fueling marsh respiration. As a consequence of the tidal coupling between Delaware Bay and the Murderkill Estuary, ecosystem productivity and metabolism in the Bay and Estuary are linked, generating an ecosystem feedback mechanism. Storms modulate this tidally-coupled biogeochemical reactor, by generating significant nitrate and salinity changes. Depending on their magnitude and duration, storms induce large phytoplankton blooms in the Delaware Bay. Such large phytoplankton blooms may occur more often with climate change, since century-long discharge records document an increase in storm frequency.

  18. Effects of Secondary Circuit Modeling on Results of Pressurized Water Reactor Main Steam Line Break Benchmark Calculations with New Coupled Code TRAB-3D/SMABRE

    SciTech Connect

    Daavittila, Antti; Haemaelaeinen, Anitta; Kyrki-Rajamaeki, Riitta

    2003-05-15

    All of the three exercises of the Organization for Economic Cooperation and Development/Nuclear Regulatory Commission pressurized water reactor main steam line break (PWR MSLB) benchmark were calculated at VTT, the Technical Research Centre of Finland. For the first exercise, the plant simulation with point-kinetic neutronics, the thermal-hydraulics code SMABRE was used. The second exercise was calculated with the three-dimensional reactor dynamics code TRAB-3D, and the third exercise with the combination TRAB-3D/SMABRE. VTT has over ten years' experience of coupling neutronic and thermal-hydraulic codes, but this benchmark was the first time these two codes, both developed at VTT, were coupled together. The coupled code system is fast and efficient; the total computation time of the 100-s transient in the third exercise was 16 min on a modern UNIX workstation. The results of all the exercises are similar to those of the other participants. In order to demonstrate the effect of secondary circuit modeling on the results, three different cases were calculated. In case 1 there is no phase separation in the steam lines and no flow reversal in the aspirator. In case 2 the flow reversal in the aspirator is allowed, but there is no phase separation in the steam lines. Finally, in case 3 the drift-flux model is used for the phase separation in the steam lines, but the aspirator flow reversal is not allowed. With these two modeling variations, it is possible to cover a remarkably broad range of results. The maximum power level reached after the reactor trip varies from 534 to 904 MW, the range of the time of the power maximum being close to 30 s. Compared to the total calculated transient time of 100 s, the effect of the secondary side modeling is extremely important.

  19. Colloidal entanglement in highly twisted chiral nematic colloids: twisted loops, Hopf links, and trefoil knots.

    PubMed

    Jampani, V S R; Škarabot, M; Ravnik, M; Čopar, S; Žumer, S; Muševič, I

    2011-09-01

    The topology and geometry of closed defect loops is studied in chiral nematic colloids with variable chirality. The colloidal particles with perpendicular surface anchoring of liquid crystalline molecules are inserted in a twisted nematic cell with the thickness that is only slightly larger than the diameter of the colloidal particle. The total twist of the chiral nematic structure in cells with parallel boundary conditions is set to 0, π, 2π, and 3π, respectively. We use the laser tweezers to discern the number and the topology of the -1/2 defect loops entangling colloidal particles. For a single colloidal particle, we observe that a single defect loop is winding around the particle, with the winding pattern being more complex in cells with higher total twist. We observe that colloidal dimers and colloidal clusters are always entangled by one or several -1/2 defect loops. For colloidal pairs in π-twisted cells, we identify at least 17 different entangled structures, some of them exhibiting linked defect loops-Hopf link. Colloidal entanglement is even richer with a higher number of colloidal particles, where we observe not only linked, but also colloidal clusters knotted into the trefoil knot. The experiments are in good agreement with numerical modeling using Landau-de Gennes theory coupled with geometrical and topological considerations using the method of tetrahedral rotation. PMID:22060386

  20. Developing Fully Coupled Dynamical Reactor Core Isolation System Models in RELAP-7 for Extended Station Black-Out Analysis

    SciTech Connect

    Haihua Zhao; Ling Zou; Hongbin Zhang; David Andrs; Richard Martineau

    2014-04-01

    The reactor core isolation cooling (RCIC) system in a boiling water reactor (BWR) provides makeup water to the reactor vessel for core cooling when the main steam lines are isolated and the normal supply of water to the reactor vessel is lost. It was one of the very few safety systems still available during the Fukushima Daiichi accidents after the tsunamis hit the plants and the system successfully delayed the core meltdown for a few days for unit 2 & 3. Therefore, detailed models for RCIC system components are indispensable to understand extended station black-out accidents (SBO) for BWRs. As part of the effort to develop the new generation reactor system safety analysis code RELAP-7, major components to simulate the RCIC system have been developed. This paper describes the models for those components such as turbine, pump, and wet well. Selected individual component test simulations and a simplified SBO simulation up to but before core damage is presented. The successful implementation of the simplified RCIC and wet well models paves the way to further improve the models for safety analysis by including more detailed physical processes in the near future.

  1. Azo dye removal in a membrane-free up-flow biocatalyzed electrolysis reactor coupled with an aerobic bio-contact oxidation reactor.

    PubMed

    Cui, Dan; Guo, Yu-Qi; Cheng, Hao-Yi; Liang, Bin; Kong, Fan-Ying; Lee, Hyung-Sool; Wang, Ai-Jie

    2012-11-15

    Azo dyes that consist of a large quantity of dye wastewater are toxic and persistent to biodegradation, while they should be removed before being discharged to water body. In this study, Alizarin Yellow R (AYR) as a model azo dye was decolorized in a combined bio-system of membrane-free, continuous up-flow bio-catalyzed electrolysis reactor (UBER) and subsequent aerobic bio-contact oxidation reactor (ABOR). With the supply of external power source 0.5 V in the UBER, AYR decolorization efficiency increased up to 94.8±1.5%. Products formation efficiencies of p-phenylenediamine (PPD) and 5-aminosalicylic acid (5-ASA) were above 90% and 60%, respectively. Electron recovery efficiency based on AYR removal in cathode zone was nearly 100% at HRTs longer than 6 h. Relatively high concentration of AYR accumulated at higher AYR loading rates (>780 gm(-3) d(-1)) likely inhibited acetate oxidation of anode-respiring bacteria on the anode, which decreased current density in the UBER; optimal AYR loading rate for the UBER was 680 gm(-3) d(-1) (HRT 2.5 h). The subsequent ABOR further improved effluent quality. Overall the Chroma decreased from 320 times to 80 times in the combined bio-system to meet the textile wastewater discharge standard II in China. PMID:23009797

  2. Simulations of flux uniformity for Cl2, BCl3, and N2 chemistries in the Sandia inductively coupled GEC reactor

    SciTech Connect

    Veerasingam, R.; Choi, S.J.; Campbell, R.B.

    1997-12-31

    Numerical simulations are performed to estimate the flux uniformity at the wafer surface for various mixtures of Cl2, BCl3 and N2, in the Sandia laboratory ICP reactor. To improve metal etch uniformity, it is desirably that the ion and neutral fluxes have uniform profiles across the wafer surface. The authors also investigate the effect of a ceramic focus ring on the flux uniformity reactor. The focus ring plays an important role in influencing the boundary conditions for the particle fluxes at the wafer edge thereby effecting the flux uniformity across the wafer surface. Numerical simulations will provide insight into the various conditions that may affect flux uniformity. In addition, the authors also perform parametric studies of Cl2, BCl3 and N2 mixtures for the bulk plasma and compare with experimental data. These simulations include variations in pressure, mixture ratio and power. The calculations will be performed using the HPEM and MPRES reactor simulation models.

  3. Coaxial rings and H2 knots in Hubble 12

    NASA Astrophysics Data System (ADS)

    Hsia, Chih-Hao; Kwok, Sun; Chau, Wayne; Zhang, Yong

    2016-07-01

    Hubble 12 (Hb 12) is a young planetary nebula (PN) exhibiting nested shells. We present new near-infrared narrow-band imaging observations of Hb 12 using the Canada-France- Hawaii Telescope (CFHT). A number of co-axial rings aligned with the bipolar lobes and two pairs of separate H2 knots with different orientations are detected.

  4. Material Properties of Hagfish Skin, with Insights into Knotting Behaviors.

    PubMed

    Clark, Andrew J; Crawford, Callie H; King, Brooke D; Demas, Andrew M; Uyeno, Theodore A

    2016-06-01

    Hagfishes (Myxinidae) often integrate whole-body knotting movements with jawless biting motions when reducing large marine carcasses to ingestible items. Adaptations for these behaviors include complex arrangements of axial muscles and flexible, elongate bodies without vertebrae. Between the axial muscles and the hagfish skin is a large, blood-filled subcutaneous sinus devoid of the intricate, myoseptal tendon networks characteristic of the taut skins of other fishes. We propose that the loose-fitting skin of the hagfish facilitates the formation and manipulation of body knots, even if it is of little functional significance to steady swimming. Hagfish skin is a relatively thick, anisotropic, multilayered composite material comprising a superficial, thin, and slimy epidermis, a middle dermal layer densely packed with fibrous tissues, and a deep subdermal layer comprised of adipose tissue. Hagfish skin is stiffer when pulled longitudinally than circumferentially. Stress-strain data from uniaxial tensile tests show that hagfish skins are comparable in tensile strength and stiffness to the taut skins of elongate fishes that do not engage in knotting behaviors (e.g., sea lamprey and penpoint gunnel). Sheath-core-constructed ropes, which serve as more accurate models for hagfish bodies, demonstrate that loose skin (extra sheathing) enhances flexibility of the body (rope). Along with a loose-fitting skin, the morphologies of hagfish skin parallel those of moray eels, which are also known for generating and manipulating figure-eight-style body knots when struggling with prey. PMID:27365419

  5. WEEDS AS HOSTS FOR THE SOUTHERN ROOT-KNOT NEMATODE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The southern root-knot nematode, Meloidogyne incognita, can reproduce on many different plants, including many weeds, but the amount of reproduction that occurs on weeds is not well documented. This study was conducted to document the relative host status of weeds common in Georgia. Seeds of cotton,...

  6. Utilization of biological control for managing root-knot nematodes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Our research goal is to enhance and conserve introduced and naturally occurring antagonists of root-knot nematodes (Meloidogyne spp.) to improve biological control. Towards that end, we have evaluated the effect of crop production practices such as rotation, nematicide application, and cover crops,...

  7. Knot invariants and the thermodynamics of lattice gas automata

    SciTech Connect

    Meyer, D.A.

    1992-01-01

    The goal of this project is to build on the understanding of the connections between knot invariants, exactly solvable statistical mechanics models and discrete dynamical systems that we have gained in earlier work, toward an answer to the question of how early and robust thermodynamic behavior appears in lattice gas automata.

  8. Untangling Some Knots in K-8 Writing Instruction.

    ERIC Educational Resources Information Center

    Peterson, Shelley, Ed.

    This book brings together the perspectives of teachers, administrators, consultants, and researchers on teaching writing to create a bridge between theory and practice. The book's 11 chapters are organized into three sections that tackle some persistent knots of writing instruction and assessment. Under Section I-Students' and Teachers' Learning…

  9. The New Polynomial Invariants of Knots and Links.

    ERIC Educational Resources Information Center

    Lickorish, W. B. R.; Millett, K. C.

    1988-01-01

    Knot theory has been inspirational to algebraic and geometric topology. The principal problem has been to ascertain whether two links are equivalent. New methods have been discovered which are effective and simple. Considered are background information; the oriented polynomial; the Jones polynomial; the semioriented polynomial; and calculations,…

  10. The multivariable Alexander polynomial and modern knot theory

    SciTech Connect

    Saleur, H. . Dept. of Physics)

    1992-06-01

    This paper is a summary of several recent works (by the author and collaborators) that study the Conway-Alexander link invariant in the light of quantum groups and topological quantum field theories. Their purpose is to understand connections between modern knot theory and more classical topological concepts.

  11. Homochiral and meso figure eight knots and a Solomon link.

    PubMed

    Ponnuswamy, Nandhini; Cougnon, Fabien B L; Pantoş, G Dan; Sanders, Jeremy K M

    2014-06-11

    A homochiral naphthalenediimide-based building block forms in water a disulfide library of macrocycles containing topological isomers. We attempted to identify each of these isomers, and explored the mechanisms leading to their formation. The two most abundant species of the library were assigned as a topologically chiral Solomon link (60% of the library, as measured by high-performance liquid chromatography (HPLC)) and a topologically achiral figure eight knot (18% by HPLC), competing products with formally different geometries but remarkably similar 4-fold symmetries. In contrast, a racemic mixture of building blocks gives the near-quantitative formation of another new and more stable structure, assigned as a meso figure eight knot. Taken together, these results seem to uncover a correlation between the point chirality of the building block used and the topological chirality of the major structure formed. These and the earlier discovery of a trefoil knot also suggest that the number of rigid components in the building block may translate into corresponding knot symmetry and could set the basis of a new strategy for constructing complex topologies. PMID:24831779

  12. Resistance of Watermelon Germplasm to Root-Knot Nematodes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Root-knot nematodes (Meloidogyne spp.) seriously impact yields of watermelon throughout the southern U.S. Pre-plant fumigation of soil with methyl bromide is the primary method for controlling these pests in watermelon. Although host resistance would be one of the most economical and environmental...

  13. Wall-crossing invariants: from quantum mechanics to knots

    NASA Astrophysics Data System (ADS)

    Galakhov, D.; Mironov, A.; Morozov, A.

    2015-03-01

    We offer a pedestrian-level review of the wall-crossing invariants. The story begins from the scattering theory in quantum mechanics where the spectrum reshuffling can be related to permutations of S-matrices. In nontrivial situations, starting from spin chains and matrix models, the S-matrices are operatorvalued and their algebra is described in terms of R- and mixing (Racah) U-matrices. Then the Kontsevich-Soibelman (KS) invariants are nothing but the standard knot invariants made out of these data within the Reshetikhin-Turaev-Witten approach. The R and Racah matrices acquire a relatively universal form in the semiclassical limit, where the basic reshufflings with the change of moduli are those of the Stokes line. Natural from this standpoint are matrices provided by the modular transformations of conformal blocks (with the usual identification R = T and U = S), and in the simplest case of the first degenerate field (2, 1), when the conformal blocks satisfy a second-order Shrödinger-like equation, the invariants coincide with the Jones ( N = 2) invariants of the associated knots. Another possibility to construct knot invariants is to realize the cluster coordinates associated with reshufflings of the Stokes lines immediately in terms of check-operators acting on solutions of the Knizhnik-Zamolodchikov equations. Then the R-matrices are realized as products of successive mutations in the cluster algebra and are manifestly described in terms of quantum dilogarithms, ultimately leading to the Hikami construction of knot invariants.

  14. Wall-crossing invariants: from quantum mechanics to knots

    SciTech Connect

    Galakhov, D. E-mail: galakhov@physics.rutgers.edu; Mironov, A. Morozov, A.

    2015-03-15

    We offer a pedestrian-level review of the wall-crossing invariants. The story begins from the scattering theory in quantum mechanics where the spectrum reshuffling can be related to permutations of S-matrices. In nontrivial situations, starting from spin chains and matrix models, the S-matrices are operatorvalued and their algebra is described in terms of R- and mixing (Racah) U-matrices. Then the Kontsevich-Soibelman (KS) invariants are nothing but the standard knot invariants made out of these data within the Reshetikhin-Turaev-Witten approach. The R and Racah matrices acquire a relatively universal form in the semiclassical limit, where the basic reshufflings with the change of moduli are those of the Stokes line. Natural from this standpoint are matrices provided by the modular transformations of conformal blocks (with the usual identification R = T and U = S), and in the simplest case of the first degenerate field (2, 1), when the conformal blocks satisfy a second-order Shrödinger-like equation, the invariants coincide with the Jones (N = 2) invariants of the associated knots. Another possibility to construct knot invariants is to realize the cluster coordinates associated with reshufflings of the Stokes lines immediately in terms of check-operators acting on solutions of the Knizhnik-Zamolodchikov equations. Then the R-matrices are realized as products of successive mutations in the cluster algebra and are manifestly described in terms of quantum dilogarithms, ultimately leading to the Hikami construction of knot invariants.

  15. Minimum lattice length and ropelength of 2-bridge knots and links

    NASA Astrophysics Data System (ADS)

    Huh, Youngsik; Hong, Kyungpyo; Kim, Hyoungjun; No, Sungjong; Oh, Seungsang

    2014-11-01

    Knots are commonly found in molecular chains such as DNA and proteins, and they have been considered to be useful models for structural analysis of these molecules. One interested quantity is the minimum number of monomers necessary to realize a molecular knot. The minimum lattice length Len(K) of a knot K indicates the minimum length necessary to construct K in the cubic lattice. Another important quantity in physical knot theory is the ropelength which is one of the knot energies measuring the complexity of knot conformation. The minimum ropelength Rop(K) is the minimum length of an ideally flexible rope necessary to tie a given knot K. Much effort has been invested in the research project for finding upper bounds on both quantities in terms of the minimum crossing number c(K) of the knot. It is known that Len(K) and Rop(K) lie between O(c(K)^{3/4}) and O(c(K)[ln (c(K))]5), but unknown yet whether any family of knots has superlinear growth. In this paper, we focus on 2-bridge knots and links. Linear growth upper bounds on the minimum lattice length and minimum ropelength for nontrivial 2-bridge knots or links are presented as Len(K) ⩽ 8c(K) + 2 and Rop(K) ⩽ 11.39c(K) + 12.37.

  16. Coupling of acrylic dyeing wastewater treatment by heterogeneous Fenton oxidation in a continuous stirred tank reactor with biological degradation in a sequential batch reactor.

    PubMed

    Esteves, Bruno M; Rodrigues, Carmen S D; Boaventura, Rui A R; Maldonado-Hódar, F J; Madeira, Luís M

    2016-01-15

    This work deals with the treatment of a recalcitrant effluent, from the dyeing stage of acrylic fibres, by combination of the heterogeneous Fenton's process in a continuous stirred tank reactor (CSTR) with biological degradation in a sequential batch reactor (SBR). Three different catalysts (a commercial Fe/ZSM-5 zeolite and two distinct Fe-containing activated carbons - ACs - prepared by wet impregnation of iron acetate and iron nitrate) were employed on the Fenton's process, and afterwards a parametric study was carried out to determine the effect of the main operating conditions, namely the hydrogen peroxide feed concentration, temperature and contact time. Under the best operating conditions found, using the activated carbon impregnated with iron nitrate, 62.7% of discolouration and 39.9% of total organic carbon (TOC) reduction were achieved, at steady-state. Furthermore, a considerable increase in the effluent's biodegradability was attained (BOD5:COD ratio increased from <0.001 to 0.27 and SOUR - specific oxygen uptake rate - from <0.2 to 11.1 mg O2/(gVSS·h)), alongside a major decrease in its toxicity (from 92.1 to 94.0% of Vibrio fischeri inhibition down to 6.9-9.9%). This allowed the application of the subsequent biological degradation stage. The combination of the two processes provided a treated effluent that clearly complies with the legislated discharge limits. It was also found that the iron leaching from the three catalysts tested was very small in all runs, a crucial factor for the stability and long-term use of such materials. PMID:26513317

  17. Plasma properties in a large-volume, cylindrical and asymmetric radio-frequency capacitively coupled industrial-prototype reactor

    NASA Astrophysics Data System (ADS)

    Lazović, Saša; Puač, Nevena; Spasić, Kosta; Malović, Gordana; Cvelbar, Uroš; Mozetič, Miran; Radetić, Maja; Petrović, Zoran Lj

    2013-02-01

    We have developed a large-volume low-pressure cylindrical plasma reactor with a size that matches industrial reactors for treatment of textiles. It was shown that it efficiently produces plasmas with only a small increase in power as compared with a similar reactor with 50 times smaller volume. Plasma generated at 13.56 MHz was stable from transition to streamers and capable of long-term continuous operation. An industrial-scale asymmetric cylindrical reactor of simple design and construction enabled good control over a wide range of active plasma species and ion concentrations. Detailed characterization of the discharge was performed using derivative, Langmuir and catalytic probes which enabled determination of the optimal sets of plasma parameters necessary for successful industry implementation and process control. Since neutral atomic oxygen plays a major role in many of the material processing applications, its spatial profile was measured using nickel catalytic probe over a wide range of plasma parameters. The spatial profiles show diffusion profiles with particle production close to the powered electrode and significant wall losses due to surface recombination. Oxygen atom densities range from 1019 m-3 near the powered electrode to 1017 m-3 near the wall. The concentrations of ions at the same time are changing from 1016 to the 1015 m-3 at the grounded chamber wall.

  18. The Treatment of PPCP-Containing Sewage in an Anoxic/Aerobic Reactor Coupled with a Novel Design of Solid Plain Graphite-Plates Microbial Fuel Cell

    PubMed Central

    Chang, Yi-Tang; Yang, Chu-Wen; Chang, Yu-Jie; Chang, Ting-Chieh; Wei, Da-Jiun

    2014-01-01

    Synthetic sewage containing high concentrations of pharmaceuticals and personal care products (PPCPs, mg/L level) was treated using an anoxic/aerobic (A/O) reactor coupled with a microbial fuel cell (MFC) at hydraulic retention time (HRT) of 8 h. A novel design of solid plain graphite plates (SPGRPs) was used for the high surface area biodegradation of the PPCP-containing sewage and for the generation of electricity. The average CODCr and total nitrogen removal efficiencies achieved were 97.20% and 83.75%, respectively. High removal efficiencies of pharmaceuticals, including acetaminophen, ibuprofen, and sulfamethoxazole, were also obtained and ranged from 98.21% to 99.89%. A maximum power density of 532.61 mW/cm2 and a maximum coulombic efficiency of 25.20% were measured for the SPGRP MFC at the anode. Distinct differences in the bacterial community were presented at various locations including the mixed liquor suspended solids and biofilms. The bacterial groups involved in PPCP biodegradation were identified as Dechloromonas spp., Sphingomonas sp., and Pseudomonas aeruginosa. This design, which couples an A/O reactor with a novel design of SPGRP MFC, allows the simultaneous removal of PPCPs and successful electricity production. PMID:25197659

  19. Chemical signals from plants previously infected with root knot nematodes affect behavior of infective juvenile root knot nematodes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nematodes are a worldwide problem in agriculture, with losses estimated to $100 billion per year in the US. Damage caused by root-knot nematodes (Meloidogyne spp.) (RKN) disrupts the flow of water and nutrients to the plant and increases the plant’s vulnerability to other pathogens. While studies ...

  20. Optimization of a coupling scheme between MCNP5 and SUBCHANFLOW for high fidelity modeling of LWR reactors

    SciTech Connect

    Ivanov, A.; Sanchez, V.; Imke, U.; Ivanov, K.

    2012-07-01

    In order to increase the accuracy and the degree of spatial resolution of core design studies, coupled Three-Dimensional (3D) neutronics (deterministic and Monte Carlo) and 3D thermal hydraulics (CFD and sub-channel) codes are being developed worldwide. In this paper the optimization of a coupling between MCNP5 code and an in-house development thermal-hydraulics code SUBCHANFLOW is presented. Various improvements of the coupling methodology are presented. With the help of novel interpolation tool a consistent methodology for the preparation of thermal scattering data library have been developed, ensuring that inelastic scattering from bound nuclei is treated at the correct moderator temperature. Trough the utilization of a hybrid coupling with discrete energy Monte-Carlo code KENO a methodology for acceleration of the coupled calculation is being demonstrated. In this approach an additional coupling between KENO and SUBCHANFLOW was developed, the converged results of which are used as initial conditions for the MCNP-SUBCHANFLOW coupling. Acceleration of fission source distribution convergence, by sampling fission source distribution from the power distribution obtained by KENO is also demonstrated. (authors)

  1. REACTOR CONTROL

    DOEpatents

    Fortescue, P.; Nicoll, D.

    1962-04-24

    A control system employed with a high pressure gas cooled reactor in which a control rod is positioned for upward and downward movement into the neutron field from a position beneath the reactor is described. The control rod is positioned by a coupled piston cylinder releasably coupled to a power drive means and the pressurized coolant is directed against the lower side of the piston. The coolant pressure is offset by a higher fiuid pressure applied to the upper surface of the piston and means are provided for releasing the higher pressure on the upper side of the piston so that the pressure of the coolant drives the piston upwardly, forcing the coupled control rod into the ncutron field of the reactor. (AEC)

  2. Thermal-Hydraulic Analyses of Heat Transfer Fluid Requirements and Characteristics for Coupling A Hydrogen Production Plant to a High-Temperature Nuclear Reactor

    SciTech Connect

    C. B. Davis; C. H. Oh; R. B. Barner; D. F. Wilson

    2005-06-01

    The Department of Energy is investigating the use of high-temperature nuclear reactors to produce hydrogen using either thermochemical cycles or high-temperature electrolysis. Although the hydrogen production processes are in an early stage of development, coupling either of these processes to the hightemperature reactor requires both efficient heat transfer and adequate separation of the facilities to assure that off-normal events in the production facility do not impact the nuclear power plant. An intermediate heat transport loop will be required to separate the operations and safety functions of the nuclear and hydrogen plants. A next generation high-temperature reactor could be envisioned as a single-purpose facility that produces hydrogen or a dual-purpose facility that produces hydrogen and electricity. Early plants, such as the proposed Next Generation Nuclear Plant, may be dual-purpose facilities that demonstrate both hydrogen and efficient electrical generation. Later plants could be single-purpose facilities. At this stage of development, both single- and dual-purpose facilities need to be understood. Seven possible configurations for a system that transfers heat between the nuclear reactor and the hydrogen and/or electrical generation plants were identified. These configurations included both direct and indirect cycles for the production of electricity. Both helium and liquid salts were considered as the working fluid in the intermediate heat transport loop. Methods were developed to perform thermalhydraulic and cycle-efficiency evaluations of the different configurations and coolants. The thermalhydraulic evaluations estimated the sizes of various components in the intermediate heat transport loop for the different configurations. The relative sizes of components provide a relative indication of the capital cost associated with the various configurations. Estimates of the overall cycle efficiency of the various configurations were also determined. The

  3. Reductive Transformation of p-chloronitrobenzene in the upflow anaerobic sludge blanket reactor coupled with microbial electrolysis cell: performance and microbial community.

    PubMed

    Xu, Xiangyang; Shao, Junjie; Li, Mengyan; Gao, Kaituo; Jin, Jie; Zhu, Liang

    2016-10-01

    A microbial electrolysis cell (MEC) combined with an upflow anaerobic sludge blanket (UASB) reactor was operated to degrade p-chloronitrobenzenes (p-ClNB) effectively. The results indicated that p-ClNB was transformed to p-chloroaniline (p-ClAn) and then reduced via dechlorination pathways. In the MEC-UASB coupled system, p-ClNB, p-ClAn removal efficiency and dechlorination efficiency reached 99.63±0.37%, 40.39±9.26% and 32.16±8.12%, respectively, which was significantly improved in comparison with the control UASB system. In addition, the coupled system could maintain appropriate pH and promote anaerobic sludge granulation to exert a positive effect on reductive transformation of p-ClNB. PCR-DGGE experiment and 454 pyrophosphate sequencing analysis indicated that applied voltage would significantly influence the succession of microbial community and promote oriented enrichment of the functional bacteria, which could be the underlying reasons for the improved performance. This study demonstrated that MEC-UASB coupled system had a promising application prospect to remove the recalcitrant pollutants effectively. PMID:27455127

  4. Knots as a Topological Order Parameter for Semiflexible Polymers

    NASA Astrophysics Data System (ADS)

    Marenz, Martin; Janke, Wolfhard

    2016-03-01

    Using a combination of the multicanonical Monte Carlo algorithm and the replica-exchange method, we investigate the influence of bending stiffness on the conformational phases of a bead-stick homopolymer model and present the pseudophase diagram for the complete range of semiflexible polymers, from flexible to stiff. Although it is a simple model, we observe a rich variety of conformational phases, reminiscent of conformations observed for synthetic polymers or biopolymers. Depending on the bending stiffness, the model exhibits different pseudophases like bent, hairpin, or toroidal. In particular, we find thermodynamically stable knots and unusual transitions into these knotted phases with a clear phase coexistence, but almost constant mean total energy, and hence almost no latent heat.

  5. Unexpected connections between Burnside groups and knot theory.

    PubMed

    Dabkowski, Mieczyslaw K; Przytycki, Józef H

    2004-12-14

    In classical knot theory and the theory of quantum invariants substantial effort was directed toward the search for unknotting moves on links. We solve, in this article, several classical problems concerning unknotting moves. Our approach uses a concept, Burnside groups of links, that establishes an unexpected relationship between knot theory and group theory. Our method has the potential to be used in computational biology in the analysis of DNA via tangle embedding theory, as developed by D. W. Sumners [Sumners, D. W., ed. (1992) New Scientific Applications of Geometry and Topology (Am Math. Soc., Washington, DC) and Ernst, C. & Sumners, D. W. (1999) Math. Proc. Cambridge Philos. Soc. 126, 23-36]. PMID:15576510

  6. Self-Organizing Knotted Magnetic Structures in Plasma.

    PubMed

    Smiet, C B; Candelaresi, S; Thompson, A; Swearngin, J; Dalhuisen, J W; Bouwmeester, D

    2015-08-28

    We perform full-magnetohydrodynamics simulations on various initially helical configurations and show that they reconfigure into a state where the magnetic field lines span nested toroidal surfaces. This relaxed configuration is not a Taylor state, as is often assumed for relaxing plasma, but a state where the Lorentz force is balanced by the hydrostatic pressure, which is lowest on the central ring of the nested tori. Furthermore, the structure is characterized by a spatially slowly varying rotational transform, which leads to the formation of a few magnetic islands at rational surfaces. We then obtain analytic expressions that approximate the global structure of the quasistable linked and knotted plasma configurations that emerge, using maps from S^{3} to S^{2} of which the Hopf fibration is a special case. The knotted plasma configurations have a highly localized magnetic energy density and retain their structure on time scales much longer than the Alfvénic time scale. PMID:26371659

  7. Knots as a Topological Order Parameter for Semiflexible Polymers.

    PubMed

    Marenz, Martin; Janke, Wolfhard

    2016-03-25

    Using a combination of the multicanonical Monte Carlo algorithm and the replica-exchange method, we investigate the influence of bending stiffness on the conformational phases of a bead-stick homopolymer model and present the pseudophase diagram for the complete range of semiflexible polymers, from flexible to stiff. Although it is a simple model, we observe a rich variety of conformational phases, reminiscent of conformations observed for synthetic polymers or biopolymers. Depending on the bending stiffness, the model exhibits different pseudophases like bent, hairpin, or toroidal. In particular, we find thermodynamically stable knots and unusual transitions into these knotted phases with a clear phase coexistence, but almost constant mean total energy, and hence almost no latent heat. PMID:27058105

  8. The life of a vortex knot (in experiment)

    NASA Astrophysics Data System (ADS)

    Kleckner, Dustin; Scheeler, Martin; Proment, Davide; Irvine, William T. M.

    2013-11-01

    In recent experiments on linked and knotted vortices in classical fluids, we have found that they undergo a spontaneous change in topology: they untie themselves through a series of local reconnections. This outcome is at odds with the notion that fluid helicity (knottedness) should be conserved, as it should be for a dissipation-less fluid. Remarkably similar behavior is found for simulations of superfluid knots using the Gross-Pitaevskii equation. We will discuss our search for the missing helicity and the possibility of a universal driving mechanism for reconnections in topological vortices. This work was supported by the National Science Foundation Materials Research and Engineering Centers (MRSEC) Program at the University of Chicago (DMR-0820054) and the Packard Foundation through a Packard fellowship.

  9. Probability of DNA knotting and the effective diameter of the DNA double helix.

    PubMed Central

    Rybenkov, V V; Cozzarelli, N R; Vologodskii, A V

    1993-01-01

    During the random cyclization of long polymer chains, knots of different types are formed. We investigated experimentally the distribution of knot types produced by random cyclization of phage P4 DNA via its long cohesive ends. The simplest knots (trefoils) predominated, but more complex knots were also detected. The fraction of knots greatly diminished with decreasing solution Na+ concentration. By comparing these experimental results with computer simulations of knotting probability, we calculated the effective diameter of the DNA double helix. This important excluded-volume parameter is a measure of the electrostatic repulsion between segments of DNA molecules. The calculated effective DNA diameter is a sensitive function of electrolyte concentration and is several times larger than the geometric diameter in solutions of low monovalent cation concentration. Images Fig. 1 PMID:8506378

  10. Shepherd model for knot-limited polymer ejection from a capsid.

    PubMed

    Antal, Tibor; Krapivsky, P L; Redner, S

    2009-12-01

    We construct a tractable model to describe the rate at which a knotted polymer is ejected from a spherical capsid via a small pore. Knots are too large to fit through the pore and must reptate to the end of the polymer for ejection to occur. The reptation of knots is described by symmetric exclusion on the line, with the internal capsid pressure represented by an additional biased particle that drives knots to the end of the chain. We compute the exact ejection speed for a finite number of knots L and find that it scales as 1/L. We establish a mapping to the solvable zero-range process. We also construct a continuum theory for many knots that matches the exact discrete theory for large L. PMID:19703473

  11. In-vitro comparison of 3 knotting techniques for lateral fabellotibial suture stabilization

    PubMed Central

    Dycus, David L.; Wardlaw, Jennifer L.; Rowe, Dennis; Elder, Steve

    2013-01-01

    This study evaluated the biomechanical characteristics of a single self-locking knot (sSLK) and a double self-locking knot (dSLK) compared with the square knot (SQ) for stabilization of cranial cruciate ligament rupture. Each knot underwent monotonic tensile and cyclical loading. Starting tension, elongation, stiffness, and load to failure were all evaluated. A value of P < 0.05 was considered significant. Starting tension, overall stiffness, and load to failure were all significantly greater in both the sSLK and dSLK compared with the SQ. There was no difference in elongation among the knots. There were no significant differences in starting tension, elongation, stiffness, and load to failure between the sSLK and the dSLK. The self-locking knots were stronger and stiffer than the SQ; there is no biomechanical advantage in using the dSLK compared with the sSLK. PMID:24082161

  12. "Security loop" tie: a new technique to overcome loosening of surgical knots.

    PubMed

    Alzacko, Saadallah Mohammad; Majid, Omer Waleed

    2007-11-01

    Sutures require knots so as to ensure optimal tissue closure strength. Loosening of surgical knots during or after tying can lead to an ineffective suture and compromise the final result. Loosening is affected mainly by the type of suture material and nature of surgical field. In palatal surgery, tying secure knots is a major consideration and may present a technical challenge. In this article, and after a review of the literature, we present a new modification of the usual knot-tying technique to maximize knot security and prevent knot loosening after the first throw is done. This technique was found to be effective, simple, fast, easy to learn, and saves time and material. PMID:17964468

  13. Folding analysis of the most complex Stevedore's protein knot.

    PubMed

    Wang, Iren; Chen, Szu-Yu; Hsu, Shang-Te Danny

    2016-01-01

    DehI is a homodimeric haloacid dehalogenase from Pseudomonas putida that contains the most complex 61 Stevedore's protein knot within its folding topology. To examine how DehI attains such an intricate knotted topology we combined far-UV circular dichroism (CD), intrinsic fluorescence spectroscopy and small angle X-ray scattering (SAXS) to investigate its folding mechanism. Equilibrium unfolding of DehI by chemical denaturation indicated the presence of two highly populated folding intermediates, I and I'. While the two intermediates vary in secondary structure contents and tertiary packing according to CD and intrinsic fluorescence, respectively, their overall dimension and compactness are similar according to SAXS. Three single-tryptophan variants (W34, W53, and W196) were generated to probe non-cooperative unfolding events localized around the three fluorophores. Kinetic fluorescence measurements indicated that the transition from the intermediate I' to the unfolded state is rate limiting. Our multiparametric folding analyses suggest that DehI unfolds through a linear folding pathway with two distinct folding intermediates by initial hydrophobic collapse followed by nucleation condensation, and that knotting precedes the formation of secondary structures. PMID:27527519

  14. High energy mechanism from the knot of OJ 287

    NASA Astrophysics Data System (ADS)

    Kushwaha, Pankaj; Sahayanathan, Sunder; Singh, K. P.

    The detection of gamma-ray flare from the BL Lac object, OJ 287 during October 2009 is associated with the ejection of a superluminal radio knot as suggested by discrete cross-correlation analysis of gamma-ray and 1 mm radio light curve. We study plausible mechanisms responsible for the high energy emission from this knot. We reproduce the quasi-simultaneous broadband spectral energy distribution from the knot considering synchrotron and inverse Compton emission from a broken power-law particle distribution. Explanation of X-ray and gamma-ray by either synchrotron-self Compton (SSC) or external Compton (EC) alone cannot reproduce the broadband spectrum and/or require unphysical set of parameters. Hence we model the high energy emission as an outcome of both SSC and EC models. The temperature of external photon field inferred from this model suggests that the gamma-ray emission must be resulting from the inverse Compton scattering of infra-red photon from the warm region surrounding the super massive black hole in OJ 287.

  15. Elastic knots of Space-Time may improve QED, QCD

    NASA Astrophysics Data System (ADS)

    Kriske, Richard

    2016-03-01

    This author had previously suggested that the time dimension of Electric fields and Magnetic fields are different. This matter was apparently settled with the Special Theory, in which each Observer, has his own Dimension of Time, that is ``elastic'' with one Dimension of Space. The independence of E and M, when they are not varying with time, leads one wonder if they are the same time. For a moving Observer, the two fields are joined through Faraday and Ampere's law. Particle Physics has made the simple Special Relativity interpretation murky. A photon does not simply become either an Electric field or a Magnetic field when viewed in its ''rest frame''. Because of this all kinds of extra sub theories are used, such as the Photon is quantized, and is massless in its rest frame, and always moves at the velocity of light. As for the Photon of the magnetic, or just the electric field, it is ``off the mass shell''. Perhaps a better theory is that the elasticity of time and the fact the ``Two'' observers show up in the theory, is that there has to be two dimensions of time, tied in a knot, in order for a field to become a Particle. The knot tying in EM is simple, when the E field varies it produces M, and vice-versa. For massive particles the knots are more complicated, more dimensions.

  16. Insecticidal plant cyclotides and related cystine knot toxins.

    PubMed

    Gruber, Christian W; Cemazar, Masa; Anderson, Marilyn A; Craik, David J

    2007-03-15

    Cyclotides are small disulphide-rich peptides found in plants from the violet (Violaceae), coffee (Rubiaceae) and cucurbit (Cucurbitaceae) families. They have the distinguishing structural features of a macrocyclic peptide backbone and a cystine knot made up of six conserved cysteine residues, which makes cyclotides exceptionally stable. Individual plants express a suite of cyclotides in a wide range of tissue types, including leaves, flowers, stems and roots and it is thought that their natural function in plants is as defence agents. This proposal is supported by their high expression levels in plants and their toxic and growth retardant activity in feeding trials against Helicoverpa spp. insect pests. This review describes the structures and activities of cyclotides with specific reference to their insecticidal activity and compares them with structurally similar cystine knot proteins from peas (Pisum sativum) and an amaranthus crop plant (Amaranthus hypocondriancus). More broadly, cystine knot proteins are common in a wide range of organisms from fungi to mammals, and it appears that this interesting structural motif has evolved independently in different organisms as a stable protein framework that has a variety of biological functions. PMID:17224167

  17. Endopathogenic lifestyle of Pseudomonas savastanoi pv. savastanoi in olive knots

    PubMed Central

    Rodríguez‐Moreno, Luis; Jiménez, Antonio J.; Ramos, Cayo

    2009-01-01

    Summary The endophytic phase of Pseudomonas savastanoi pv. savastanoi in olive stems and the structural and ultrastructural histogenesis of olive knots have been studied. Construction of a stable plasmid vector expressing the green fluorescent protein, in combination with the use of in vitro olive plants, allowed real‐time monitoring of P. savastanoi pv. savastanoi infection. The infection process was also examined by bright field and epifluorescence microscopy as well as by scanning and transmission electron microscopy. Hypertrophy of the stem tissue was concomitant with the formation of bacterial aggregates, microcolonies and multilayer biofilms, over the cell surfaces and the interior of plasmolysed cells facing the air‐tissue interface of internal opened fissures, and was followed by invasion of the outer layers of the hypertrophied tissue. Pathogenic invasion of the internal lumen of newly formed xylem vessels, which were connected with the stem vascular system, was also observed in late stages of infection. Ultrastructural analysis of knot sections showed the release of outer membrane vesicles from the pathogen surface, a phenomenon not described before for bacterial phytopathogens during host infection. This is the first real‐time monitoring of P. savastanoi disease development and the first illustrated description of the ultrastructure of P. savastanoi‐induced knots. PMID:21255279

  18. Environmentally friendly efficient coupling of n-heptane by sulfated tri-component metal oxides in slurry bubble column reactor.

    PubMed

    Ma, Hongzhu; Xiao, Jing; Wang, Bo

    2009-07-30

    SO(4)(2-)/M(x)O(y) is of the greatest interest in solid catalysts and green catalysts. Slurry bubble column reactors are of considerable interest in industrial processes and various biochemical processes. The cetane number (CN) has widely used diesel fuel quality parameter related to the ignition delay time (and combustion quality) of a fuel. CN improvement of diesel fuels is a difficult task that refiners will face in the near future. For that purpose, the tests were designed in which n-heptane is used as the reactant in the air or ozone atmosphere at room temperature (RT) and local atmospheric pressure (LAP) using different catalysts of sulfated tri-component metal oxides SO(4)(2-)/Fe(2)O(3)-TiO2-SnO(2) (SFTSn) and SO(4)(2-)/MnO(2)-TiO2-SnO(2) (SMTSn) in slurry bubble column reactor. The products distribution was analyzed by gas chromatography-mass spectrometry (GC-MS) method and the results show that the relative selectivity of long linear alkane (C(12)-C(28)) reaches the maximum (87.330%) when SMTSn is used as catalyst in flow air at 60 min. Diesel fuel components with higher cetane numbers can be easily obtained from this study. PMID:19124196

  19. Metabolic Toxicity Screening Using Electrochemiluminescence Arrays Coupled with Enzyme-DNA Biocolloid Reactors and Liquid Chromatography–Mass Spectrometry

    PubMed Central

    Hvastkovs, Eli G.; Schenkman, John B.; Rusling, James F.

    2012-01-01

    New chemicals or drugs must be guaranteed safe before they can be marketed. Despite widespread use of bioassay panels for toxicity prediction, products that are toxic to a subset of the population often are not identified until clinical trials. This article reviews new array methodologies based on enzyme/DNA films that form and identify DNA-reactive metabolites that are indicators of potentially genotoxic species. This molecularly based methodology is designed in a rapid screening array that utilizes electrochemiluminescence (ECL) to detect metabolite-DNA reactions, as well as biocolloid reactors that provide the DNA adducts and metabolites for liquid chromatography–mass spectrometry (LC-MS) analysis. ECL arrays provide rapid toxicity screening, and the biocolloid reactor LC-MS approach provides a valuable follow-up on structure, identification, and formation rates of DNA adducts for toxicity hits from the ECL array screening. Specific examples using this strategy are discussed. Integration of high-throughput versions of these toxicity-screening methods with existing drug toxicity bioassays should allow for better human toxicity prediction as well as more informed decision making regarding new chemical and drug candidates. PMID:22482786

  20. Application of membrane-coupled sequencing batch reactor for oilfield produced water recycle and beneficial re-use.

    PubMed

    Fakhru'l-Razi, A; Pendashteh, Alireza; Abidin, Zurina Zainal; Abdullah, Luqman Chuah; Biak, Dayang Radiah Awang; Madaeni, Sayed Siavash

    2010-09-01

    Oil and gas field wastewater or produced water is a significant waste stream in the oil and gas industries. In this study, the performance of a membrane sequencing batch reactor (MSBR) and membrane sequencing batch reactor/reverse osmosis (MSBR/RO) process treating produced wastewater were investigated and compared. The MSBR was operated in different hydraulic residence time (HRT) of 8, 20 and 44 h. Operation results showed that for a HRT of 20 h, the combined process effluent chemical oxygen demand (COD), total organic carbon (TOC) and oil and grease (O&G) removal efficiencies were 90.9%, 92% and 91.5%, respectively. The MSBR effluent concentration levels met the required standard for oil well re-injection. The RO treatment reduced the salt and organic contents to acceptable levels for irrigation and different industrial re-use. Foulant biopsy demonstrated that the fouling on the membrane surface was mainly due to inorganic (salts) and organic (microorganisms and their products, hydrocarbon constituents) matters. PMID:20434905

  1. Metabolic Toxicity Screening Using Electrochemiluminescence Arrays Coupled with Enzyme-DNA Biocolloid Reactors and Liquid Chromatography-Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Hvastkovs, Eli, G.; Schenkman, John B.; Rusling, James, F.

    2012-07-01

    New chemicals or drugs must be guaranteed safe before they can be marketed. Despite widespread use of bioassay panels for toxicity prediction, products that are toxic to a subset of the population often are not identified until clinical trials. This article reviews new array methodologies based on enzyme/DNA films that form and identify DNA-reactive metabolites that are indicators of potentially genotoxic species. This molecularly based methodology is designed in a rapid screening array that utilizes electrochemiluminescence (ECL) to detect metabolite-DNA reactions, as well as biocolloid reactors that provide the DNA adducts and metabolites for liquid chromatography-mass spectrometry (LC-MS) analysis. ECL arrays provide rapid toxicity screening, and the biocolloid reactor LC-MS approach provides a valuable follow-up on structure, identification, and formation rates of DNA adducts for toxicity hits from the ECL array screening. Specific examples using this strategy are discussed. Integration of high-throughput versions of these toxicity-screening methods with existing drug toxicity bioassays should allow for better human toxicity prediction as well as more informed decision making regarding new chemical and drug candidates.

  2. The effects of neutral gas heating on H mode transition and maintenance currents in a 13.56 MHz planar coil inductively coupled plasma reactor

    SciTech Connect

    Jayapalan, Kanesh K.; Chin, Oi-Hoong

    2012-09-15

    The H mode transition and maintenance currents in a 13.56 MHz laboratory 6 turn planar coil inductively coupled plasma (ICP) reactor are simulated for low pressure argon discharge range of 0.02-0.3 mbar with neutral gas heating and at ambient temperature. An experimentally fitted 3D power evolution plot for 0.02 mbar argon pressure is also shown to visualize the effects of hysteresis in the system. Comparisons between simulation and experimental measurements show good agreement in the pressure range of 0.02-0.3 mbar for transition currents and 0.02-0.1 mbar for maintenance currents only when neutral gas heating is considered. This suggests that neutral gas heating plays a non-negligible role in determining the mode transition points of a rf ICP system.

  3. Development of Tritium Permeation Analysis Code and Tritium Transport in a High Temperature Gas-Cooled Reactor Coupled with Hydrogen Production System

    SciTech Connect

    Chang H. Oh; Eung S. Kim; Mike Patterson

    2010-06-01

    Abstract – A tritium permeation analyses code (TPAC) was developed by Idaho National Laboratory for the purpose of analyzing tritium distributions in very high temperature reactor (VHTR) systems, including integrated hydrogen production systems. A MATLAB SIMULINK software package was used in developing the code. The TPAC is based on the mass balance equations of tritium-containing species and various forms of hydrogen coupled with a variety of tritium sources, sinks, and permeation models. In the TPAC, ternary fission and neutron reactions with 6Li, 7Li 10B, and 3He were taken into considerations as tritium sources. Purification and leakage models were implemented as main tritium sinks. Permeation of tritium and H2 through pipes, vessels, and heat exchangers were considered as main tritium transport paths. In addition, electroyzer and isotope exchange models were developed for analyzing hydrogen production systems, including high temperature electrolysis and sulfur-iodine processes.

  4. Measurements and Simulations of the Energy Distributions of Ions Bombarding Radio-frequency Biased Electrodes in an Inductively Coupled Plasma Reactor

    NASA Astrophysics Data System (ADS)

    Edelberg, Erik A.; Perry, Andrew; Benjamin, Neil; Aydil, Eray S.

    1998-10-01

    A compact retarding field ion energy analyzer has been designed and built to measure the energy distribution of ions bombarding the surface of radio frequency (rf) biased electrodes in high-density plasma reactors. Specifically, the analyzer was installed in the rf biased electrostatic chuck of a high-density, transformer-coupled plasma (TCP) reactor. The effects of TCP power, rf bias power, pressure, and gas composition on the measured ion energy distributions are demonstrated through Ar, Ne, Ar/Ne, O2 and CF4/O2 discharges. To complement the experimental results, a numerical sheath model that predicts the spatio-temporal variations of the potential across the sheath in a high density plasma has been developed. The energy distribution of ions bombarding the rf biased surface is then calculated using Monte Carlo simulations of the ion trajectories. Bimodal ion energy distributions resulting from ion energy modulation in the sheath were observed and simulated. Multiple peaks in the IEDs measured in gas mixtures were identified as signatures of ions with different masses falling through the sheath. The simulations predict both the energy separation of the bimodal IEDs as well as the ratio of the peak heights as measured by the ion energy analyzer.

  5. Fine-structure infrared lines from the Cassiopeia A knots

    NASA Astrophysics Data System (ADS)

    Docenko, D.; Sunyaev, R. A.

    2010-01-01

    Aims: Archival observations of infrared fine-structure lines of the young Galactic supernova remnant Cassiopeia A allow us to test existing models and determine the physical parameters of various regions of the fast-moving knots, which are metal-dominated clouds of material ejected by the supernova explosion. Methods: The fluxes of far-infrared [O i] and [O iii] lines are extracted from previously unpublished archival ISO data. The archival Spitzer data are used to determine the fluxes of the O, Ne, Si, S, Ar, and Fe ion fine-structure lines originating in the fast-moving knots. The ratios of these line fluxes are used as plasma diagnostics. We also determine the infrared line flux ratios with respect to the optical [O iii] 5007 Å line in the knots with previously measured reddening. Additionally, we analyze several optical and near-infrared observations of the fast-moving knots to obtain clearer insight into the post-shock photoionized region structure. Results: We show that the infrared oxygen line flux predictions of all existing theoretical models are correct only to within a factor of a several. Comparison of the model predictions shows that to reproduce the observations it is essential to include the effects of the electron conductivity and dust. Detailed analysis of the diagnostic line flux ratios of various ions allows us to qualitatively confirm the general model of fast-moving knot emission and determine observationally for the first time the physical conditions in the photoionized region after the shock. We infer from the [O iii] line flux ratios that the pre-shock cloud densities are higher than assumed in existing theoretical models and most probably correspond to several hundred particles per cm3. We also determine the Cas A luminosity in the infrared continuum and lines. We show that accounting for the charge exchange processes in the post-shock photoionized region allows us to reproduce most of the relevant spectral line ratios even in the frame of

  6. Computational study on the progressive factorization of composite polymer knots into separated prime components

    NASA Astrophysics Data System (ADS)

    Tubiana, Luca

    2014-05-01

    Using Monte Carlo simulations and advanced knot localization methods, we analyze the length and distribution of prime components in composite knots tied on freely jointed rings. For increasing contour length, we observe the progressive factorization of composite knots into separated prime components. However, we observe that a complete factorization, equivalent to the "decorated ring" picture, is not obtained even for rings of contour lengths N ≃3N0, about tens of times the most probable length of the prime knots tied on the rings. The decorated ring hypothesis has been used in the literature to justify the factorization of composite knot probabilities into the knotting probabilities of their prime components. Following our results, we suggest that such a hypothesis may not be necessary to explain the factorization of the knotting probabilities, at least when polymers excluding volume is not relevant. We rationalize the behavior of the system through a simple one-dimensional model in which prime knots are replaced by slip links randomly placed on a circle, with the only constraint being that the length of the loops has the same distribution as that of the length of the corresponding prime knots.

  7. Kauffman knot polynomials in classical abelian Chern-Simons field theory

    SciTech Connect

    Liu Xin

    2010-12-15

    Kauffman knot polynomial invariants are discovered in classical abelian Chern-Simons field theory. A topological invariant t{sup I(L)} is constructed for a link L, where I is the abelian Chern-Simons action and t a formal constant. For oriented knotted vortex lines, t{sup I} satisfies the skein relations of the Kauffman R-polynomial; for un-oriented knotted lines, t{sup I} satisfies the skein relations of the Kauffman bracket polynomial. As an example the bracket polynomials of trefoil knots are computed, and the Jones polynomial is constructed from the bracket polynomial.

  8. Determination of hydrogen peroxide by micro-flow injection-chemiluminescence using a coupled flow cell reactor chemiluminometer.

    PubMed

    Nozaki, O; Kawamoto, H

    2000-01-01

    A novel flow cell reactor was developed for micro-flow injection determination of hydrogen peroxide (H(2)O(2)) using horseradish peroxide (HRP)-catalysed luminol chemiluminescence. The newly developed flow cell reactor for a chemiluminometer allowed mixing of the chemiluminescent reagents in front of a photomultiplier for maximum detection of the emitted light. The rapid mixing allowed a decrease in the flow rate of the pump to 0.1-0.01 mL/min, resulting in increased sensitivity of detection of light. The flow cell reactor was made by packing HRP-immobilized gels into a flow cell (Teflon tube; 6 cm x 0.98 mm i.d.) located in the cell holder of a chemiluminometer (flow-through type). The HRP-immobilized gels were made by immobilizing HRP onto the Chitopearl gel by the periodate method. H(2)O(2) specimens (50 microL) were injected into a stream of water delivered at a flow rate of 0.1 mL/min and mixed with a luminol solution (0.56 mmol/L in Tricine buffer, pH 9.2) delivered at 0.1 mL/min in the flow cell reactor. Within-run reproducibility of the assay of H(2)O(2) was 2.4% (4.85 micromol/L; flow rate 0.1 mL/min, injection interval 10 min). The reproducibility of the H(2)O(2) assay was influenced by the flow rates and the injection intervals of the H(2)O(2) specimens. As the flow rates decreased, both the light intensity and the light duration increased. Optimal light intensity was obtained at a luminol concentration of 3-8 mmol/L, but 0.56 mmol/L was sufficient for assay of H(2)O(2) in clinical specimens. At a luminol concentration of 0.56 mmol/L, the regression equation of the standard curve for H(2)O(2) (0-9.7 micromol/L) was Y = 27.5 X(2) + 394 X + 58.9 (Y = light intensity; X = concentration of H(2)O(2)) and the detection limit of H(2)O(2) was 0.2 micromol/L. This method was used to assay glucose (2.7-16.7 mmol/L) based on a glucose oxidase (20 U/mL, pH 7.4) reaction. The standard curve for glucose was Y = 167 X(2) - 351 X + 1484 (Y = light intensity; X = glucose

  9. Fundamental Processes of Coupled Radiation Damage and Mechanical Behavior in Nuclear Fuel Materials for High Temperature Reactors

    SciTech Connect

    Phillpot, Simon; Tulenko, James

    2011-09-08

    The objective of this work has been to elucidate the relationship among microstructure, radiation damage and mechanical properties for nuclear fuel materials. As representative nuclear materials, we have taken an hcp metal (Mg as a generic metal, and Ti alloys for fast reactors) and UO2 (representing fuel). The degradation of the thermo-mechanical behavior of nuclear fuels under irradiation, both the fissionable material itself and its cladding, is a longstanding issue of critical importance to the nuclear industry. There are experimental indications that nanocrystalline metals and ceramics may be more resistant to radiation damage than their coarse-grained counterparts. The objective of this project look at the effect of microstructure on radiation damage and mechanical behavior in these materials. The approach to be taken was state-of-the-art, large-scale atomic-level simulation. This systematic simulation program of the effects of irradiation on the structure and mechanical properties of polycrystalline Ti and UO2 identified radiation damage mechanisms. Moreover, it will provided important insights into behavior that can be expected in nanocrystalline microstructures and, by extension, nanocomposites. The fundamental insights from this work can be expected to help in the design microstructures that are less susceptible to radiation damage and thermomechanical degradation.

  10. The validation of an instrumented simulator for the assessment of performance and outcome of knot tying skill: a pilot study.

    PubMed

    Rojas, David; Cristancho, Sayra; Rueda, Claudia; Grierson, Lawrence; Monclou, Alex; Dubrowski, Adam

    2011-01-01

    The construct validity of a surgical bench-top simulator with built-in computer acquired assessments was examined. It features two parallel elastic tubes instrumented with flexion sensors that simulate the walls of a wound. Participants from three groups (9 novices, 7 intermediates, 9 experts) performed 10 two-handed, double square knots. The peak tensions at the initiation of the first knot, the completion of the first knot and the completion of the second knot, as well as measures of movement economy indicated technical performance. Product quality was indicated by knot stability defined as the amount of slippage of the knot under the tension. There were significant differences between experts and novices for peak tension on first knot (p=.03), movement economy (p=.02), and knot stability (p=.002). The results support the construct validity of these objective measures. PMID:21335849

  11. Cotton Cultivar Response to Root-Knot Nematodes in Two Tillage Regimes, 2008

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Six cotton cultivars were evaluated for yield response to the root-knot nematode in a naturally infested field at E. V. Smith Research and Extension Center, near Shorter, Alabama. The field had a long history of root-knot nematode infestation, and the soil type was classified as a sandy loam. Plots ...

  12. PA-560, A Southern Root-knot Nematode Resistant, Yellow-fruited, Habanero-type Pepper

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The USDA has developed a yellow-fruited, Habanero-type pepper (Capsicum chinense Jacq.) that is highly resistant to root-knot nematodes. The new breeding line, designated PA-560, is the product of a backcross/pedigree breeding procedure to incorporate a root-knot nematode resistance gene from the S...

  13. Response of Watermelon Germplasm to Southern Root-Knot Nematode in Field Tests

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Southern root-knot nematode (Meloidogyne incognita) is a serious pest of cultivated watermelon (Citrullus lanatus var. lanatus) in southern regions of the US. While there is no known resistance to southern root-knot nematode in watermelon cultivars to date, wild watermelon relatives (C. lanatus var...

  14. Percutaneous Retrieval of a Pulmonary Artery Catheter Knot in Pacing Electrodes

    SciTech Connect

    Valenzuela-Garcia, Luis Felipe Almendro-Delia, Manuel; Gonzalez-Valdayo, Miguel; Munoz-Campos, Juan; Dorado-Garcia, Jose C.; Gomez-Rosa, Francisco; Vazquez-Garcia, Rafael; Calderon-Leal, Jose M.

    2007-09-15

    To illustrate a successful approach to resolving a pulmonary artery catheter knot in the pacing leads of a cardiac resynchronization device. When planning invasive monitoring for patients having right chamber electrodes, fluoroscopic-guided catheter insertion and extraction is advisable. In the event of coiling or knotting, an interventional radiologist should be contacted as soon as possible to avoid serious complications.

  15. Translocation dynamics of knotted polymers under a constant or periodic external field.

    PubMed

    Narsimhan, Vivek; Renner, C Benjamin; Doyle, Patrick S

    2016-06-14

    We perform Brownian dynamics simulations to examine how knots alter the dynamics of polymers moving through nanopores under an external field. In the first part of this paper, we study the situation when the field is constant. Here, knots halt translocation above a critical force with jamming occurring at smaller forces for twist topologies compared to non-twist topologies. Slightly below the jamming transition, the polymer's transit times exhibit large fluctuations. This phenomenon is an example of the knot's molecular individualism since the conformation of the knot plays a large role in the chain's subsequent dynamics. In the second part of the paper, we study the motion of the chain when one cycles the field on and off. If the off time is comparable to the knot's relaxation time, one can adjust the swelling of the knot at the pore and hence design strategies to ratchet the polymer in a controllable fashion. We examine how the off time affects the ratcheting dynamics. We also examine how this strategy alters the fluctuations in the polymer's transit time. We find that cycling the force field can reduce fluctuations near the knot's jamming transition, but can enhance the fluctuations at very high forces since knots get trapped in metastable states during the relaxation process. The latter effect appears to be more prominent for non-torus topologies than torus ones. We conclude by discussing the feasibility of this approach to control polymer motion in biotechnology applications such as sequencing. PMID:27181288

  16. High finesse microfiber knot resonators made from double-ended tapered fibers.

    PubMed

    Xiao, Limin; Birks, T A

    2011-04-01

    We fabricated optical microfiber knot resonators from thin tapered fibers (diameter down to 1 μm) linked to untapered fiber at both ends. We demonstrated a finesse of about 100, over twice as high as previously reported for microfiber resonators. Low-loss encapsulation of microfiber knot resonators in hydrophobic silica aerogel was also investigated. PMID:21478995

  17. Ethnomathematics in Arfak (West Papua-Indonesia): Hidden Mathematics on Knot of Rumah Kaki Seribu

    ERIC Educational Resources Information Center

    Haryanto; Nusantara, Toto; Subanji; Abadyo

    2016-01-01

    This ethnomathematics article focused on the models of knot which is used in the frame of "Rumah Kaki Seribu." The knot model itself was studied mathematically. The results of this study revealed the way Arfak tribal communities think mathematically. This article uses exploration, documentation, interview, experiments and literature…

  18. Resistance to tomato spotted wilt virus and root-knot nematode in peanut interspecific breeding lines

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The peanut root-knot nematode [Meloidogyne arenaria (Neal) Chitwood race 1] and tomato spotted wilt virus Tospovirus (TSWV) are economically significant pathogens of peanut in the southeastern United States. Peanut cultivars are available that have resistance to either the peanut root-knot nematode...

  19. Expression of almond KNOTTED1 homologue (PdKn1) anticipates adventitious shoot initiation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background and Aims: The transcription factor encoded by the gene Knotted1 is a nuclear homeodomain protein, regulating meristematic cells at the shoot apical meristem. It has been proven that Knotted1 (KN1) has a role in the switch from an indeterminate to determinate cell fate and as such this gen...

  20. Macromolecular knot in good and poor solvents: a Monte Carlo simulation.

    PubMed

    Sun, Huan-Quan; Zhang, Lu; Liao, Qi

    2010-09-30

    The probability and dimension of the simple macromolecular knots over a wide range of temperatures corresponding from good to poor solvents are investigated by Monte Carlo simulation. Macromolecular knots are modeled as rings of self-avoiding walks on a simple cubic lattice with the nearest neighbor attractions. We found that there is a minimum probability for the unknotted ring at a certain temperature. The size dependence of trivial, trefoil, and figure-eight knots on chain lengths and temperatures is presented. The simulation results for the size dependence on the knot's complication in different solvents are in good qualitative agreement with prediction of the scaling model proposed by Grosberg et al. The critical exponent for long chain is independent of the knot types based on the simulation results, although the mean square radius of gyration is influenced significantly by the knot types for a shorter length macromolecular ring. We calculated the ratio of the topological invariant p of trefoil knot and figure-eight knot and found that the ratio is approaching to 1.3 with the increasing of the chain length. PMID:20825151

  1. Unraveling the Helix Nebula: Its Structure and Knots

    NASA Astrophysics Data System (ADS)

    O'Dell, C. R.; McCullough, Peter R.; Meixner, Margaret

    2004-11-01

    Through Hubble Space Telescope (HST) imaging of the inner part of the main ring of the Helix Nebula, together with CTIO 4 m images of the fainter outer parts, we have a view of unprecedented quality of the nearest bright planetary nebula. These images have allowed us to determine that the main ring of the nebula is composed of an inner disk of about 499" diameter (0.52 pc) surrounded by an outer ring (in reality a torus) of 742" diameter (0.77 pc) whose plane is highly inclined to the plane of the disk. This outer ring is surrounded by an outermost ring of 1500" (1.76 pc) diameter, which is flattened on the side colliding with the ambient interstellar medium. The inner disk has an extended distribution of low-density gas along its rotational axis of symmetry, and the disk is optically thick to ionizing radiation, as is the outer ring. Published radial velocities of the knots provide support for the two-component structure of the main ring of the nebula and for the idea that the knots found there are expanding along with the nebular material from which they recently originated. These velocities indicate a spatial expansion velocity of the inner disk of 40 and 32 km s-1 for the outer ring, which yields expansion ages of 6560 and 12,100 yr, respectively. The outermost ring may be partially ionized through scattered recombination continuum from the inner parts of the nebula, but shocks certainly are occurring in it. This outermost ring probably represents a third period of mass loss by the central star. There is one compact, outer object that is unexplained, showing shock structures indicating a different orientation of the gas flow from that of the nebula. There is a change in the morphology of the knots as a function of the distance from the local ionization front. This supports a scenario in which the knots are formed in or near the ionization front and are then sculpted by the stellar radiation from the central star as the ionization front advances beyond them

  2. Design and performance of the APPLE-Knot undulator

    PubMed Central

    Ji, Fuhao; Chang, Rui; Zhou, Qiaogen; Zhang, Wei; Ye, Mao; Sasaki, Shigemi; Qiao, Shan

    2015-01-01

    Along with the development of accelerator technology, synchrotron emittance has continuously decreased. This results in increased brightness, but also causes a heavy heat load on beamline optics. Recently, optical surfaces with 0.1 nm micro-roughness and 0.05 µrad slope error (r.m.s.) have become commercially available and surface distortions due to heat load have become a key factor in determining beamline performance, and heat load has become a serious problem at modern synchrotron radiation facilities. Here, APPLE-Knot undulators which can generate photons with arbitrary polarization, with low on-axis heat load, are reported. PMID:26134793

  3. Racah matrices and hidden integrability in evolution of knots

    NASA Astrophysics Data System (ADS)

    Mironov, A.; Morozov, A.; Morozov, An.; Sleptsov, A.

    2016-09-01

    We construct a general procedure to extract the exclusive Racah matrices S and S bar from the inclusive 3-strand mixing matrices by the evolution method and apply it to the first simple representations R = [ 1 ], [2], [3] and [ 2 , 2 ]. The matrices S and S bar relate respectively the maps (R ⊗ R) ⊗ R bar ⟶ R with R ⊗ (R ⊗ R bar) ⟶ R and (R ⊗ R bar) ⊗ R ⟶ R with R ⊗ (R bar ⊗ R) ⟶ R. They are building blocks for the colored HOMFLY polynomials of arbitrary arborescent (double fat) knots. Remarkably, the calculation realizes an unexpected integrability property underlying the evolution matrices.

  4. Writhe-induced knotting in a lattice polymer

    NASA Astrophysics Data System (ADS)

    Dagrosa, E.; Owczarek, A. L.; Prellberg, T.

    2015-02-01

    We consider a simple lattice model of a topological phase transition in open polymers. To be precise, we study a model of self-avoiding walks on the simple cubic lattice tethered to a surface and weighted by an appropriately defined writhe. We also consider the effect of pulling the untethered end of the polymer from the surface. Regardless of the force we find a first-order phase transition which we argue is a consequence of increased knotting in the lattice polymer, rather than due to other effects such as the formation of plectonemes.

  5. Fully Coupled Modeling of Burnup-Dependent (U1- y , Pu y )O2- x Mixed Oxide Fast Reactor Fuel Performance

    NASA Astrophysics Data System (ADS)

    Liu, Rong; Zhou, Wenzhong; Zhou, Wei

    2016-03-01

    During the fast reactor nuclear fuel fission reaction, fission gases accumulate and form pores with the increase of fuel burnup, which decreases the fuel thermal conductivity, leading to overheating of the fuel element. The diffusion of plutonium and oxygen with high temperature gradient is also one of the important fuel performance concerns as it will affect the fuel material properties, power distribution, and overall performance of the fuel pin. In order to investigate these important issues, the (U1- y Pu y )O2- x fuel pellet is studied by fully coupling thermal transport, deformation, oxygen diffusion, fission gas release and swelling, and plutonium redistribution to evaluate the effects on each other with burnup-dependent models, accounting for the evolution of fuel porosity. The approach was developed using self-defined multiphysics models based on the framework of COMSOL Multiphysics to manage the nonlinearities associated with fast reactor mixed oxide fuel performance analysis. The modeling results showed a consistent fuel performance comparable with the previous results. Burnup degrades the fuel thermal conductivity, resulting in a significant fuel temperature increase. The fission gas release increased rapidly first and then steadily with the burnup increase. The fuel porosity increased dramatically at the beginning of the burnup and then kept constant as the fission gas released to the fuel free volume, causing the fuel temperature to increase. Another important finding is that the deviation from stoichiometry of oxygen affects greatly not only the fuel properties, for example, thermal conductivity, but also the fuel performance, for example, temperature distribution, porosity evolution, grain size growth, fission gas release, deformation, and plutonium redistribution. Special attention needs to be paid to the deviation from stoichiometry of oxygen in fuel fabrication. Plutonium content will also affect the fuel material properties and performance

  6. Introduction of "Papazian Pusher: " A Modified-Design Knot Pusher for Surgical Repair of Cleft Palates.

    PubMed

    Papazian, Nazareth J; Chahine, Fadl; Atiyeh, Bishara; Deeba, Samer; Zgheib, Elias; Abu-Sittah, Ghassan

    2015-09-01

    Tying sutures is an integral aspect of any surgery and reliable instruments are essential for hassle-free procedures including craniofacial surgeries. Knot pushers have been widely known for their application in various laparoscopic, arthroscopic, and anal surgeries. The literature reveals numerous articles pertaining to knot pushers, as well as improvements on existing designs. Nevertheless, no application of knot pushers in the surgical repair of cleft palates has been described. We describe a new knot pusher "Papazian Pusher" (PP) finely designed for application in oral surgeries in general and repair of cleft palates in particular. The instrument was used satisfactorily in repair of cleft palate surgeries and no complications were encountered. The PP was found, overall, to be easy to use, and helps in performing faster, stronger, smooth, and secure knots. PMID:26355980

  7. Untangling the mechanics and topology in the frictional response of long overhand elastic knots.

    PubMed

    Jawed, M K; Dieleman, P; Audoly, B; Reis, P M

    2015-09-11

    We combine experiments and theory to study the mechanics of overhand knots in slender elastic rods under tension. The equilibrium shape of the knot is governed by an interplay between topology, friction, and bending. We use precision model experiments to quantify the dependence of the mechanical response of the knot as a function of the geometry of the self-contacting region, and for different topologies as measured by their crossing number. An analytical model based on the nonlinear theory of thin elastic rods is then developed to describe how the physical and topological parameters of the knot set the tensile force required for equilibrium. Excellent agreement is found between theory and experiments for overhand knots over a wide range of crossing numbers. PMID:26406861

  8. Effect of Rf Ground Location in an Inductively Coupled Plasma Reactor on the Plasma Density and Ion Energy

    NASA Astrophysics Data System (ADS)

    Radovanov, Svetlana; Anderson, Harold; Bell, Gary; Zhang, Hong-Mei; Hoffman, Dan; Resta, Victoria; Rasmussen, Dave

    1996-10-01

    Measurements of the electromagnetic (EM) fields, plasma density and ion energy distribution (IED)were performed in a high density ICP etch tool.The obtained EM fields have shown that a virtual radio frequency (RF) ground exists on the current strap. A set of experiments were performed to investigate the impact of altering the location of this RF ground on the EM fields produced and on the uniformity of the plasma density and ion energy distribution. Vacuum RF field measurements for "virtual" and "imposed" ground configurations show a dramatic effect on the electric and magnetic fields. In the standard "virtual" ground case (ground located near the outer edge of the coil), the electric field magnitude is center peaked, while in the "imposed" ground mode (ground shifted toward the coil center), the electric field magnitude has an annular shape. A miniaturized retarding grid ion energy analyzer (mini-IEA) was used to determine radial profiles of the ion saturation current and ion energy distribution (IED)[1]. Radial profiles of the ion current in the "virtual" ground mode are uniform and IEDs are sharp and narrow. In the "imposed" ground mode an annular shaped profile was obtained. The IEDs are significantly broadened, suggesting a larger electrostatic coupling component to the discharge. The changes in the IED are important owing to their impact on the isotropy of etching of microelectronic devices and uniformity of plasma generation. ( G.W. Gibson, Jr, H.H. Sawin, I. Tepermeister, D.E.Ibbotson, and J.T.C. Lee, J. Vac. Sci. Technol. B, 12, 2333 (1994).)

  9. TRITIUM PERMEATION AND TRANSPORT IN THE GASOLINE PRODUCTION SYSTEM COUPLED WITH HIGH TEMPERATURE GAS-COOLED REACTORS (HTGRS)

    SciTech Connect

    Chang H. Oh; Eung S. Kim; Mike Patterson

    2011-05-01

    This paper describes scoping analyses on tritium behaviors in the HTGR-integrated gasoline production system, which is based on a methanol-to-gasoline (MTG) plant. In this system, the HTGR transfers heat and electricity to the MTG system. This system was analyzed using the TPAC code, which was recently developed by Idaho National Laboratory. The global sensitivity analyses were performed to understand and characterize tritium behaviors in the coupled HTGR/MTG system. This Monte Carlo based random sampling method was used to evaluate maximum 17,408 numbers of samples with different input values. According to the analyses, the average tritium concentration in the product gasoline is about 3.05×10-3 Bq/cm3, and 62 % cases are within the tritium effluent limit (= 3.7x10-3 Bq/cm3[STP]). About 0.19% of released tritium is finally transported from the core to the gasoline product through permeations. This study also identified that the following four parameters are important concerning tritium behaviors in the HTGR/MTG system: (1) tritium source, (2) wall thickness of process heat exchanger, (3) operating temperature, and (4) tritium permeation coefficient of process heat exchanger. These four parameters contribute about 95 % of the total output uncertainties. This study strongly recommends focusing our future research on these four parameters to improve modeling accuracy and to mitigate tritium permeation into the gasol ine product. If the permeation barrier is included in the future study, the tritium concentration will be significantly reduced.

  10. Extension of the supercritical carbon dioxide brayton cycle to low reactor power operation: investigations using the coupled anl plant dynamics code-SAS4A/SASSYS-1 liquid metal reactor code system.

    SciTech Connect

    Moisseytsev, A.; Sienicki, J. J.

    2012-05-10

    Significant progress has been made on the development of a control strategy for the supercritical carbon dioxide (S-CO{sub 2}) Brayton cycle enabling removal of power from an autonomous load following Sodium-Cooled Fast Reactor (SFR) down to decay heat levels such that the S-CO{sub 2} cycle can be used to cool the reactor until decay heat can be removed by the normal shutdown heat removal system or a passive decay heat removal system such as Direct Reactor Auxiliary Cooling System (DRACS) loops with DRACS in-vessel heat exchangers. This capability of the new control strategy eliminates the need for use of a separate shutdown heat removal system which might also use supercritical CO{sub 2}. It has been found that this capability can be achieved by introducing a new control mechanism involving shaft speed control for the common shaft joining the turbine and two compressors following reduction of the load demand from the electrical grid to zero. Following disconnection of the generator from the electrical grid, heat is removed from the intermediate sodium circuit through the sodium-to-CO{sub 2} heat exchanger, the turbine solely drives the two compressors, and heat is rejected from the cycle through the CO{sub 2}-to-water cooler. To investigate the effectiveness of shaft speed control, calculations are carried out using the coupled Plant Dynamics Code-SAS4A/SASSYS-1 code for a linear load reduction transient for a 1000 MWt metallic-fueled SFR with autonomous load following. No deliberate motion of control rods or adjustment of sodium pump speeds is assumed to take place. It is assumed that the S-CO{sub 2} turbomachinery shaft speed linearly decreases from 100 to 20% nominal following reduction of grid load to zero. The reactor power is calculated to autonomously decrease down to 3% nominal providing a lengthy window in time for the switchover to the normal shutdown heat removal system or for a passive decay heat removal system to become effective. However, the

  11. Complexity of knotting in chaotic 3D eigenfunctions

    NASA Astrophysics Data System (ADS)

    Taylor, Alexander; Dennis, Mark

    Quantised vortices occur generically in disordered 3D complex scalar fields, forming a geometrically complex and statistically random large scale tangle even in systems with very different origins of complexity such as turbulent superfluids, optical volume speckle, the quantum eigenfunctions of chaotic 3D cavities, and liquid crystal phases. Although all such systems are random and fractal on large scales, it has previously been established that topological measures such as the probability of vortices knotting or linking with one another are sensitive to the local physics. We use the wave chaos as a universal model system with just one physical lengthscale, the wavelength, beyond which its vortices are Brownian. To access finite-volume realisations of wavefields, vortices are traced numerically in three different random degenerate eigenfunction systems, each approximating the random isotropic limit but with different constraints and symmetries that significantly impact topological statistics even at high energies. By a simple mode counting argument, we observe that the probability of a generic eigenfunction containing a knotted vortex line reaches 50% by around its 1000-3000th mode.

  12. High Proteolytic Resistance of Spider-Derived Inhibitor Cystine Knots

    PubMed Central

    Kikuchi, Kyoko; Sugiura, Mika; Kimura, Tadashi

    2015-01-01

    Proteolytic stability in gastrointestinal tract and blood plasma is the major obstacle for oral peptide drug development. Inhibitor cystine knots (ICKs) are linear cystine knot peptides which have multifunctional properties and could become promising drug scaffolds. ProTx-I, ProTx-II, GTx1-15, and GsMTx-4 were spider-derived ICKs and incubated with pepsin, trypsin, chymotrypsin, and elastase in physiological conditions to find that all tested peptides were resistant to pepsin, and ProTx-II, GsMTx-4, and GTx1-15 showed resistance to all tested proteases. Also, no ProTx-II degradation was observed in rat blood plasma for 24 hours in vitro and ProTx-II concentration in circulation decreased to half in 40 min, indicating absolute stability in plasma and fast clearance from the system. So far, linear peptides are generally thought to be unsuitable in vivo, but all tested ICKs were not degraded by pepsin and stomach could be selected for the alternative site of drug absorption for fast onset of the drug action. Since spider ICKs are selective inhibitors of various ion channels which are related to the pathology of many diseases, engineered ICKs will make a novel class of peptide medicines which can treat variety of bothering symptoms. PMID:26843868

  13. A one-step preparation method of monolithic enzyme reactor for highly efficient sample preparation coupled to mass spectrometry-based proteomics studies.

    PubMed

    Jiang, Shan; Zhang, Zichuan; Li, Lingjun

    2015-09-18

    Mass spectrometry (MS) coupled to sample preparation and separation techniques has become a primary tool for proteomics studies. However, due to sample complexity, it is often challenging to achieve fast and efficient sample preparation prior to MS analysis. In recent decades, monolithic materials have been developed not only as chromatographic media, but also as efficient solid supports for immobilizing multiple types of affinity reagents. Herein, the N-acryloxysuccinimide-co-acrylamide-co-N,N'-methylenebisacrylamide (NAS-AAm-Bis) monolith was fabricated within silanized 200 μm i.d. fused-silica capillaries and was used as an immobilized enzyme reactor (IMER). The column was conjugated with trypsin/Lys-C and Lys-N enzymes to allow enzymatic digestions to occur while protein mixture was loaded onto the IMER column followed by MS-based proteomics analysis. Similar MS signal and protein sequence coverage were observed using protein standard bovine serum albumin (BSA) compared to in-solution digestion. Furthermore, mouse serum, yeast, and human cell lysate samples were also subjected to enzymatic digestion by both IMER (in seconds to minutes) and conventional in solution digestion (overnight) for comparison in large-scale proteomics studies. Comparable protein identification results obtained by the two methods highlighted the potential of employing NAS-based IMER column for fast and highly efficient sample preparation for MS analysis in proteomics studies. PMID:26300481

  14. Simulation of decay heat removal by natural convection in a pool type fast reactor model-ramona-with coupled 1D/2D thermal hydraulic code system

    SciTech Connect

    Kasinathan, N.; Rajakumar, A.; Vaidyanathan, G.; Chetal, S.C.

    1995-09-01

    Post shutdown decay heat removal is an important safety requirement in any nuclear system. In order to improve the reliability of this function, Liquid metal (sodium) cooled fast breeder reactors (LMFBR) are equipped with redundant hot pool dipped immersion coolers connected to natural draught air cooled heat exchangers through intermediate sodium circuits. During decay heat removal, flow through the core, immersion cooler primary side and in the intermediate sodium circuits are also through natural convection. In order to establish the viability and validate computer codes used in making predictions, a 1:20 scale experimental model called RAMONA with water as coolant has been built and experimental simulation of decay heat removal situation has been performed at KfK Karlsruhe. Results of two such experiments have been compiled and published as benchmarks. This paper brings out the results of the numerical simulation of one of the benchmark case through a 1D/2D coupled code system, DHDYN-1D/THYC-2D and the salient features of the comparisons. Brief description of the formulations of the codes are also included.

  15. An Indwelling Urethral Catheter Knotted Around a Double-J Ureteral Stent: An Unusual Complication after Kidney Transplantation

    PubMed Central

    Warmerdam, E. G.; Toorop, R. J.; Abrahams, A. C.; Berger, P.

    2011-01-01

    Urethral catheterization is a common procedure with a relatively low complication rate. Knotting of an indwelling urethral catheter is a very rare complication, and there are only a few case reports on knotted catheters, most of them concerning children. We report an especially rare case where a urethral catheter formed a knot around a double-J ureteral stent after a kidney transplantation. We will discuss the various risk factors for knotting of a catheter and the methods to untangle a knot. PMID:24533194

  16. In vitro and in situ characterization of arthroscopic loop security and knot security of braided polyblend sutures: a biomechanical study.

    PubMed

    Armstrong, Lucas C; Chong, Alexander; Livermore, Ryan W; Prohaska, Daniel J; Doyon, Amanda N; Wooley, Paul H

    2015-04-01

    We conducted a study to evaluate biomechanical performance during destructive testing of several different suture materials in various arthroscopic knot configurations under both in vitro and in situ conditions. Surgeons of different levels of experience tied the knots. Three different arthroscopic knots (static surgeon's, Weston, Tennessee slider) with 3 reverse half-hitches on alternating posts were tested using Fiberwire, ForceFiber, Orthocord, and Ultrabraid suture materials under both in vitro and in situ (blood plasma at 37°C) conditions. Three surgeons of different experience levels tied the knots on a post 30 mm in circumference. A single load-to-failure test was performed. There were no significant in vitro-in situ differences for Ultrabraid in the different knot configurations or with the different experience levels. Surgeon B (intermediate experience) showed no significant differences between test conditions for any knot configuration or suture material. With Tennessee slider knots, surgeon C (least experience) showed significantly lower clinical failure load under both test conditions and had a higher percentage of complete knot slippage. Surgeon B had no knot slippage with use of Fiberwire. Both the aqueous environment and the surgeon's familiarity with certain knots have an effect on knot security. PMID:25844588

  17. Energy landscape and multiroute folding of topologically complex proteins adenylate kinase and 2ouf-knot.

    PubMed

    Li, Wenfei; Terakawa, Tsuyoshi; Wang, Wei; Takada, Shoji

    2012-10-30

    While fast folding of small proteins has been relatively well characterized by experiments and theories, much less is known for slow folding of larger proteins, for which recent experiments suggested quite complex and rich folding behaviors. Here, we address how the energy landscape theory can be applied to these slow folding reactions. Combining the perfect-funnel approximation with a multiscale method, we first extended our previous atomic-interaction based coarse grained (AICG) model to take into account local flexibility of protein molecules. Using this model, we then investigated the energy landscapes and folding routes of two proteins with complex topologies: a multidomain protein adenylate kinase (AKE) and a knotted protein 2ouf-knot. In the AKE folding, consistent with experimental results, the kinetic free energy surface showed several substates between the fully unfolded and native states. We characterized the structural features of these substates and transitions among them, finding temperature-dependent multiroute folding. For protein 2ouf-knot, we found that the improved atomic-interaction based coarse-grained model can spontaneously tie a knot and fold the protein with a probability up to 96%. The computed folding rate of the knotted protein was much slower than that of its unknotted counterpart, in agreement with experimental findings. Similar to the AKE case, the 2ouf-knot folding exhibited several substates and transitions among them. Interestingly, we found a dead-end substate that lacks the knot, thus suggesting backtracking mechanisms. PMID:22753508

  18. Effects of horseshoe crab harvest in delaware bay on red knots: Are harvest restrictions working?

    USGS Publications Warehouse

    Niles, L.J.; Bart, J.; Sitters, H.P.; Dey, A.D.; Clark, K.E.; Atkinson, P.W.; Baker, A.J.; Bennett, K.A.; Kalasz, K.S.; Clark, N.A.; Clark, J.; Gillings, S.; Gates, A.S.; Gonzalez, P.M.; Hernandez, D.E.; Minton, C.D.T.; Morrison, R.I.G.; Porter, R.R.; Ross, R.K.; Veitch, C.R.

    2009-01-01

    Each May, red knots (Calidris canutus rufa) congregate in Delaware Bay during their northward migration to feed on horseshoe crab eggs (Limulus polyphemus) and refuel for breeding in the Arctic. During the 1990s, the Delaware Bay harvest of horseshoe crabs for bait increased 10-fold, leading to a more than 90% decline in the availability of their eggs for knots. The proportion of knots achieving weights of more than 180 grams by 26-28 May, their main departure period, dropped from 0.6-0.8 to 0.14-0.4 over 1997-2007. During the same period, the red knot population stopping in Delaware Bay declined by more than 75%, in part because the annual survival rate of adult knots wintering in Tierra del Fuego declined. Despite restrictions, the 2007 horseshoe crab harvest was still greater than the 1990 harvest, and no recovery of knots was detectable. We propose an adaptive management strategy with recovery goals and annual monitoring that, if adopted, will both allow red knot and horseshoe crab populations to recover and permit a sustainable harvest of horseshoe crabs.

  19. Slipknotting upon native-like loop formation in a trefoil knot protein.

    PubMed

    Noel, Jeffrey K; Sułkowska, Joanna I; Onuchic, José N

    2010-08-31

    Protein knots and slipknots, mostly regarded as intriguing oddities, are gradually being recognized as significant structural motifs. Recent experimental results show that knotting, starting from a fully extended polypeptide, has not yet been observed. Understanding the nucleation process of folding knots is thus a natural challenge for both experimental and theoretical investigation. In this study, we employ energy landscape theory and molecular dynamics to elucidate the entire folding mechanism. The full free energy landscape of a knotted protein is mapped using an all-atom structure-based protein model. Results show that, due to the topological constraint, the protein folds through a three-state mechanism that contains (i) a precise nucleation site that creates a correctly twisted native loop (first barrier) and (ii) a rate-limiting free energy barrier that is traversed by two parallel knot-forming routes. The main route corresponds to a slipknot conformation, a collapsed configuration where the C-terminal helix adopts a hairpin-like configuration while threading, and the minor route to an entropically limited plug motion, where the extended terminus is threaded as through a needle. Knot formation is a late transition state process and results show that random (nonspecific) knots are a very rare and unstable set of configurations both at and below folding temperature. Our study shows that a native-biased landscape is sufficient to fold complex topologies and presents a folding mechanism generalizable to all known knotted protein topologies: knotting via threading a native-like loop in a preordered intermediate. PMID:20702769

  20. Multiple folding pathways of proteins with shallow knots and co-translational folding

    NASA Astrophysics Data System (ADS)

    Chwastyk, Mateusz; Cieplak, Marek

    2015-07-01

    We study the folding process in the shallowly knotted protein MJ0366 within two variants of a structure-based model. We observe that the resulting topological pathways are much richer than identified in previous studies. In addition to the single knot-loop events, we find novel, and dominant, two-loop mechanisms. We demonstrate that folding takes place in a range of temperatures and the conditions of most successful folding are at temperatures which are higher than those required for the fastest folding. We also demonstrate that nascent conditions are more favorable to knotting than off-ribosome folding.

  1. Multiple folding pathways of proteins with shallow knots and co-translational folding.

    PubMed

    Chwastyk, Mateusz; Cieplak, Marek

    2015-07-28

    We study the folding process in the shallowly knotted protein MJ0366 within two variants of a structure-based model. We observe that the resulting topological pathways are much richer than identified in previous studies. In addition to the single knot-loop events, we find novel, and dominant, two-loop mechanisms. We demonstrate that folding takes place in a range of temperatures and the conditions of most successful folding are at temperatures which are higher than those required for the fastest folding. We also demonstrate that nascent conditions are more favorable to knotting than off-ribosome folding. PMID:26233164

  2. Ball lightning as a force-free magnetic knot

    PubMed

    Ranada; Soler; Trueba

    2000-11-01

    The stability of fireballs in a recent model of ball lightning is studied. It is shown that the balls shine while relaxing in an almost quiescent expansion, and that three effects contribute to their stability: (i) the formation in each one during a process of Taylor relaxation of a force-free magnetic field, a concept introduced in 1954 in order to explain the existence of large magnetic fields and currents in stable configurations of astrophysical plasmas; (ii) the so called Alfven conditions in magnetohydrodynamics; and (iii) the approximate conservation of the helicity integral. The force-free fields that appear are termed "knots" because their magnetic lines are closed and linked. PMID:11102074

  3. Effusive molecular beam-sampled Knudsen flow reactor coupled to vacuum ultraviolet single photon ionization mass spectrometry using an external free radical source

    SciTech Connect

    Leplat, N.; Rossi, M. J.

    2013-11-15

    A new apparatus using vacuum ultraviolet single photon ionization mass spectrometry (VUV SPIMS) of an effusive molecular beam emanating from a Knudsen flow reactor is described. It was designed to study free radical-molecule kinetics over a significant temperature range (300–630 K). Its salient features are: (1) external free radical source, (2) counterpropagating molecular beam and diffuse VUV photon beam meeting in a crossed-beam ion source of a quadrupole mass spectrometer with perpendicular ion extraction, (3) analog detection of the photocurrent of the free radical molecular cation, and (4) possibility of detecting both free radicals and closed shell species in the same apparatus and under identical reaction conditions owing to the presence of photoelectrons generated by the photoelectric effect of the used VUV-photons. The measured thermal molecular beam-to-background ratio was 6.35 ± 0.39 for Ar and 10.86 ± 1.59 for i-C{sub 4}H{sub 10} at 300 K, a factor of 2.52 and 1.50 smaller, respectively, than predicted from basic gas-dynamic considerations. Operating parameters as well as the performance of key elements of the instrument are presented and discussed. Coupled to an external free radical source a steady-state specific exit flow of 1.6 × 10{sup 11} and 5.0 × 10{sup 11} molecule s{sup −1} cm{sup −3} of C{sub 2}H{sub 5}{sup •} (ethyl) and t-C{sub 4}H{sub 9}{sup •} (t-butyl) free radicals have been detected using VUV SPIMS at their molecular ion m/z 29 and 57, respectively, at 300 K.

  4. An experimental study on the oxidative coupling of methane in a direct current corona discharge reactor over Sr/La{sub 2}O{sub 3} catalyst

    SciTech Connect

    Marafee, A.; Liu, C.; Xu, G.; Mallinson, R.; Lobban, L.

    1997-03-01

    The homogeneous and catalytic oxidative coupling of methane (OCM) for converting methane directly into higher hydrocarbons has been the subject of a large body of research. The present study on conversion of methane in dc corona discharge packed bed reactors may significantly improve the process economics. Experimental investigations have been conducted in which all the reactive gases pass through a catalyst bed which is situated within the corona-induced plasma zone. In this study, a typical OCM catalyst, Sr/La{sub 2}O{sub 3}, was used to investigate experimentally the corona discharge OCM reactions. Experiments were conducted over a wide range of temperatures (823--1,023 K) and input powers (0--6 W) with both positive and negative corona processes. Compared to the catalytic process in the absence of corona discharge, the corona discharge results in higher methane conversion and larger yield of C{sub 2} products even at temperatures at which there is no C{sub 2} activity for the catalyst alone. The methane conversion and C{sub 2} yield increase with O{sub 2} partial pressure during the corona-enhanced catalytic reactions, while the selectivity decreases slightly with increasing O{sub 2} partial pressure. Compared to results obtained in the absence of corona discharges, methane conversion in the presence of the dc corona was nearly five times larger and the selectivity for C{sub 2} over eight times higher at 853 K. A great enhancement in catalytic activity has also been achieved at a temperature at which the catalyst alone shows no C{sub 2} activity. The conversion at higher temperature (more than 953 K) is limited by the poor corona performance and the availability of active oxygen species.

  5. Effusive molecular beam-sampled Knudsen flow reactor coupled to vacuum ultraviolet single photon ionization mass spectrometry using an external free radical source.

    PubMed

    Leplat, N; Rossi, M J

    2013-11-01

    A new apparatus using vacuum ultraviolet single photon ionization mass spectrometry (VUV SPIMS) of an effusive molecular beam emanating from a Knudsen flow reactor is described. It was designed to study free radical-molecule kinetics over a significant temperature range (300-630 K). Its salient features are: (1) external free radical source, (2) counterpropagating molecular beam and diffuse VUV photon beam meeting in a crossed-beam ion source of a quadrupole mass spectrometer with perpendicular ion extraction, (3) analog detection of the photocurrent of the free radical molecular cation, and (4) possibility of detecting both free radicals and closed shell species in the same apparatus and under identical reaction conditions owing to the presence of photoelectrons generated by the photoelectric effect of the used VUV-photons. The measured thermal molecular beam-to-background ratio was 6.35 ± 0.39 for Ar and 10.86 ± 1.59 for i-C4H10 at 300 K, a factor of 2.52 and 1.50 smaller, respectively, than predicted from basic gas-dynamic considerations. Operating parameters as well as the performance of key elements of the instrument are presented and discussed. Coupled to an external free radical source a steady-state specific exit flow of 1.6 × 10(11) and 5.0 × 10(11) molecule s(-1) cm(-3) of C2H5(●) (ethyl) and t-C4H9(●) (t-butyl) free radicals have been detected using VUV SPIMS at their molecular ion m/z 29 and 57, respectively, at 300 K. PMID:24289411

  6. Ileoileal Knot as a Content of Obstructed Hernia: What Are the Odds?

    PubMed Central

    Gopivallabh, Madhusudhan Madihalli; Jaganmaya, Kajekar; Hanumanthaiah, Kunthurdoddi Sanjeevaiah; Babannavar, Prashantha; Crithic, Vilas

    2016-01-01

    An obstructed inguinal hernia is a common surgical emergency, which presents with a variety of contents like the small intestine, omentum, and colon. Intestinal knotting is a rare entity encountered in surgical practice; it occurs when one coil of intestine wraps around the other and eventually leads to complications such as intestinal obstruction, ischemia, and gangrene. Both conditions are considered surgical emergencies and should be dealt with through appropriate surgical measures forthwith. We report the case of an obstructed inguinal hernia, which, on exploration, showed an ileoileal knot as its content. Ileoileal knotting is a very rare phenomenon and, to the best of our knowledge, such an ileoileal knot as a content of obstructed inguinal hernia has not been reported in the surgical literature so far. PMID:27175047

  7. Syncytial knots and intervillous bridges in the human placenta: an ultrastructural study.

    PubMed

    Jones, C J; Fox, H

    1977-11-01

    An electron microscopic study has shown that the syncytial knots of the villi of the human placenta contain aggregated nuclei which exhibit marked degenerative changes; within the cytoplasm there is an abundance of cytoplasmic filaments and many stacks of annulate lamellae. It is suggested that syncytial knots are a sequestration phenomenon in which senescent nuclear material is aggregated and removed from metabolically active areas of the syncytiotrophoblast. Intervillous bridges appear to be formed chiefly by fusion of syncytial knots from adjacent villi, and it seems reasonable that the effete material in a syncytial knot should be used for this purpose. The intervillous bridges hava a fine structure which suggests that they have a mechanical function, and this lends support to the theory that they form an internal strut system within the placenta. PMID:591426

  8. New conformational search method using genetic algorithm and knot theory for proteins.

    PubMed

    Sakae, Y; Hiroyasu, T; Miki, M; Okamoto, Y

    2011-01-01

    We have proposed a parallel simulated annealing using genetic crossover as one of powerful conformational search methods, in order to find the global minimum energy structures for protein systems. The simulated annealing using genetic crossover method, which incorporates the attractive features of the simulated annealing and the genetic algorithm, is useful for finding a minimum potential energy conformation of protein systems. However, when we perform simulations by using this method, we often find obviously unnatural stable conformations, which have "knots" of a string of an amino-acid sequence. Therefore, we combined knot theory with our simulated annealing using genetic crossover method in order to avoid the knot conformations from the conformational search space. We applied this improved method to protein G, which has 56 amino acids. As the result, we could perform the simulations, which avoid knot conformations. PMID:21121049

  9. Folding of small knotted proteins: Insights from a mean field coarse-grained model

    SciTech Connect

    Najafi, Saeed; Potestio, Raffaello

    2015-12-28

    A small but relevant number of proteins whose native structure is known features nontrivial topology, i.e., they are knotted. Understanding the process of folding from a swollen unknotted state to the biologically relevant native conformation is, for these proteins, particularly difficult, due to their rate-limiting topological entanglement. To shed some light into this conundrum, we introduced a structure-based coarse-grained model of the protein, where the information about the folded conformation is encoded in bonded angular interactions only, which do not favor the formation of native contacts. A stochastic search scheme in parameter space is employed to identify a set of interactions that maximizes the probability to attain the knotted state. The optimal knotting pathways of the two smallest knotted proteins, obtained through this approach, are consistent with the results derived by means of coarse-grained as well as full atomistic simulations.

  10. Tightening slip knots in raw and degummed silk to increase toughness without losing strength.

    PubMed

    Pantano, Maria F; Berardo, Alice; Pugno, Nicola M

    2016-01-01

    Knots are fascinating topological elements, which can be found in both natural and artificial systems. While in most of the cases, knots cannot be loosened without breaking the strand where they are tightened, herein, attention is focused on slip or running knots, which on the contrary can be unfastened without compromising the structural integrity of their hosting material. Two different topologies are considered, involving opposite unfastening mechanisms, and their influence on the mechanical properties of natural fibers, as silkworm silk raw and degummed single fibers, is investigated and quantified. Slip knots with optimized shape and size result in a significant enhancement of fibers energy dissipation capability, up to 300-400%, without affecting their load bearing capacity. PMID:26868855

  11. Tightening slip knots in raw and degummed silk to increase toughness without losing strength

    NASA Astrophysics Data System (ADS)

    Pantano, Maria F.; Berardo, Alice; Pugno, Nicola M.

    2016-02-01

    Knots are fascinating topological elements, which can be found in both natural and artificial systems. While in most of the cases, knots cannot be loosened without breaking the strand where they are tightened, herein, attention is focused on slip or running knots, which on the contrary can be unfastened without compromising the structural integrity of their hosting material. Two different topologies are considered, involving opposite unfastening mechanisms, and their influence on the mechanical properties of natural fibers, as silkworm silk raw and degummed single fibers, is investigated and quantified. Slip knots with optimized shape and size result in a significant enhancement of fibers energy dissipation capability, up to 300-400%, without affecting their load bearing capacity.

  12. Tightening slip knots in raw and degummed silk to increase toughness without losing strength

    PubMed Central

    Pantano, Maria F.; Berardo, Alice; Pugno, Nicola M.

    2016-01-01

    Knots are fascinating topological elements, which can be found in both natural and artificial systems. While in most of the cases, knots cannot be loosened without breaking the strand where they are tightened, herein, attention is focused on slip or running knots, which on the contrary can be unfastened without compromising the structural integrity of their hosting material. Two different topologies are considered, involving opposite unfastening mechanisms, and their influence on the mechanical properties of natural fibers, as silkworm silk raw and degummed single fibers, is investigated and quantified. Slip knots with optimized shape and size result in a significant enhancement of fibers energy dissipation capability, up to 300–400%, without affecting their load bearing capacity. PMID:26868855

  13. Management of root-knot nematode (Meloidogyne incognita) in bottle gourd using different botanicals in pots.

    PubMed

    Singh, Tulika; Patel, B A

    2015-09-01

    A pot experiment was conducted to study the efficacy of different botanicals in varying doses for management of root-knot nematode, M. incognita in bottle gourd. The results exhibited that madar (Calotropis procera) and neem (Azadirachta indica) leaves application proved to be more effective in improving plant growth characters and reducing root-knot index and final nematode population. Among the doses tested, higher dose of 1.5 % (w/w) was more effective than lower ones. PMID:26345048

  14. Tightening the knot in phytochrome by single-molecule atomic force microscopy.

    PubMed

    Bornschlögl, Thomas; Anstrom, David M; Mey, Elisabeth; Dzubiella, Joachim; Rief, Matthias; Forest, Katrina T

    2009-02-18

    A growing number of proteins have been shown to adopt knotted folds. Yet the biological roles and biophysical properties of these knots remain poorly understood. We used protein engineering and atomic force microscopy to explore the single-molecule mechanics of the figure-eight knot in the chromophore-binding domain of the red/far-red photoreceptor, phytochrome. Under load, apo phytochrome unfolds at forces of approximately 47 pN, whereas phytochrome carrying its covalently bound tetrapyrrole chromophore unfolds at approximately 73 pN. These forces are not unusual in mechanical protein unfolding, and thus the presence of the knot does not automatically indicate a superstable protein. Our experiments reveal a stable intermediate along the mechanical unfolding pathway, reflecting the sequential unfolding of two distinct subdomains in phytochrome, potentially the GAF and PAS domains. For the first time (to the best of our knowledge), our experiments allow a direct determination of knot size under load. In the unfolded chain, the tightened knot is reduced to 17 amino acids, resulting in apparent shortening of the polypeptide chain by 6.2 nm. Steered molecular-dynamics simulations corroborate this number. Finally, we find that covalent phytochrome dimers created for these experiments retain characteristic photoreversibility, unexpectedly arguing against a dramatic rearrangement of the native GAF dimer interface upon photoconversion. PMID:19217867

  15. Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field

    PubMed Central

    a Beccara, Silvio; Škrbić, Tatjana; Covino, Roberto; Micheletti, Cristian; Faccioli, Pietro

    2013-01-01

    We report on atomistic simulation of the folding of a natively-knotted protein, MJ0366, based on a realistic force field. To the best of our knowledge this is the first reported effort where a realistic force field is used to investigate the folding pathways of a protein with complex native topology. By using the dominant-reaction pathway scheme we collected about 30 successful folding trajectories for the 82-amino acid long trefoil-knotted protein. Despite the dissimilarity of their initial unfolded configuration, these trajectories reach the natively-knotted state through a remarkably similar succession of steps. In particular it is found that knotting occurs essentially through a threading mechanism, involving the passage of the C-terminal through an open region created by the formation of the native -sheet at an earlier stage. The dominance of the knotting by threading mechanism is not observed in MJ0366 folding simulations using simplified, native-centric models. This points to a previously underappreciated role of concerted amino acid interactions, including non-native ones, in aiding the appropriate order of contact formation to achieve knotting. PMID:23555232

  16. Spatial Distributions of Electron, CF, and CF2 Radical Densities and Gas Temperature in DC-Superposed Dual-Frequency Capacitively Coupled Plasma Etch Reactor Employing Cyclic-C4F8/N2/Ar Gas

    NASA Astrophysics Data System (ADS)

    Yamaguchi, Tsuyoshi; Kimura, Tetsuya; Koshimizu, Chishio; Takeda, Keigo; Kondo, Hiroki; Ishikawa, Kenji; Sekine, Makoto; Hori, Masaru

    2011-05-01

    On a plasma etch reactor for a wafer of 300 mm in diameter, the spatial distributions of the absolute densities of CF and CF2 radicals, electron density (ne), and the gas temperature (Tg) of N2 were measured employing the dual frequency of negative dc voltage superposed to a very high frequency (VHF) of 60 MHz capacitively coupled plasma (DS-2f-CCP) with the cyclic- (c-)C4F8/Ar/N2 gas mixture. The dc bias was superposed on the upper electrode with a frequency of 60 MHz. The distributions of electron and radical densities were uniform within a diameter of about 260 mm, and took a monotonic decay in regions outside a diameter of 260 mm on the reactor for 300 mm wafers in the reactor. It was found that only CF2 density at the radial position between 150 and 180 mm, corresponding to the position of the Si focus ring, dropped, while CF density took a uniform distribution over a diameter of 260 mm. Additionally, at this position, the rotational temperature of N2 gas increased to be 100 K larger than that at the center position. CF2 radical density was markedly affected by the modified surface loss probability of the material owing to coupling with surface temperature.

  17. Development of a plant dynamics computer code for analysis of a supercritical carbon dioxide Brayton cycle energy converter coupled to a natural circulation lead-cooled fast reactor.

    SciTech Connect

    Moisseytsev, A.; Sienicki, J. J.

    2007-03-08

    STAR-LM is a lead-cooled pool-type fast reactor concept operating under natural circulation of the coolant. The reactor core power is 400 MWt. The open-lattice core consists of fuel pins attached to the core support plate, (the does not consist of removable fuel assemblies). The coolant flows outside of the fuel pins. The fuel is transuranic nitride, fabricated from reprocessed LWR spent fuel. The cladding material is HT-9 stainless steel; the steady-state peak cladding temperature is 650 C. The coolant is single-phase liquid lead under atmospheric pressure; the core inlet and outlet temperatures are 438 C and 578 C, respectively. (The Pb coolant freezing and boiling temperatures are 327 C and 1749 C, respectively). The coolant is contained inside of a reactor vessel. The vessel material is Type 316 stainless steel. The reactor is autonomous meaning that the reactor power is self-regulated based on inherent reactivity feedbacks and no external power control (through control rods) is utilized. The shutdown (scram) control rods are used for startup and shutdown and to stop the fission reaction in case of an emergency. The heat from the reactor is transferred to the S-CO{sub 2} Brayton cycle in in-reactor heat exchangers (IRHX) located inside the reactor vessel. The IRHXs are shell-and-tube type heat exchangers with lead flowing downwards on the shell side and CO{sub 2} flowing upwards on the tube side. No intermediate circuit is utilized. The guard vessel surrounds the reactor vessel to contain the coolant, in the very unlikely event of reactor vessel failure. The Reactor Vessel Auxiliary Cooling System (RVACS) implementing the natural circulation of air flowing upwards over the guard vessel is used to cool the reactor, in the case of loss of normal heat removal through the IRHXs. The RVACS is always in operation. The gap between the vessels is filled with liquid lead-bismuth eutectic (LBE) to enhance the heat removal by air by significantly reducing the thermal

  18. Evaluation of the effect of 4 types of knots on the mechanical properties of 4 types of suture material used in small animal practice.

    PubMed

    Avoine, Xytilis; Lussier, Bertrand; Brailovski, Vladimir; Inaekyan, Karine; Beauchamp, Guy

    2016-04-01

    The influence of the type of material used, knot configuration, and use of an additional throw on the tensile force at failure, the elongation, and the mode of failure of different configurations of linear sutures and knotted suture loops was evaluated in this in-vitro mechanical study. We hypothesized that all types of knots would significantly influence the initial force and elongation of suture materials and would influence the force and elongation at which the knotted loops break, but not their mode of failure. A total of 432 samples of 4 types of size 3-0 suture material (polydioxanone, polyglecaprone 25, polyglactin 910, and nylon), representing 9 configurations, were tested in a tensiometer. The configurations were 1 linear suture without a knot and the following loops: square (SQ) knot; surgeon's (SU) knot; granny (GR) knot; and sliding half-hitch (SHH) knot using either 4 and 5 or 3 and 4 throws, depending on the material. For polydioxanone, SQ and SU knots did not decrease the initial force at failure of the suture. Granny (GR) and SHH knots decreased the tensile force at failure and elongation by premature failure of the loop. For polyglecaprone 25, all knots decreased the initial force at failure of the suture, with SHH being weaker than the other knots. For coated polyglactin 910, all knots decreased the initial force at failure of the suture and slippage increased significantly compared with the other 3 sutures. The use of SQ knots with 3 throws did not result in a safe knot. For nylon, knots did not alter the original mechanics of the suture. In conclusion, all knots and types of suture material do not necessarily have the same effect on the initial tensile force at failure of suture materials. PMID:27127344

  19. On the correspondence between three nodes W states in quantum network theory and the oriented links in knot theory

    NASA Astrophysics Data System (ADS)

    Gu, Zhi-Yu; Qian, Shang-Wu

    2015-04-01

    The GHZ states and W states are two fundamental types of three qubits quantum entangled states. For finding the knotted pictures of three nodes W states, on the one side, we empty any one node, thus obtaining three degenerated two-node W states, then we find the nonzero submatrix of the corresponding covariance correlation tensor in quantum network theory. On the other side, excepting the linkage 41 corresponding to Bell bases, we conjecture that the another one possible oriented link (which is composed of two-component knots entangled with each other and has four crossings) would be the required knotted pictures of the two nodes W states, thence obtain the nonzero submatrix of the Alexander relation matrix in the theory of knot crystals for these knotted pictures. The equality of the two nonzero submatrices of different kinds thus verify the exactness of our conjecture. The superposition of three knotted pictures of two-node W states from different choices of the emptied node gives the knotted pictures of three-node W states, thus shows the correspondence between three-node W states in quantum network theory and the oriented links in knot theory. Finally we point out that there is an intimate and simple relationship between the knotted pictures of GHZ states and W states.

  20. Optical vortex knots - one photon at a time.

    PubMed

    Tempone-Wiltshire, Sebastien J; Johnstone, Shaun P; Helmerson, Kristian

    2016-01-01

    Feynman described the double slit experiment as "a phenomenon which is impossible, absolutely impossible, to explain in any classical way and which has in it the heart of quantum mechanics". The double-slit experiment, performed one photon at a time, dramatically demonstrates the particle-wave duality of quantum objects by generating a fringe pattern corresponding to the interference of light (a wave phenomenon) from two slits, even when there is only one photon (a particle) at a time passing through the apparatus. The particle-wave duality of light should also apply to complex three dimensional optical fields formed by multi-path interference, however, this has not been demonstrated. Here we observe particle-wave duality of a three dimensional field by generating a trefoil optical vortex knot - one photon at a time. This result demonstrates a fundamental physical principle, that particle-wave duality implies interference in both space (between spatially distinct modes) and time (through the complex evolution of the superposition of modes), and has implications for topologically entangled single photon states, orbital angular momentum multiplexing and topological quantum computing. PMID:27087642

  1. BRIGHT KNOT APPEARS IN SUPERNOVA 1987A RING

    NASA Technical Reports Server (NTRS)

    2002-01-01

    [RIGHT] - This NASA Hubble Space Telescope Wide Field and Planetary Camera 2 image shows the glowing gas ring around supernova 1987A, as it appeared in 1994. The gas, excited by light from the explosion, has been fading for a decade. [LEFT] - Recent Hubble telescope observations show a brightening knot on the upper right side of the ring. This is the site of a powerful collision between an outward moving blast wave and the innermost parts of the circumstellar ring. The collision heats the gas and has caused it to brighten in recent months. This is likely to be the first sign of a dramatic and violent collision that will take place over the next few years, rejuvenating SN1987A as a powerful source of X-ray and radio emissions. The white sickle-shaped material in the center is the visible part of the shredded star, rushing outward at 3,000 kilometers per second, which is heated by radioactive elements created in the supernova explosion. The bright dot in the lower left is a star, which is the same direction as SN1987A, but is not physically part of the system. Both images were made from separate images taken in blue light, visual light and the narrow emission from glowing hydrogen. Computer image processing techniques were used to enhance details in the ring. Credit: Peter Garnavich (Harvard-Smithsonian Center for Astrophysics), and NASA

  2. The magnetic resonance appearance of surfers' knots: a case report.

    PubMed

    McManus, Luke J; Thomson, Andrew; Whan, Andrew

    2016-09-01

    Athletes are at increased risk of developing soft-tissue lesions of the lower limbs. Although the majority of these will be benign, the differential diagnosis is broad and increasingly, doctors are turning to magnetic resonance imaging (MRI) as a first-line investigation when presented with these sorts of lesions, both to narrow the differential diagnosis and exclude malignancy. We report the case of a 28-year-old Caucasian man who presented with 2 soft-tissue lesions of the right foot. History and examination of the nodules fitted with a diagnosis of surfers' knots, an unusual form of acquired, benign, connective tissue nodule that may appear over the tibial tuberosities, dorsum of the feet, and occasionally on the chest of surfers in association with repetitive microtrauma during surfing. MRI findings were consistent with this diagnosis with both lesions exhibiting T1 hypointensity and speckled T2 hypointensity with no significant blooming artifact on gradient echo imaging. When imaged with gadolinium, they demonstrated only mild contrast enhancement. MRI is a valuable tool when investigating athletes with soft-tissue lesions over the lower limbs where the possibility of malignancy must be addressed. In selected cases, MRI may be sufficient to permit a conservative approach to the management of these patients. PMID:27594950

  3. Optical vortex knots – one photon at a time

    NASA Astrophysics Data System (ADS)

    Tempone-Wiltshire, Sebastien J.; Johnstone, Shaun P.; Helmerson, Kristian

    2016-04-01

    Feynman described the double slit experiment as “a phenomenon which is impossible, absolutely impossible, to explain in any classical way and which has in it the heart of quantum mechanics”. The double-slit experiment, performed one photon at a time, dramatically demonstrates the particle-wave duality of quantum objects by generating a fringe pattern corresponding to the interference of light (a wave phenomenon) from two slits, even when there is only one photon (a particle) at a time passing through the apparatus. The particle-wave duality of light should also apply to complex three dimensional optical fields formed by multi-path interference, however, this has not been demonstrated. Here we observe particle-wave duality of a three dimensional field by generating a trefoil optical vortex knot – one photon at a time. This result demonstrates a fundamental physical principle, that particle-wave duality implies interference in both space (between spatially distinct modes) and time (through the complex evolution of the superposition of modes), and has implications for topologically entangled single photon states, orbital angular momentum multiplexing and topological quantum computing.

  4. Temperature Sensing in Seawater Based on Microfiber Knot Resonator

    PubMed Central

    Yang, Hongjuan; Wang, Shanshan; Wang, Xin; Liao, Yipeng; Wang, Jing

    2014-01-01

    Ocean internal-wave phenomena occur with the variation in seawater vertical temperature, and most internal-wave detections are dependent on the measurement of seawater vertical temperature. A seawater temperature sensor based on a microfiber knot resonator (MKR) is designed theoretically and demonstrated experimentally in this paper. Especially, the dependences of sensing sensitivity on fiber diameter and probing wavelength are studied. Calculated results show that sensing sensitivity increases with the increasing microfiber diameter with the range of 2.30–3.91 μm and increases with the increasing probing wavelength, which reach good agreement with results obtained by experiments. By choosing the appropriate parameters, the maximum sensitivity measured can reach to be 22.81 pm/°C. The seawater temperature sensor demonstrated here shows advantages of small size, high sensitivity, easy fabrication, and easy integration with fiber systems, which may offer a new optical method to detect temperature of seawater or ocean internal-wave phenomenon and offer valuable reference for assembling micro sensors used for other parameters related to seawater, such as salinity, refractive index, concentration of NO3− and so on. PMID:25299951

  5. Novel Inhibitor Cystine Knot Peptides from Momordica charantia

    PubMed Central

    Clark, Richard J.; Tang, Jun; Zeng, Guang-Zhi; Franco, Octavio L.; Cantacessi, Cinzia; Craik, David J.; Daly, Norelle L.; Tan, Ning-Hua

    2013-01-01

    Two new peptides, MCh-1 and MCh-2, along with three known trypsin inhibitors (MCTI-I, MCTI-II and MCTI-III), were isolated from the seeds of the tropical vine Momordica charantia. The sequences of the peptides were determined using mass spectrometry and NMR spectroscopy. Using a strategy involving partial reduction and stepwise alkylation of the peptides, followed by enzymatic digestion and tandem mass spectrometry sequencing, the disulfide connectivity of MCh-1 was elucidated to be CysI-CysIV, CysII-CysV and CysIII-CysVI. The three-dimensional structures of MCh-1 and MCh-2 were determined using NMR spectroscopy and found to contain the inhibitor cystine knot (ICK) motif. The sequences of the novel peptides differ significantly from peptides previously isolated from this plant. Therefore, this study expands the known peptide diversity in M. charantia and the range of sequences that can be accommodated by the ICK motif. Furthermore, we show that a stable two-disulfide intermediate is involved in the oxidative folding of MCh-1. This disulfide intermediate is structurally homologous to the proposed ancestral fold of ICK peptides, and provides a possible pathway for the evolution of this structural motif, which is highly prevalent in nature. PMID:24116036

  6. Feedback in clinical education: untying the Gordian knot.

    PubMed

    Weinstein, Debra F

    2015-05-01

    Feedback is essential to clinical education, especially in the era of competencies, milestones, and entrustable professional activities. It is, however, an area where medical educators often fall short. Although educational leaders and faculty supervisors provide feedback in a variety of clinical settings, surveys show important gaps in medical student and resident satisfaction with the feedback received, suggesting lost opportunities to identify performance problems as well as to help each learner reach his or her greatest potential.In this issue of Academic Medicine, Telio and colleagues extend the empirically validated concept of a "therapeutic alliance" to propose the "educational alliance" as a framework for enhancing feedback in medical education. They highlight the importance of source credibility, which depends on the teacher-learner relationship and alignment of values, the teacher's understanding of the learner's role and goals, the teacher's direct observation of the learner, and the learner's perception of the teacher's good intentions. The author of this Commentary suggests that the educational alliance framework should prompt medical educators to reconsider feedback and explore opportunities for optimizing it. Most medical schools and graduate medical education programs are not designed in a way that supports the education alliance model, but the Commentary author offers suggestions for cultivating educational alliances, including rethinking supervisor selection criteria. Such interventions should be combined with ongoing faculty development and efforts to improve coaching and mentoring for students, residents, and fellows. Untying the Gordian knot of effective feedback will require innovative approaches, exchange of successful strategies, and continued research. PMID:25406602

  7. Optical vortex knots – one photon at a time

    PubMed Central

    Tempone-Wiltshire, Sebastien J.; Johnstone, Shaun P.; Helmerson, Kristian

    2016-01-01

    Feynman described the double slit experiment as “a phenomenon which is impossible, absolutely impossible, to explain in any classical way and which has in it the heart of quantum mechanics”. The double-slit experiment, performed one photon at a time, dramatically demonstrates the particle-wave duality of quantum objects by generating a fringe pattern corresponding to the interference of light (a wave phenomenon) from two slits, even when there is only one photon (a particle) at a time passing through the apparatus. The particle-wave duality of light should also apply to complex three dimensional optical fields formed by multi-path interference, however, this has not been demonstrated. Here we observe particle-wave duality of a three dimensional field by generating a trefoil optical vortex knot – one photon at a time. This result demonstrates a fundamental physical principle, that particle-wave duality implies interference in both space (between spatially distinct modes) and time (through the complex evolution of the superposition of modes), and has implications for topologically entangled single photon states, orbital angular momentum multiplexing and topological quantum computing. PMID:27087642

  8. Induction of Tolerance to Root-Knot Nematode by Oxycom

    PubMed Central

    Anwar, Safdar A.; McKenry, M. V.; Yang, Kwang-Yeol; Anderson, A. J.

    2003-01-01

    Oxycom applications increased plant growth and population levels of Meloidogyne incognita on susceptible tomato. A single Oxycom drench at 2,500 ppm applied 7 days prior to inoculation with M. incognita provided remediation of plant growth measured 63 days later. This occurred without reducing nematode population levels. Follow-up drenches at 2,500 ppm at 10-day intervals stunted shoots and roots (P = 0.05). The same application rates at 20-day intervals did not reduce plant growth. Plants receiving multiple drenches had more galls (P = 0.05), females, and second-stage juveniles (J2) per root system compared to plants receiving only the single treatment. Foliar mass and height of plants treated with a single pre-inoculation Oxycom drench were indistinguishable from plants without nematodes. Oxycom treatments activated signaling pathways for plant defense as confirmed by detection of elevated defense gene transcripts in root tissues. The finding of increased reproduction of root-knot nematode without loss of plant growth is consistent with the definition of induced tolerance. Frequency, rate, and timing of applications need further study with other nematodes and various field settings. PMID:19262766

  9. Characterization of the Inner Knot of the Crab: The Site of the Gamma-Ray Flares?

    NASA Astrophysics Data System (ADS)

    Rudy, Alexander; Horns, Dieter; DeLuca, Andrea; Kolodziejczak, Jeffery; Tennant, Allyn; Yuan, Yajie; Buehler, Rolf; Arons, Jonathon; Blandford, Roger; Caraveo, Patrizia; Costa, Enrico; Funk, Stephan; Hays, Elizabeth; Lobanov, Andrei; Max, Claire; Mayer, Michael; Mignani, Roberto; O'Dell, Stephen L.; Romani, Roger; Tavani, Marco; Weisskopf, Martin C.

    2015-09-01

    A particularly intriguing recent result from γ-ray astronomy missions is the detection of powerful flares from the Crab Nebula, which challenges the current understanding of pulsar wind nebulae and acceleration mechanisms. To search for the production site(s) of these flares, we conducted a multi-wavelength observing campaign using Keck, the Hubble Space Telescope (HST), and the Chandra X-ray Observatory. As the short timescales of the γ-ray flares (≲ 1 day) suggest a small emitting region, the Crab’s inner knot (about 0.6 arcsec from the pulsar) is a candidate site for such flaring. This paper describes observations of the inner knot, seeking to understand its nature and possible relationship with γ-ray flares. Using singular-value decomposition, analysis of the HST images yielded results consistent with traditional methods while substantially reducing some uncertainties. These analyses show that the knot’s intrinsic properties (especially size and brightness) are correlated with its (projected) separation from the pulsar. This characterization of the inner knot helps in constraining standard shock model parameters, under the assumption that the knot lies near the shocked surface. While the standard shock model gives good agreement in several respects, two puzzles persist: (a) the observed angular size of the knot relative to the pulsar-knot separation is much smaller than expected; and (b) the variable high degree of polarization (reported by others) is difficult to reconcile with a highly relativistic downstream flow. However, the IR-optical flux of the inner knot is marginally consistent with the shock accelerating most of the Nebula’s optical-emitting particles.

  10. DYNAMICS OF VERTICAL THREADS AND DESCENDING KNOTS IN A HEDGEROW PROMINENCE

    SciTech Connect

    Chae, Jongchul

    2010-05-01

    The existence and behavior of vertical fine structures of plasma-threads and knots-are a significant observational clue to understanding the magnetic structure and dynamics of quiescent prominences on the quiet Sun. Based on the equation of motion in ideal MHD, we reason that the non-hydrostatic support of plasma against gravity in general requires either the motion of plasma with a high value of downward acceleration (dynamical support) or the role of horizontal magnetic fields (magnetic support). By carefully tracking the motion of several bright threads seen in a hedgerow prominence observed by the Solar Optical Telescope aboard Hinode, we confirm that these threads are essentially static and stable, which negates the dynamic support. The application of the Kippenhahn-Schlueter solution suggests that they may be supported by sagged magnetic field lines with a sag angle of about 43{sup 0}. We also track several bright descending knots and find that their descending speeds range from 10 to 30 km s{sup -1}, with a mean value of 16 km s{sup -1}, and their vertical accelerations from -0.10 to 0.10 km s{sup -2}, with a mean of practically zero. This finding suggests that these knots are basically supported by horizontal magnetic fields against gravity even when they descend, and the complex variations of their descending speeds should be attributed to small imbalances between gravity and the force of magnetic tension. Furthermore, some knots are observed to impulsively get accelerated downward from time to time. We conjecture that these impulsive accelerations are a result of magnetic reconnection and the subsequent interchange of magnetic configuration between a knot and its surrounding structure. It is proposed that this process of reconnection and interchange not only initiates the descending motion of the knots, but also allows knots to keep falling long distance through the medium permeated by horizontal magnetic fields.

  11. Knots in rings. The circular knotted protein Momordica cochinchinensis trypsin inhibitor-II folds via a stable two-disulfide intermediate.

    PubMed

    Cemazar, Masa; Daly, Norelle L; Häggblad, Sara; Lo, Kai Pong; Yulyaningsih, Ernie; Craik, David J

    2006-03-24

    The aim of this work was to elucidate the oxidative folding mechanism of the macrocyclic cystine knot protein MCoTI-II. We aimed to investigate how the six-cysteine residues distributed on the circular backbone of the reduced unfolded peptide recognize their correct partner and join up to form a complex cystine-knotted topology. To answer this question, we studied the oxidative folding of the naturally occurring peptide using a range of spectroscopic methods. For both oxidative folding and reductive unfolding, the same disulfide intermediate species was prevalent and was characterized to be a native-like two-disulfide intermediate in which the Cys1-Cys18 disulfide bond was absent. Overall, the folding pathway of this head-to-tail cyclized protein was found to be similar to that of linear cystine knot proteins from the squash family of trypsin inhibitors. However, the pathway differs in an important way from that of the cyclotide kalata B1, in that the equivalent two-disulfide intermediate in that case is not a direct precursor of the native protein. The size of the embedded ring within the cystine knot motif appears to play a crucial role in the folding pathway. Larger rings contribute to the independence of disulfides and favor an on-pathway native-like intermediate that has a smaller energy barrier to cross to form the native fold. The fact that macrocyclic proteins are readily able to fold to a complex knotted structure in vitro in the absence of chaperones makes them suitable as protein engineering scaffolds that have remarkable stability. PMID:16547012

  12. Characterization of Optically Selected Star-Forming Knots in (U)LIRGs

    NASA Astrophysics Data System (ADS)

    Miralles-Caballero, Daniel; Colina, Luis; Arribas, Santiago; Duc, Pierre-Alain

    2011-09-01

    We present a comprehensive characterization of the general properties (luminosity functions (LFs), mass, size, ages, etc.) of optically selected compact stellar objects (knots) in a representative sample of 32 low-z luminous and ultraluminous infrared galaxies ((U)LIRGs). It is important to understand the formation and evolution of these properties in such systems, which represent the most extreme cases of starbursts in the low-z universe. We have made use of high angular resolution Advanced Camera for Surveys images from the Hubble Space Telescope in F435W (~B) and F814W (~I) bands. The galaxies in the sample represent different interaction phases (first contact, pre-merger, merger, and post-merger) and cover a wide luminosity range (11.46 <= log (L IR/L sun) <= 12.54). With a median size of 32 pc, most of the nearly 3000 knots detected consist of complexes of star clusters. Some of the knots (~15%) are so blue that their colors indicate a young (i.e., <30 Myr) and almost extinction-free population. There is a clear correlation of the mass of these blue knots with their radius, where MvpropR 1.91 ± 0.14, similar to that found in complexes of clusters in M51 and in giant molecular clouds. This suggests that the star formation within the knots is proportional to the gas density at any given radius. This relation does not depend significantly on either the infrared luminosity of the system or the interaction phase. The star formation of all the knots is characterized by LFs of the knots with slopes close to 2. Nevertheless, we see a marginally significant indication that the LF evolves with the interaction process, becoming steeper from early to advanced merger phases. Due to size-of-sample effects we are probably sampling knots in ULIRGs that intrinsically more luminous (by a factor of about four) than in less luminous systems. They also have sizes and are likely to have masses characteristic of clumps in galaxies at z >~ 1. Knots in post-mergers are on average (1

  13. DNA knots reveal a chiral organization of DNA in phage capsids

    NASA Astrophysics Data System (ADS)

    Arsuaga, Javier; Vazquez, Mariel; McGuirk, Paul; Trigueros, Sonia; Sumners, De Witt; Roca, Joaquim

    2005-06-01

    Icosahedral bacteriophages pack their double-stranded DNA genomes to near-crystalline density and achieve one of the highest levels of DNA condensation found in nature. Despite numerous studies, some essential properties of the packaging geometry of the DNA inside the phage capsid are still unknown. We present a different approach to the problems of randomness and chirality of the packed DNA. We recently showed that most DNA molecules extracted from bacteriophage P4 are highly knotted because of the cyclization of the linear DNA molecule confined in the phage capsid. Here, we show that these knots provide information about the global arrangement of the DNA inside the capsid. First, we analyze the distribution of the viral DNA knots by high-resolution gel electrophoresis. Next, we perform Monte Carlo computer simulations of random knotting for freely jointed polygons confined to spherical volumes. Comparison of the knot distributions obtained by both techniques produces a topological proof of nonrandom packaging of the viral DNA. Moreover, our simulations show that the scarcity of the achiral knot 41 and the predominance of the torus knot 51 over the twist knot 52 observed in the viral distribution of DNA knots cannot be obtained by confinement alone but must include writhe bias in the conformation sampling. These results indicate that the packaging geometry of the DNA inside the viral capsid is writhe-directed. Author contributions: D.W.S. and J.R. designed research; J.A. and J.R. performed research; J.A., M.V., P.M., S.T., and J.R. contributed new reagents/analytic tools; J.A., M.V., P.M., and J.R. analyzed data; and D.W.S. and J.R. wrote the paper.This paper was submitted directly (Track II) to the PNAS office.‡Present address: Department of Mathematics and Center for Computation in the Life Sciences, San Francisco State University, San Francisco, CA 94132.

  14. Multispecies modeling for adaptive management of horseshoe crabs and red knots in the delaware bay

    USGS Publications Warehouse

    McGowan, C.P.; Smith, D.R.; Sweka, J.A.; Martin, J.; Nichols, J.D.; Wong, R.; Lyons, J.E.; Niles, L.J.; Kalasz, K.; Brust, J.; Klopfer, M.; Spear, B.

    2011-01-01

    Adaptive management requires that predictive models be explicit and transparent to improve decisions by comparing management actions, directing further research and monitoring, and facilitating learning. The rufa subspecies of red knots (Calidris canutus rufa), which has recently exhibited steep population declines, relies on horseshoe crab (Limulus polyphemus) eggs as their primary food source during stopover in Delaware Bay during spring migration. We present a model with two different parameterizations for use in the adaptive management of horseshoe crab harvests in the Delaware Bay that links red knot mass gain, annual survival, and fecundity to horseshoe crab dynamics. The models reflect prevailing hypotheses regarding ecological links between these two species. When reported crab harvest from 1998 to 2008 was applied, projections corresponded to the observed red knot population abundances depending on strengths of the demographic relationship between these species. We compared different simulated horseshoe crab harvest strategies to evaluate whether, given this model, horseshoe crab harvest management can affect red knot conservation and found that restricting harvest can benefit red knot populations. Our model is the first to explicitly and quantitatively link these two species and will be used within an adaptive management framework to manage the Delaware Bay system and learn more about the specific nature of the linkage between the two species. ?? 2011 Wiley Periodicals, Inc.

  15. Condensates and instanton - torus knot duality. Hidden Physics at UV scale

    NASA Astrophysics Data System (ADS)

    Gorsky, A.; Milekhin, A.

    2015-11-01

    We establish the duality between the torus knot superpolynomials or the Poincaré polynomials of the Khovanov homology and particular condensates in Ω-deformed 5D supersymmetric QED compactified on a circle with 5d Chern-Simons (CS) term. It is explicitly shown that n-instanton contribution to the condensate of the massless flavor in the background of four-observable exactly coincides with the superpolynomial of the T (n, nk + 1) torus knot where k is the level of CS term. In contrast to the previously known results, the particular torus knot corresponds not to the partition function of the gauge theory but to the particular instanton contribution and summation over the knots has to be performed in order to obtain the complete answer. The instantons are sitting almost at the top of each other and the physics of the "fat point" where the UV degrees of freedom are slaved with point-like instantons turns out to be quite rich. Also we see knot polynomials in the quantum mechanics on the instanton moduli space. We consider the different limits of this correspondence focusing at their physical interpretation and compare the algebraic structures at the both sides of the correspondence. Using the AGT correspondence, we establish a connection between superpolynomials for unknots and q-deformed DOZZ factors.

  16. On Chern-Simons theory with an inhomogeneous gauge group and BF theory knot invariants

    SciTech Connect

    Naot, Gad

    2005-12-15

    We study the Chern-Simons topological quantum field theory with an inhomogeneous gauge group, a non-semi-simple group obtained from a semisimple one by taking its semidirect product with its Lie algebra. We find that the standard knot observable (i.e., trace of the holonomy along the knot) essentially vanishes, and yet, the non-semi-simplicity of the gauge group allows us to consider a class of unorthodox observables which breaks gauge invariance at one point and leads to a nontrivial theory on long knots in R{sup 3}. We have two main morals. (1) In the non-semi-simple case there is more to observe in Chern-Simons theory. There might be other interesting non-semi-simple gauge groups to study in this context beyond our example. (2) In the case of an inhomogeneous gauge group, we find that Chern-Simons theory with the unorthodox observable is actually the same as three-dimensional BF theory with the Cattaneo-Cotta-Ramusino-Martellini knot observable. This leads to a simplification of their results and enables us to generalize and solve a problem they posed regarding the relation between BF theory and the Alexander-Conway polynomial. We prove that the most general knot invariant coming from pure BF topological quantum field theory is in the algebra generated by the coefficients of the Alexander-Conway polynomial.

  17. Multispecies modeling for adaptive management of horseshoe crabs and red knots in the Delaware Bay

    USGS Publications Warehouse

    McGowan, Conor P.; Smith, David; Sweka, John A.; Martin, Julien; Nichols, James D.; Wong, Richard; Lyons, J.E.; Niles, Lawrence J.; Kalasz, Kevin S.; Brust, Jeffrey; Klopfer, Michelle; Spear, Braddock

    2011-01-01

    Adaptive management requires that predictive models be explicit and transparent to improve decisions by comparing management actions, directing further research and monitoring, and facilitating learning. The rufa subspecies of red knots (Calidris canutus rufa), which has recently exhibited steep population declines, relies on horseshoe crab (Limulus polyphemus) eggs as their primary food source during stopover in Delaware Bay during spring migration. We present a model with two different parameterizations for use in the adaptive management of horseshoe crab harvests in the Delaware Bay that links red knot mass gain, annual survival, and fecundity to horseshoe crab dynamics. The models reflect prevailing hypotheses regarding ecological links between these two species. When reported crab harvest from 1998 to 2008 was applied, projections corresponded to the observed red knot population abundances depending on strengths of the demographic relationship between these species. We compared different simulated horseshoe crab harvest strategies to evaluate whether, given this model, horseshoe crab harvest management can affect red knot conservation and found that restricting harvest can benefit red knot populations. Our model is the first to explicitly and quantitatively link these two species and will be used within an adaptive management framework to manage the Delaware Bay system and learn more about the specific nature of the linkage between the two species.

  18. Allotides: Proline-Rich Cystine Knot α-Amylase Inhibitors from Allamanda cathartica.

    PubMed

    Nguyen, Phuong Q T; Luu, Thuy T; Bai, Yang; Nguyen, Giang K T; Pervushin, Konstantin; Tam, James P

    2015-04-24

    Cystine knot α-amylase inhibitors belong to a knottin family of peptidyl inhibitors of 30-32 residues and contain two to four prolines. Thus far, only four members of the group of cystine knot α-amylase inhibitors have been characterized. Herein, the discovery and characterization of five cystine knot α-amylase inhibitors, allotides C1-C5 (Ac1-Ac5) (1-5), from the medicinal plant Allamanda cathartica are reported using both proteomic and genomic methods. Proteomic analysis showed that 1-5 are 30 amino acids in length with three or four proline residues. NMR determination of 4 revealed that it has two cis- and one trans-proline residues and adopts two equally populated conformations in solution. Determination of disulfide connectivity of 2 by differential S-reduction and S-alkylation provided clues of its unfolding process. Genomic analysis showed that allotide precursors contain a three-domain arrangement commonly found in plant cystine knot peptides with conserved residues flanking the processing sites of the mature allotide domain. This work expands the number of known cystine knot α-amylase inhibitors and furthers the understanding of both the structural and biological diversity of this type of knottin family. PMID:25832441

  19. Hemoglobinopathies: slicing the Gordian knot of Plasmodium falciparum malaria pathogenesis.

    PubMed

    Taylor, Steve M; Cerami, Carla; Fairhurst, Rick M

    2013-01-01

    Plasmodium falciparum malaria kills over 500,000 children every year and has been a scourge of humans for millennia. Owing to the co-evolution of humans and P. falciparum parasites, the human genome is imprinted with polymorphisms that not only confer innate resistance to falciparum malaria, but also cause hemoglobinopathies. These genetic traits--including hemoglobin S (HbS), hemoglobin C (HbC), and α-thalassemia--are the most common monogenic human disorders and can confer remarkable degrees of protection from severe, life-threatening falciparum malaria in African children: the risk is reduced 70% by homozygous HbC and 90% by heterozygous HbS (sickle-cell trait). Importantly, this protection is principally present for severe disease and largely absent for P. falciparum infection, suggesting that these hemoglobinopathies specifically neutralize the parasite's in vivo mechanisms of pathogenesis. These hemoglobin variants thus represent a "natural experiment" to identify the cellular and molecular mechanisms by which P. falciparum produces clinical morbidity, which remain partially obscured due to the complexity of interactions between this parasite and its human host. Multiple lines of evidence support a restriction of parasite growth by various hemoglobinopathies, and recent data suggest this phenomenon may result from host microRNA interference with parasite metabolism. Multiple hemoglobinopathies mitigate the pathogenic potential of parasites by interfering with the export of P. falciparum erythrocyte membrane protein 1 (PfEMP1) to the surface of the host red blood cell. Few studies have investigated their effects upon the activation of the innate and adaptive immune systems, although recent murine studies suggest a role for heme oxygenase-1 in protection. Ultimately, the identification of mechanisms of protection and pathogenesis can inform future therapeutics and preventive measures. Hemoglobinopathies slice the "Gordian knot" of host and parasite

  20. Specific microbial attachment to root knot nematodes in suppressive soil.

    PubMed

    Adam, Mohamed; Westphal, Andreas; Hallmann, Johannes; Heuer, Holger

    2014-05-01

    Understanding the interactions of plant-parasitic nematodes with antagonistic soil microbes could provide opportunities for novel crop protection strategies. Three arable soils were investigated for their suppressiveness against the root knot nematode Meloidogyne hapla. For all three soils, M. hapla developed significantly fewer galls, egg masses, and eggs on tomato plants in unsterilized than in sterilized infested soil. Egg numbers were reduced by up to 93%. This suggested suppression by soil microbial communities. The soils significantly differed in the composition of microbial communities and in the suppressiveness to M. hapla. To identify microorganisms interacting with M. hapla in soil, second-stage juveniles (J2) baited in the test soil were cultivation independently analyzed for attached microbes. PCR-denaturing gradient gel electrophoresis of fungal ITS or 16S rRNA genes of bacteria and bacterial groups from nematode and soil samples was performed, and DNA sequences from J2-associated bands were determined. The fingerprints showed many species that were abundant on J2 but not in the surrounding soil, especially in fungal profiles. Fungi associated with J2 from all three soils were related to the genera Davidiella and Rhizophydium, while the genera Eurotium, Ganoderma, and Cylindrocarpon were specific for the most suppressive soil. Among the 20 highly abundant operational taxonomic units of bacteria specific for J2 in suppressive soil, six were closely related to infectious species such as Shigella spp., whereas the most abundant were Malikia spinosa and Rothia amarae, as determined by 16S rRNA amplicon pyrosequencing. In conclusion, a diverse microflora specifically adhered to J2 of M. hapla in soil and presumably affected female fecundity. PMID:24532076

  1. Specific Microbial Attachment to Root Knot Nematodes in Suppressive Soil

    PubMed Central

    Adam, Mohamed; Westphal, Andreas; Hallmann, Johannes

    2014-01-01

    Understanding the interactions of plant-parasitic nematodes with antagonistic soil microbes could provide opportunities for novel crop protection strategies. Three arable soils were investigated for their suppressiveness against the root knot nematode Meloidogyne hapla. For all three soils, M. hapla developed significantly fewer galls, egg masses, and eggs on tomato plants in unsterilized than in sterilized infested soil. Egg numbers were reduced by up to 93%. This suggested suppression by soil microbial communities. The soils significantly differed in the composition of microbial communities and in the suppressiveness to M. hapla. To identify microorganisms interacting with M. hapla in soil, second-stage juveniles (J2) baited in the test soil were cultivation independently analyzed for attached microbes. PCR-denaturing gradient gel electrophoresis of fungal ITS or 16S rRNA genes of bacteria and bacterial groups from nematode and soil samples was performed, and DNA sequences from J2-associated bands were determined. The fingerprints showed many species that were abundant on J2 but not in the surrounding soil, especially in fungal profiles. Fungi associated with J2 from all three soils were related to the genera Davidiella and Rhizophydium, while the genera Eurotium, Ganoderma, and Cylindrocarpon were specific for the most suppressive soil. Among the 20 highly abundant operational taxonomic units of bacteria specific for J2 in suppressive soil, six were closely related to infectious species such as Shigella spp., whereas the most abundant were Malikia spinosa and Rothia amarae, as determined by 16S rRNA amplicon pyrosequencing. In conclusion, a diverse microflora specifically adhered to J2 of M. hapla in soil and presumably affected female fecundity. PMID:24532076

  2. Complete Mapping of a Cystine Knot and Nested Disulfides of Recombinant Human Arylsulfatase A by Multi-Enzyme Digestion and LC-MS Analysis Using CID and ETD

    NASA Astrophysics Data System (ADS)

    Ni, Wenqin; Lin, Melanie; Salinas, Paul; Savickas, Philip; Wu, Shiaw-Lin; Karger, Barry L.

    2013-01-01

    Cystine knots or nested disulfides are structurally difficult to characterize, despite current technological advances in peptide mapping with high-resolution liquid chromatography coupled with mass spectrometry (LC-MS). In the case of recombinant human arylsulfatase A (rhASA), there is one cystine knot at the C-terminal, a pair of nested disulfides at the middle, and two out of three unpaired cysteines in the N-terminal region. The statuses of these cysteines are critical structure attributes for rhASA function and stability that requires precise examination. We used a unique approach to determine the status and linkage of each cysteine in rhASA, which was comprised of multi-enzyme digestion strategies (from Lys-C, trypsin, Asp-N, pepsin, and PNGase F) and multi-fragmentation methods in mass spectrometry using electron transfer dissociation (ETD), collision induced dissociation (CID), and CID with MS3 (after ETD). In addition to generating desired lengths of enzymatic peptides for effective fragmentation, the digestion pH was optimized to minimize the disulfide scrambling. The disulfide linkages, including the cystine knot and a pair of nested cysteines, unpaired cysteines, and the post-translational modification of a cysteine to formylglycine, were all determined. In the assignment, the disulfide linkages were Cys138-Cys154, Cys143-Cys150, Cys282-Cys396, Cys470-Cys482, Cys471-Cys484, and Cys475-Cys481. For the unpaired cysteines, Cys20 and Cys276 were free cysteines, and Cys51 was largely converted to formylglycine (>70 %). A successful methodology has been developed, which can be routinely used to determine these difficult-to-resolve disulfide linkages, ensuring drug function and stability.

  3. Avian influenza virus antibodies in Pacific Coast Red Knots (Calidris canutus rufa)

    USGS Publications Warehouse

    Johnson, James A.; DeCicco, Lucas H.; Ruthrauff, Daniel R.; Krauss, Scott; Hall, Jeffrey S.

    2014-01-01

    Prevalence of avian influenza virus (AIV) antibodies in the western Atlantic subspecies of Red Knot (Calidris canutus rufa) is among the highest for any shorebird. To assess whether the frequency of detection of AIV antibodies is high for the species in general or restricted only to C. c. rufa, we sampled the northeastern Pacific Coast subspecies of Red Knot (Calidris canutus roselaari) breeding in northwestern Alaska. Antibodies were detected in 90% of adults and none of the chicks sampled. Viral shedding was not detected in adults or chicks. These results suggest a predisposition of Red Knots to AIV infection. High antibody titers to subtypes H3 and H4 were detected, whereas low to intermediate antibody levels were found for subtypes H10 and H11. These four subtypes have previously been detected in shorebirds at Delaware Bay (at the border of New Jersey and Delaware) and in waterfowl along the Pacific Coast of North America.

  4. Avian influenza virus antibodies in Pacific Coast Red Knots (Calidris canutus roselaari).

    PubMed

    Johnson, James A; DeCicco, Lucas H; Ruthrauff, Daniel R; Krauss, Scott; Hall, Jeffrey S

    2014-07-01

    Prevalence of avian influenza virus (AIV) antibodies in the western Atlantic subspecies of Red Knot (Calidris canutus rufa) is among the highest for any shorebird. To assess whether the frequency of detection of AIV antibodies is high for the species in general or restricted only to C. c. rufa, we sampled the northeastern Pacific Coast subspecies of Red Knot (Calidris canutus roselaari) breeding in northwestern Alaska. Antibodies were detected in 90% of adults and none of the chicks sampled. Viral shedding was not detected in adults or chicks. These results suggest a predisposition of Red Knots to AIV infection. High antibody titers to subtypes H3 and H4 were detected, whereas low to intermediate antibody levels were found for subtypes H10 and H11. These four subtypes have previously been detected in shorebirds at Delaware Bay (at the border of New Jersey and Delaware) and in waterfowl along the Pacific Coast of North America. PMID:24807362

  5. Slip knots and unfastening topologies enhance toughness without reducing strength of silk fibroin fibres.

    PubMed

    Berardo, Alice; Pantano, Maria F; Pugno, Nicola M

    2016-02-01

    The combination of high strength and high toughness is a desirable feature that structural materials should display. However, while in the past, engineers had to compromise on either strength or toughness depending on the requested application, nowadays, new toughening strategies are available to provide strong materials with high toughness. In this paper, we focus on one of such strategy, which requires no chemical treatment, but the implementation of slip knots with optimized shape and size in the involved material, which is silkworm silk in this case. In particular, a variety of slip knot topologies with different unfastening mechanisms are investigated, including even complex knots usually used in the textile industry, and their efficiency in enhancing toughness of silk fibres is discussed. PMID:26855750

  6. Self-assembling knots of controlled topology by designing the geometry of patchy templates

    NASA Astrophysics Data System (ADS)

    Polles, Guido; Marenduzzo, Davide; Orlandini, Enzo; Micheletti, Cristian

    2015-03-01

    The self-assembly of objects with a set of desired properties is a major goal of material science and physics. A particularly challenging problem is that of self-assembling structures with a target topology. Here we show by computer simulation that one may design the geometry of string-like rigid patchy templates to promote their efficient and reproducible self-assembly into a selected repertoire of non-planar closed folds including several knots. In particular, by controlling the template geometry, we can direct the assembly process so as to strongly favour the formation of constructs tied in trefoil or pentafoil, or even of more exotic torus knots. Polydisperse and racemic mixtures of helical fragments of variable composition add further tunability in the topological self-assembly we discovered. Our results should be relevant to the design of new ways to synthesize molecular knots, which may prove, for instance, to be efficient cargo-carriers due to their mechanical stability.

  7. A cactus-derived toxin-like cystine knot Peptide with selective antimicrobial activity.

    PubMed

    Aboye, Teshome L; Strömstedt, Adam A; Gunasekera, Sunithi; Bruhn, Jan G; El-Seedi, Hesham; Rosengren, K Johan; Göransson, Ulf

    2015-05-01

    Naturally occurring cystine knot peptides show a wide range of biological activity, and as they have inherent stability they represent potential scaffolds for peptide-based drug design and biomolecular engineering. Here we report the discovery, sequencing, chemical synthesis, three-dimensional solution structure determination and bioactivity of the first cystine knot peptide from Cactaceae (cactus) family: Ep-AMP1 from Echinopsis pachanoi. The structure of Ep-AMP1 (35 amino acids) conforms to that of the inhibitor cystine knot (or knottin) family but represents a novel diverse sequence; its activity was more than 500 times higher against bacterial than against eukaryotic cells. Rapid bactericidal action and liposome leakage implicate membrane permeabilisation as the mechanism of action. Sequence homology places Ec-AMP1 in the plant C6-type of antimicrobial peptides, but the three dimensional structure is highly similar to that of a spider neurotoxin. PMID:25821084

  8. RESISTANCE OF WATERMELON (CITRULLUS SPP.) GERMPLASM TO THE PEANUT ROOT-KNOT NEMATODE (MELOIDOGYNE ARENARIA RACE 1)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Root-knot nematodes (Meloidogyne arenaria, M. incognita, and M. javanica) are serious pests of watermelon (Citrullus lanatus) in the southern U.S. and world-wide. Currently, root-knot nematodes (RKN) are controlled in watermelon by pre-plant soil fumigation with methyl bromide or other nematicides....

  9. Host resistance and soil treatments for managing Pythium root rot and southern root-knot nematode in pepper

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Five pepper (Capsicum annuum) genotypes differing in reactions to Phytophthora capsici and southern root-knot nematode (Meloidogyne incognita) were studied in combination with four soil treatments for managing Pythium root rot and southern root-knot nematode in field trials in Charleston, SC and Cit...

  10. Unfolding knots by proteasome-like systems: simulations of the behaviour of folded and neurotoxic proteins.

    PubMed

    Wojciechowski, Michał; Gómez-Sicilia, Àngel; Carrión-Vázquez, Mariano; Cieplak, Marek

    2016-08-16

    Knots in proteins have been proposed to resist proteasomal degradation. Ample evidence associates proteasomal degradation with neurodegeneration. One interesting possibility is that indeed knotted conformers stall this machinery leading to toxicity. However, although the proteasome is known to unfold mechanically its substrates, at present there are no experimental methods to emulate this particular traction geometry. Here, we consider several dynamical models of the proteasome in which the complex is represented by an effective potential with an added pulling force. This force is meant to induce the translocation of a protein or a polypeptide into the catalytic chamber. The force is either constant or applied periodically. The translocated proteins are modelled in a coarse-grained fashion. We do comparative analysis of several knotted globular proteins and the transiently knotted polyglutamine tracts of length 60 alone and fused in exon 1 of the huntingtin protein. Huntingtin is associated with Huntington's disease, a well-known genetically determined neurodegenerative disease. We show that the presence of a knot hinders and sometimes even jams translocation. We demonstrate that the probability to do so depends on the protein, the model of the proteasome, the magnitude of the pulling force, and the choice of the pulled terminus. In any case, the net effect would be a hindrance in the proteasomal degradation process in the cell. This would then yield toxicity via two different mechanisms: one through toxic monomers compromising degradation and another by the formation of toxic oligomers. Our work paves the way for the mechanistic investigation of the mechanical unfolding of knotted structures by the proteasome and its relation to toxicity and disease. PMID:27425826

  11. Demographic consequences of migratory stopover: linking red knot survival to horseshoe crab spawning abundance

    USGS Publications Warehouse

    McGowan, Conor P.; Hines, James E.; Nichols, James D.; Lyons, James E.; Smith, David; Kalasz, Kevin S.; Niles, Lawrence J.; Dey, Amanda D.; Clark, Nigel A.; Atkinson, Philip W.; Minton, Clive D.T.; Kendall, William

    2011-01-01

    Understanding how events during one period of the annual cycle carry over to affect survival and other fitness components in other periods is essential to understanding migratory bird demography and conservation needs. Previous research has suggested that western Atlantic red knot (Calidris canutus rufa) populations are greatly affected by horseshoe crab (Limulus polyphemus) egg availability at Delaware Bay stopover sites during their spring northward migration. We present a mass-based multistate, capturerecapture/resighting model linking (1) red knot stopover mass gain to horseshoe crab spawning abundance and (2) subsequent apparent annual survival to mass state at the time of departure from the Delaware Bay stopover area. The model and analysis use capture-recapture/resighting data with over 16,000 individual captures and 13,000 resightings collected in Delaware Bay over a 12 year period from 1997–2008, and the results are used to evaluate the central management hypothesis that red knot populations can be influenced by horseshoe crab harvest regulations as part of a larger adaptive management effort. Model selection statistics showed support for a positive relationship between horseshoe crab spawning abundance during the stopover and the probability of red knots gaining mass (parameter coefficient from the top model b = 1.71, SE = 0.46). Our analyses also supported the link between red knot mass and apparent annual survival, although average estimates for the two mass classes differed only slightly. The addition of arctic snow depth as a covariate influencing apparent survival improved the fit of the data to the models (parameter coefficient from the top model b = 0.50, SE = 0.08). Our results indicate that managing horseshoe crab resources in the Delaware Bay has the potential to improve red knot population status.

  12. Modification of U-Stitch Laparoscopic Gastrostomy Technique to Minimize Suture Knot Abscess Formation.

    PubMed

    McCagg, Jillian; Markham, Sarah; Idowu, Olajire; Newton, Christopher; Palmer, Barnard; Kim, Sunghoon

    2016-06-01

    Aim U-stitch laparoscopic gastrostomy is a commonly used technique for placement of balloon gastrostomy for pediatric patients. The U-stitch method was modified by others whereby the stay sutures are placed in a subcutaneous tissue. Although this modification has been reported to be superior, it has led to suture knot abscess formation which was not reported in the original method. We developed further modification whereby the stay-suture knots are positioned within the gastrostomy tract instead of the subcutaneous tissue which minimizes suture knot abscess formation. Methods Modified U-stitch technique was used to place the balloon gastrostomy. The U-stitch stay sutures are placed to hold the stomach to the abdominal wall. These sutures are subcutaneously tunneled toward the gastrostomy tract and tied to the opposing sutures with the resulting knots lying within the tract of the gastrostomy. Chart reviews of patients who underwent this modified U-stitch method were done. Results A total of 27 consecutive patients were evaluated. Minimal follow-up period was 6 months. No suture knot abscess complication was found. One patient for whom we used a polyglactin (Vicryl; Ethicon Inc., Cincinnati, Ohio, United States) suture developed cellulitis around the gastrostomy site which cleared with antibiotic. Remaining 10 patients for whom we used Vicryl suture and 16 patients for whom polydioxanone (PDS; Ethicon Inc.) suture was used did not develop any infections. Conclusion Subcutaneous placement of stay suture within the open gastrostomy tract rather than within closed subcutaneous tissue may minimize suture knot abscess formation. PMID:26011076

  13. Characterization of the Inner Knot of the Crab: the Site of the Gamma-ray Flares?

    NASA Technical Reports Server (NTRS)

    Weisskopf, Martin C.

    2015-01-01

    One of the most intriguing recent discoveries has been the detection of powerful gamma-ray flares from the Crab Nebula. Such events, with a recurrence time of about once per year, can be so dramatic to make the system the brightest source in the gamma-ray sky as occurred, e.g. in April 2011. These flares challenge our understanding of how pulsar wind nebulae work and defy current astrophysical models for particle acceleration. We present here our study of the inner knot located within a fraction of an arcsecond from the pulsar with the aim of characterizing the feature and asking if this might be the site of the origin of the gamma-ray flares. We took data using Keck, HST, and Chandra obtained as part of our multi-wavelength campaign to identify the source of the enigmatic flares. We set an upper limit as to the gamma-ray flux from the knot. We also find that the dimensions, surface brightness, flux, etc. of the optical and infrared knot are all correlated with distance from the pulsar. This distance, in turn, varies with time. In addition to this most thorough characterization of the inner knot's properties, we examine the hypothesis that the knot may be the site of the flares by examining the knot separation versus the Fermi/LAT gamma-ray flux. Finally, as part of this research, we make use of a new approach employing singular value decomposition (SVD) for analyzing time series of images and compare the approach to more traditional methods. Our conclusions are only refined but not impacted by using the new approach.

  14. Direct Detection of the Helical Magnetic Field Geometry from 3D Reconstruction of Prominence Knot Trajectories

    NASA Astrophysics Data System (ADS)

    Zapiór, Maciej; Martínez-Gómez, David

    2016-02-01

    Based on the data collected by the Vacuum Tower Telescope located in the Teide Observatory in the Canary Islands, we analyzed the three-dimensional (3D) motion of so-called knots in a solar prominence of 2014 June 9. Trajectories of seven knots were reconstructed, giving information of the 3D geometry of the magnetic field. Helical motion was detected. From the equipartition principle, we estimated the lower limit of the magnetic field in the prominence to ≈1-3 G and from the Ampère’s law the lower limit of the electric current to ≈1.2 × 109 A.

  15. Aggregates of a hetero-oligophenylene derivative as reactors for the generation of palladium nanoparticles: a potential catalyst in the Sonogashira coupling reaction under aerial conditions.

    PubMed

    Walia, Preet Kamal; Pramanik, Subhamay; Bhalla, Vandana; Kumar, Manoj

    2015-12-18

    The utilization of Pd nanoparticles stabilized by aggregates of hetero-oligophenylene derivative 3 as an excellent catalyst in a copper/amine free Sonogashira coupling reaction under aerial conditions at room temperature has been demonstrated. PMID:26460180

  16. RGS Spectroscopy of the Cygnus Loop XA Knot

    NASA Technical Reports Server (NTRS)

    Gaetz, Terrance J.; Mushotzky, Richard F. (Technical Monitor)

    2003-01-01

    The observations were performed at the end of April 2002, and the data were received in July 2002. Unfortunately, the observations were badly compromised by high levels of background radiation; one the three observations lost entirely. Two replacement observations were scheduled for November 2002, and were only made available in January of 2003. Consequently, we have had little time to grapple with the unusual data analysis challenges. The search for a postdoctoral fellow has been successfully concluded, and Manami Sasaki began working for us in January 2003. She will be supported in part by these funds, and will be working to help understand these data. Examination of the RGS 'Orders' images indicate the presence of broad emission lines (as expected for the diffuse XA knot). However, examination of the 'Spatial' dispersion/cross-dispersion images indicate that the emission is also broad in the cross-dispersion direction. (As a crosscheck, some of the 'Lockman Hole' datasets were also examined as representative 'sky background' datasets; in these, both types of images are relatively flat (outside the calibration source regions). The quicklook plots of the spectra show the expected O VII and O VIII lines, in addition to a complex around 35 Angstroms; the approx. 35 Angstrom line is likely the C V He-beta line at 34.97 Angstrom, but identifying the additional line(s) will require a more careful reduction of the data. Consequently, there is valuable information to be extracted from these data, but it is complicated by diffuse nature of the emission. Because the angular scale is large, we will have to make use of sky background datasets in order to do the background fitting. A color composite image of OM data in the three UV bands was presented at the 'How does the Galaxy Work?' meeting, and compared to optical and X-ray imaging data. Quantitative analysis will require obtaining the effective bandpasses of the UV filters so that the predominant line and continuum

  17. Protein similarity from knot theory: geometric convolution and line weavings.

    PubMed

    Erdmann, Michael A

    2005-01-01

    Shape similarity is one of the most elusive and intriguing questions of nature and mathematics. Proteins provide a rich domain in which to test theories of shape similarity. Proteins can match at different scales and in different arrangements. Sometimes the detection of common local structure is sufficient to infer global alignment of two proteins; at other times it provides false information. Proteins with very low sequence identity may share large substructures, or perhaps just a central core. There are even examples of proteins with nearly identical primary sequences in which alpha-helices have become beta-sheets. Shape similarity can be formulated (i) in terms of global metrics, such as RMSD or Hausdorff distance, (ii) in terms of subgraph isomorphisms, such as the detection of shared substructures with similar relative locations, or (iii) purely topologically, in terms of structure preserving transformations. Existing protein structure detection programs are built on the first two types of similarity. The third forms the foundations of knot theory. The thesis of this paper is this: Protein similarity detection leads naturally to algorithms operating at the metric, relational, and isotopic scales. The paper introduces a definition of similarity based on atomic motions that preserve local backbone topology without incurring significant distance errors. Such motions are motivated by the physical requirements for rearranging subsequences of a protein. Similarity detection then seeks rigid body motions able to overlay pairs of substructures, each related by a substructure-preserving motion, without necessarily requiring global structure preservation. This definition is general enough to span a wide range of questions: One can ask for full rearrangement of one protein into another while preserving global topology, as in drug design; or one can ask for rearrangements of sets of smaller substructures, preserving local but not global topology, as in protein evolution

  18. NEUTRONIC REACTOR CONTROL

    DOEpatents

    Metcalf, H.E.

    1958-10-14

    Methods of controlling reactors are presented. Specifically, a plurality of neutron absorber members are adjustably disposed in the reactor core at different distances from the center thereof. The absorber members extend into the core from opposite faces thereof and are operated by motive means coupled in a manner to simultaneously withdraw at least one of the absorber members while inserting one of the other absorber members. This feature effects fine control of the neutron reproduction ratio by varying the total volume of the reactor effective in developing the neutronic reaction.

  19. Contribution of root-knot nematodes to aflatoxin contamination in peanut

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Peanut kernels are susceptible to colonization by Aspergillus spp. which, under conditions of drought and high temperatures, can produce aflatoxins prior to harvest. Our primary objective was to determine the mechanism by which the peanut root-knot nematode (Meloidogyne arenaria) increases aflatoxi...

  20. Managing Root-knot on Tobacco in the Southeastern United States

    PubMed Central

    Johnson, Charles S.

    1989-01-01

    Root-knot nematodes suppress yields of flue-cured tobacco an estimated 0.1 to 4.8% annually in the southeastern United States, even though nematode management practices have been widely adopted. Although Meloidogyne incognita races 1 and 3 have predominated, M. arenaria, M. javanica, and M. incognita races 2 and 4 are increasingly important. Seventy-five percent of the flue-cured tobacco hectarage in North Carolina and Virginia is rotated on 2-year or 3-year intervals. Over half of the hectarage in the southeastern United States was planted with tobacco cultivars resistant to M. incognita races 1 and 3 in 1986. Resistance to other species or races of root-knot nematodes is not available in commercially available flue-cured tobacco cultivars. Most producers plow and (or) disc-out flue-cured tobacco roots and stalks after harvest. Nematicide use ranges from virtually 100% in Florida and Georgia to 60% in Virginia. Continued research is needed to develop management strategies for mixed populations of root-knot nematodes and to incorporate resistance to more root-knot nematode species and races into tobacco cultivars. Nematode advisory programs that allow producers to optimize nematicide use from an economical and ecological point of view are also needed. PMID:19287655

  1. Southern root-knot nematode affects common cocklebur (Xanthium strumarium) interference with cotton

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Southern root-knot nematode and common cocklebur will both interfere with cotton growth and yield. A greater understanding of the interaction of these pests on cotton growth and yield is needed for effective IPM (integrated pest management). An additive design was used in outdoor micro-plots with fi...

  2. PA-559: A New, Root-knot Nematode Resistant, Red-fruited, Habanero-type Pepper

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Efforts to develop a root-knot nematode resistant, red-fruited, Habanero-type pepper (Capsicum chinense Jacq.) were completed with the official release of PA-559 on September 18, 2008. The new breeding line is the product of a backcross/pedigree breeding procedure to incorporate a dominant root-kno...

  3. Celtic Knots: Interweaving the Elements of Effective Teacher Professional Development in ICT

    ERIC Educational Resources Information Center

    Lloyd, Margaret; Cochrane, Janet

    2006-01-01

    Professional development for teachers is often described as a journey. This paper, using the findings from a small-scale study interrogating professional development in ICT, offers the alternate metaphor of an interwoven Celtic knot to explain this phenomenon. It will show how the four key elements identified as being critical to creating the most…

  4. Over-expression of MIC3 reduces cotton susceptibility to root-knot nematode

    Technology Transfer Automated Retrieval System (TEKTRAN)

    While the inheritance of root-knot nematode (Meloidogyne incognita; RKN) resistance in cotton (Gossypium hirsutum) has been the focus of much research, the mechanism of the resistance at the molecular level remains largely unknown. To date, increased transcript and protein levels of MIC3 (Meloidogy...

  5. Transcriptome analysis of resistant and susceptible alfalfa cultivars infected with root-knot nematode Meloidogyne incognita

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nematodes are one of the major limiting factors in alfalfa production. Root knot nematodes (RKN, Meloidogyne spp.) are widely distributed and economically important sedentary endoparasites of agricultural crops (Castagnone-Sereno et al. 2013) and they may inflict significant damage to alfalfa fields...

  6. Field level risk assessment for root-knot nematodes in lima beans

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Southern Root-Knot Nematode (RKN), Meloidogyne incognita, is a major yield limiting pest in lima beans (Phaseolus lunatus). RKN are not evenly distributed through fields and population dynamics are fluid making whole field management challenging. The objectives of this research were to characterize ...

  7. Hairy Nightshade Undermines Resistance of Potato Breeding Lines to Columbia Root-Knot Nematode

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Columbia root-knot nematode, Meloidogyne chitwoodi, is a major pest of potato in the Pacific Northwest of the USA and is controlled by costly soil fumigation. Potato breeding lines have been developed with resistance to the predominant race 1 (CRN-1) of M. chitwoodi. Hairy nightshade, Solanum sarr...

  8. Rootstock assessment for root-knot nematode management in grafted honeydew melon

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Root-knot nematodes (RKN) are one of the most damaging soilborne pathogens of honeydew melon (Cucumis melo var. inodorus). Currently their management is dependent on soil fumigation. Vegetable grafting with resistant rootstocks may be an effective approach for RKN management in the sustainable produ...

  9. Post-transcriptional gene silencing of root knot-nematode in transformed soybean roots

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plant-parasitic nematodes cause about $100 billion in crop losses annually. Root-knot nematodes (RKN; Meloidogyne spp.) are sedentary endoparasites, and the genus has been found on more than 3000 host plant species. In this study four different gene constructs were designed to produce RNA interferen...

  10. Synthesis of Ga 2O 3 chains with closely spaced knots connected by nanowires

    NASA Astrophysics Data System (ADS)

    Dai, L.; You, L. P.; Duan, X. F.; Lian, W. C.; Qin, G. G.

    2004-07-01

    Chains of closely spaced metal or semiconductor particles have potential applications in optoelectronics and single electron devices. We report, for the first time, the synthesis of Ga 2O 3 chains with closely spaced knots connected by nanowires using the thermal evaporation method with a specially designed quartz boat. The Ga 2O 3 chains grew only on the Si substrates where Au catalyst or Ga droplets were coated. The average diameter of the knots is about 450 nm and that of the nanowires is about 50 nm. The selected area electron diffraction of either a knot or a connecting nanowire includes two sets of overlapped single crystal electron diffraction patterns which belong to the [1 0 2] and [1 0 1¯] crystal zone axes of the monoclinic β-Ga 2O 3 phase, respectively. The knot and its neighbor nanowire have the common ( 2¯ 0 1) growth planes at their interface. A mechanism model for the Ga 2O 3 chains synthesis based on the vapor-liquid-solid mechanism is discussed.

  11. Phytotoxicity of Clove Oil to Vegetable Crop Seedlings and Nematotoxicity to Root-knot Nematodes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Clove oil derived from the plant Syzygium aromaticum is active against various soilborne plant pathogens, and therefore has potential for use as a biobased pesticide. A clove oil formulation previously found to be toxic to the root-knot nematode Meloidogyne incognita in laboratory assays was invest...

  12. New meniscus repair by an all-inside knot suture technique.

    PubMed

    Fukushima, Kazumasa; Okano, Tatsumasa; Negishi, Shinichi; Horaguchi, Takashi; Sato, Kenji; Saito, Akiyoshi; Ryu, Junnosuke

    2005-06-01

    The indications for the all-inside knot suture technique include tears in the red-red zone or red-white zone in the meniscus, and a horizontal tear, a vertical tear, and a peripheral tear. First, find an appropriate place for a suture insertion site with a Kateran needle or a spinal needle. Make sure it exits beyond the tear in the meniscus. Once the insertion site is chosen, a suture is passed into and through the joint. The suture is slowly pulled back. You should be able to feel the tip of the suture come out of the joint capsule. If you want to make a vertical suture to suture the tear, move the suture vertically apex. Then insert the suture back into the joint through the capsule. Make sure the suture stays inside the joint. Find and grab the suture with a punch inserted from the clear cannula. Pull the suture out of the joint through the clear cannula with the punch. Tighten the knot with a knot pusher. Then confirm the stability of the sutured site with the probe. Our all-inside knot suture technique can be performed arthroscopically, allowing reliable repair of the torn meniscus. PMID:15944646

  13. MIC3 over-expression reduces cotton susceptibility to root-knot nematode

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The inheritance of root-knot nematode (RKN) resistance in cotton has been the focus of much research; however, the mechanism of the resistance at the molecular level remains largely unknown. To date, increased transcript and protein levels of MIC3 in galls of resistant plants remains the only examp...

  14. Proper motions of radiative knots in simulations of stellar jets. An alternative to pulsating inflow conditions

    NASA Astrophysics Data System (ADS)

    Rubini, F.; Lorusso, S.; Del Zanna, L.; Bacciotti, F.

    2007-09-01

    Aims:Elongated jets from young stellar objects typically present a nodular structure, formed by a chain of bright knots of enhanced emission with individual proper motions. Though it is generally accepted that internal shocks play an important role in the formation and dynamics of such structures, their precise origin and the mechanisms behind the observed proper motions is still a matter of debate. Our goal is to study numerically the origin, dynamics, and emission properties of such knots. Methods: Axisymmetric simulations are performed with a shock-capturing code for gas dynamics, allowing for molecular, atomic, and ionized hydrogen in non-equilibrium concentrations subject to ionization/recombination processes. Radiative losses in [S ii] lines are computed, and the resulting synthetic emission maps are compared with observations. Results: We show that a pattern of regularly spaced internal oblique shocks, characterized by individual proper motions, is generated by the pressure gradient between the propagating jet and the time variable external cocoon. In the case of under-expanded, light jets the resulting emission knots are found to move downstream with the jet flow, with increasing velocity and decaying brightness toward the leading bow shock. This suggests that the basic properties of the knots observed in stellar jets can be reproduced even without invoking ad hoc pulsating conditions at the jet inlet, though an interplay between the two scenarios is certainly possible.

  15. Resistance in peanut cultivars and breeding lines to three root-knot nematode species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Three major species of root-knot nematode infect peanut: Meloidogyne arenaria race 1 (Ma), M. hapla (Mh), and M. javanica race 3 (Mj). Sources of resistance to all three nematodes are needed for developing novel peanut cultivars with broad resistance to Meloidogyne spp. Cultivars and breeding lines ...

  16. A knotted1-like homeobox protein regulates abscission in tomato by modulating the auxin pathway

    Technology Transfer Automated Retrieval System (TEKTRAN)

    KD1, a gene encoding a KNOTTED1-LIKE HOMEOBOX transcription factor is known to be involved, in tomato, in ontogeny of the compound leaf. KD1 is also highly expressed in both leaf and flower abscission zones. Reducing abundance of transcripts of this gene in tomato, using both virus induced gene sile...

  17. Comparison of ultrasonic suture welding and traditional knot tying in a rabbit rotator cuff repair model.

    PubMed

    Nho, Shane J; Cole, Brian J; Mazzocca, Augustus D; Williams, James M; Romeo, Anthony A; Bush-Joseph, Charles A; Bach, Bernard R; Hallab, Nadim J

    2006-01-01

    The purpose of this study is to evaluate ultrasonic suture welding of monofilament suture in an animal model of rotator cuff repair with biomechanical and histologic analyses. We randomly assigned 46 shoulders in 23 rabbits to 1 of 3 treatment groups: sham-operated (n = 15), knotted (n = 15), and welded (n = 16). Supraspinatus defects were surgically created and acutely repaired with suture anchors loaded with either No. 2-0 Ethibond for knotted group or No. 2-0 nylon for welded shoulders. Eighteen weeks postoperatively, all animals were killed, and the shoulders underwent either biomechanical testing or histologic analysis. The maximum stress of the sham-operated group (20.6 N/mm2) was significantly greater than that of both the knotted (10.2 N/mm2) and welded (8.3 N/mm2) groups (P < .05), but no differences were observed between the knotted and welded groups. Although some histologic changes were noted, none was considered to be significant to distinguish either group. PMID:16979062

  18. New Discoveries in Resistances to Columbia Root-knot Nematode and Corky Ringspot Disease

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Columbia root-knot nematode CRKN (Meloidogyne chitwoodi) is a serious pest of potato in the Pacific Northwest. In the warmer zones, with longer growing seasons, this nematode builds up to high populations and damages the potato tubers by invading and causing discoloration and galling. It is pr...

  19. Mustard seed meal for management of root-knot nematode and weeds in tomato production

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mustard seed meals of indian mustard [InM (Brassica juncea)] and yellow mustard [YeM (Sinapis alba)], alone and combined, were tested for effects on tomato (Solanum lycopersicum) plants and for suppression of southern root-knot nematode [RKN (Meloidogyne incognita)] and weed populations. In the gree...

  20. Mutually tangled colloidal knots and induced defect loops in nematic fields

    NASA Astrophysics Data System (ADS)

    Martinez, Angel; Ravnik, Miha; Lucero, Brice; Visvanathan, Rayshan; Žumer, Slobodan; Smalyukh, Ivan I.

    2014-03-01

    Colloidal dispersions in liquid crystals can serve as asoft-matter toolkit for the self-assembly of composite materials with pre-engineered properties and structures that are highly dependent on particle-induced topological defects. Here, we demonstrate that bulk and surface defects in nematic fluids can be patterned by tuning the topology of colloidal particles dispersed in them. In particular, by taking advantage of two-photon photopolymerization techniques to make knot-shaped microparticles, we show that the interplay of the topologies of the knotted particles, the nematic field and the induced defects leads to knotted, linked and other topologically non-trivial field configurations. These structures match theoretical predictions made on the basis of the minimization of the elastic free energy and satisfy topological constraints. Our approach may find uses in self-assembled topological superstructures of knotted particles linked by nematic fields, in topological scaffolds supporting the decoration of defect networks with nanoparticles, and in modelling other physical systems exhibiting topologically analogous phenomena.

  1. Transgressive segregation of root-knot nematode resistance in cotton determined by QTL analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Transgressive resistance to root-knot nematode, Meloidogyne incognita, was found in intraspecific (Gossypium hirsutum; resistant Acala NemX x susceptible Acala SJ-2) and interspecific (G. barbadense susceptible Pima-S7 x Acala NemX) cotton recombinant inbred line (RIL) populations. Similar contribut...

  2. Theory and experiment in concert: templated synthesis of amide rotaxanes, catenanes, and knots.

    PubMed

    Schalley, Christoph A; Reckien, Werner; Peyerimhoff, Sigrid; Baytekin, Bilge; Vögtle, Fritz

    2004-10-01

    The synthesis of amide rotaxanes, amide catenanes, and trefoil amide knots is based on template effects mediated by hydrogen bonds. While a large body of experimental data is available, in-depth theoretical studies of these template syntheses are virtually unavailable, although they would provide a more profound insight into the exact details of the hydrogen-bonding patterns involved in the formation of these mechanically interlocked species. In this article we present a density functional study of the conformational properties of tetralactam macrocycles and the threading mechanism that produces the immediate precursor for rotaxane and catenane formation. Predictions of the geometries and relative energies made on the basis of semi-empirical AM1 calculations are compared with these results in order to judge the reliability of the simpler approach. Since these calculations yield good agreement with the structural features, they have been used to extend the calculations in order to understand the mechanism of formation of a trefoil dodecaamide knot that has recently been synthesized. The inherent topological chirality of the knot is reflected in the intermediates generated during its formation; these involve helical loops. These loops parallel the rotaxane and catenane wheels with respect to the arrangement of the functional groups that mediate the template effect and may well serve as wheel analogues through which one of the precursor molecules can be threaded. This threading step finally results in the knotted structure. Good agreement between the results of the calculations presented here and experimental findings is achieved. PMID:15372695

  3. Introgression of root-knot nematode (RKN) resistance into tetraploid cottons.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The introgression of root-knot nematode (RKN) resistance into tetraploid cotton (Gossypium ssp.) and its ancestral genome origin were examined. Three major germplasm sources (Acala NemX, Clevewilt 6, and Auburn 623 RNR) of RKN resistance were compared with diverse germplasm using selected SSR marker...

  4. Managing root-knot nematodes: A case for cover crops in establishing peach orchards

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Root-knot nematodes (Meloidogyne spp.) are an important pathogen of peach in the United States. Several Meloidogyne spp. have been reported to cause damage to stone fruits, but M. incognita and M. javanica are the predominant species on peach. Preplant fumigant nematicides have traditionally been ...

  5. Does infection by southern root-knot nematode influence development of Phytophthora blight in pepper?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The southern root-knot nematode, Meloidogyne incognita, and Phytophthora capsici, the causal agent of Phytophthora blight, are both important pathogens of pepper (Capsicum annuum L.) in the U.S. and worldwide. Although there is significant information in the literature about the responses of pepper...

  6. Tolerance of a Knotted Near-Infrared Fluorescent Protein to Random Circular Permutation.

    PubMed

    Pandey, Naresh; Kuypers, Brianna E; Nassif, Barbara; Thomas, Emily E; Alnahhas, Razan N; Segatori, Laura; Silberg, Jonathan J

    2016-07-12

    Bacteriophytochrome photoreceptors (BphP) are knotted proteins that have been developed as near-infrared fluorescent protein (iRFP) reporters of gene expression. To explore how rearrangements in the peptides that interlace into the knot within the BphP photosensory core affect folding, we subjected iRFPs to random circular permutation using an improved transposase mutagenesis strategy and screened for variants that fluoresce. We identified 27 circularly permuted iRFPs that display biliverdin-dependent fluorescence in Escherichia coli. The variants with the brightest whole cell fluorescence initiated translation at residues near the domain linker and knot tails, although fluorescent variants that initiated translation within the PAS and GAF domains were discovered. Circularly permuted iRFPs retained sufficient cofactor affinity to fluoresce in tissue culture without the addition of biliverdin, and one variant displayed enhanced fluorescence when expressed in bacteria and tissue culture. This variant displayed a quantum yield similar to that of iRFPs but exhibited increased resistance to chemical denaturation, suggesting that the observed increase in the magnitude of the signal arose from more efficient protein maturation. These results show how the contact order of a knotted BphP can be altered without disrupting chromophore binding and fluorescence, an important step toward the creation of near-infrared biosensors with expanded chemical sensing functions for in vivo imaging. PMID:27304983

  7. On the implications of recent observations of the inner knot in the Crab nebula

    NASA Astrophysics Data System (ADS)

    Yuan, Yajie; Blandford, Roger D.

    2015-12-01

    Recent observations of the Crab nebula (Rudy et al.) have maintained its reputation for high-energy astrophysical enlightenment and its use as a test-bed for theories of the behaviour of magnetized, relativistic plasma. In particular, new observations of the inner knot located 0.65 arcsec SE from the pulsar confirm that it is compact, elongated transversely to the symmetry axis and curved concave towards the pulsar. 60 per cent polarization has been measured along the symmetry axis (Moran et al.). The knot does not appear to be involved in the gamma-ray flares. The new observations both reinforce the interpretation of the knot as dissipation of the pulsar wind at a strong shock and challenge the details of existing models of this process. In particular, it is argued that the compactness, high polarization, and curvature are difficult to reconcile with simple relativistic shock models. Alternative possibilities include deflection of the outflow ahead of the shock and spatial variation in which the knot is interpreted as a caustic. Some future observations are proposed and new theoretical investigations are suggested.

  8. Percutaneous Untying of a Knot in a Retained Swan-Ganz Catheter

    SciTech Connect

    Bhatti, Waqar A.; Sinha, Sankar; Rowlands, Peter

    2000-03-15

    A patient was referred to us with a tightly knotted Swan-Ganz catheter. The catheter could not be removed by conventional simple methods. We describe a minimally invasive means of removal of the catheter using an Amplatz gooseneck snare and an angioplasty balloon. This allowed the catheter to be removed without trauma.

  9. Black knot [Apiosporina morbosa (Schw.)] resistance in imported and domestic Prunus domestica L. germplasm and cultivars

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Black knot (BK) Apisporina morbosa (Schw.) is an important fungal disease of Prunus domestica and other Prunus species in North America. BK causes economic losses in the plum growing regions of northern and eastern U.S. and eastern Canada. Relatively few P. domestica commercial cultivars are resis...

  10. Splitting, linking, knotting, and solitonic escape of topological defects in nematic drops with handles.

    PubMed

    Tasinkevych, Mykola; Campbell, Michael G; Smalyukh, Ivan I

    2014-11-18

    Topologically nontrivial field excitations, including solitonic, linked, and knotted structures, play important roles in physical systems ranging from classical fluids and liquid crystals, to electromagnetism, classic, and quantum field theories. These excitations can appear spontaneously during symmetry-breaking phase transitions. For example, in cosmological theories, cosmic strings may have formed knotted configurations influencing the Early Universe development, whereas in liquid crystals transient tangled defect lines were observed during isotropic-nematic transitions, eventually relaxing to defect-free states. Knotted and solitonic fields and defects were also obtained using optical manipulation, complex-shaped colloids, and frustrated cholesterics. Here we use confinement of nematic liquid crystal by closed surfaces with varied genus and perpendicular boundary conditions for a robust control of appearance and stability of such field excitations. Theoretical modeling and experiments reveal structure of defect lines as a function of the surface topology and material and geometric parameters, establishing a robust means of controlling solitonic, knotted, linked, and other field excitations. PMID:25369931

  11. Splitting, linking, knotting, and solitonic escape of topological defects in nematic drops with handles

    PubMed Central

    Tasinkevych, Mykola; Campbell, Michael G.; Smalyukh, Ivan I.

    2014-01-01

    Topologically nontrivial field excitations, including solitonic, linked, and knotted structures, play important roles in physical systems ranging from classical fluids and liquid crystals, to electromagnetism, classic, and quantum field theories. These excitations can appear spontaneously during symmetry-breaking phase transitions. For example, in cosmological theories, cosmic strings may have formed knotted configurations influencing the Early Universe development, whereas in liquid crystals transient tangled defect lines were observed during isotropic–nematic transitions, eventually relaxing to defect-free states. Knotted and solitonic fields and defects were also obtained using optical manipulation, complex-shaped colloids, and frustrated cholesterics. Here we use confinement of nematic liquid crystal by closed surfaces with varied genus and perpendicular boundary conditions for a robust control of appearance and stability of such field excitations. Theoretical modeling and experiments reveal structure of defect lines as a function of the surface topology and material and geometric parameters, establishing a robust means of controlling solitonic, knotted, linked, and other field excitations. PMID:25369931

  12. Resistant Citrullus lanatus var. citroides Rootstocks for Managing Root-knot Nematodes in Grafted Watermelon

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Southern root-knot nematode (RKN), Meloidogyne incognita, is an important re-emerging pest of watermelon. Several factors have contributed to re-emergence of RKN including: 1) ban of methyl bromide for soil fumigation; 2) reduced land area for crop rotation; and 3) continuous cropping of cucurbits u...

  13. A new class of magnetic confinement device in the shape of a knot

    SciTech Connect

    Hudson, S. R. Startsev, E.; Feibush, E.

    2014-01-15

    We describe a new class of magnetic confinement device, with the magnetic axis in the shape of a knot. We call such devices “knotatrons.” An example is given that has a large volume filled with magnetic surfaces, with significant rotational-transform, and with the magnetic field produced entirely by external circular coils.

  14. Truhart-NR, A Root-knot Nematode Resistant, Pimento-type Pepper Cultivar

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Efforts to develop a high-yielding, pimento-type pepper (Capsicum annuum L.) cultivar that is highly resistant to root-knot nematodes were completed with the official release of Truhart-NR on October 20, 2009. The new cultivar is homozygous for the dominant N gene that conditions a high level of re...

  15. PA-559, a Root-knot Nematode Resistant, Red-fruited, Habanero-type Pepper

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Agricultural Research Service of the U.S. Department of Agriculture has released a new Habanero-type pepper designated PA-559. The new breeding line is the product of a recurrent backcross breeding procedure to incorporate a dominant root-knot nematode resistance gene from the Scotch Bonnet-typ...

  16. PA-560, A Root-Knot Nematode Resistant, Yellow-fruited, Habanero-type Pepper

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Efforts to develop a yellow-fruited, Habanero-type pepper (Capsicum chinense Jacq.) that is highly resistant to root-knot nematodes were completed with the official release of PA-560 on October 20, 2009. PA-560, an advanced breeding line, is the product of a backcross/pedigree breeding procedure to...

  17. Is Grafting Useful for Managing Root-Knot Nematodes in Watermelon?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Five Citrullus lanatus var. citroides germplasm lines, four Lagenaria siceraria cultivars, one Cucurbita moschata x C. maxima hybrid, and one commercial wild watermelon (Citrullus lanatus spp.) cultivar were evaluated as rootstocks for watermelon in a field infested with the southern root-knot nemat...

  18. Resistance of Wild Watermelon (Citrullus lanatus var. citroides) Rootstocks to Southern Root-Knot Nematode

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Seedless watermelon (Citrullus lanatus var. lanatus) ‘Tri-X 313’ scions were grafted on ten different cucurbit rootstocks and evaluated in a field infested with southern root-knot nematode (RKN), Meloidogyne incognita, in Charleston, SC in 2009. The rootstocks evaluated included five wild watermelo...

  19. Root vs Pod Infection by Root-Knot Nematodes on Aflatoxin Contamination of Peanut

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aflatoxins are potent carcinogens produced by some Aspergillus spp. Infection of peanut (Arachis hypogaea) by root-knot nematodes (Meloidogyne arenaria) can lead to an increase in aflatoxin contamination of kernels when the plants are subjected to drought stress during pod maturation. It is not cle...

  20. Response of root-knot nematodes and Palmer amaranth to tillage and rye green manure

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rye (Secale cereale L.), which produces bioactive benzoxazinoid compounds, is a frequently used winter cover crop in many agronomic production systems in the USA. Our objective was to determine whether incorporating rye into soil while still green results in greater suppression of root-knot nematod...

  1. Tomato susceptibility to root-knot nematodes requires an intact jasmonic Acid signaling pathway

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Response of tomato (Solanum lycopersicum) to root-knot nematode (RKN; Meloidogyne spp.) infection was monitored using TOM1 cDNA microarray with resistant (‘Motelle’; Mi-1) and susceptible (‘Moneymaker’; mi) tomato at 24 h after RKN infection. The array analysis identified 1497 genes and 750 genes d...

  2. Pierced Lasso Bundles are a new class of knot-like motifs.

    PubMed

    Haglund, Ellinor; Sulkowska, Joanna I; Noel, Jeffrey K; Lammert, Heiko; Onuchic, José N; Jennings, Patricia A

    2014-06-01

    A four-helix bundle is a well-characterized motif often used as a target for designed pharmaceutical therapeutics and nutritional supplements. Recently, we discovered a new structural complexity within this motif created by a disulphide bridge in the long-chain helical bundle cytokine leptin. When oxidized, leptin contains a disulphide bridge creating a covalent-loop through which part of the polypeptide chain is threaded (as seen in knotted proteins). We explored whether other proteins contain a similar intriguing knot-like structure as in leptin and discovered 11 structurally homologous proteins in the PDB. We call this new helical family class the Pierced Lasso Bundle (PLB) and the knot-like threaded structural motif a Pierced Lasso (PL). In the current study, we use structure-based simulation to investigate the threading/folding mechanisms for all the PLBs along with three unthreaded homologs as the covalent loop (or lasso) in leptin is important in folding dynamics and activity. We find that the presence of a small covalent loop leads to a mechanism where structural elements slipknot to thread through the covalent loop. Larger loops use a piercing mechanism where the free terminal plugs through the covalent loop. Remarkably, the position of the loop as well as its size influences the native state dynamics, which can impact receptor binding and biological activity. This previously unrecognized complexity of knot-like proteins within the helical bundle family comprises a completely new class within the knot family, and the hidden complexity we unraveled in the PLBs is expected to be found in other protein structures outside the four-helix bundles. The insights gained here provide critical new elements for future investigation of this emerging class of proteins, where function and the energetic landscape can be controlled by hidden topology, and should be take into account in ab initio predictions of newly identified protein targets. PMID:24945798

  3. Pierced Lasso Bundles Are a New Class of Knot-like Motifs

    PubMed Central

    Haglund, Ellinor; Sulkowska, Joanna I.; Noel, Jeffrey K.; Lammert, Heiko; Onuchic, José N.; Jennings, Patricia A.

    2014-01-01

    A four-helix bundle is a well-characterized motif often used as a target for designed pharmaceutical therapeutics and nutritional supplements. Recently, we discovered a new structural complexity within this motif created by a disulphide bridge in the long-chain helical bundle cytokine leptin. When oxidized, leptin contains a disulphide bridge creating a covalent-loop through which part of the polypeptide chain is threaded (as seen in knotted proteins). We explored whether other proteins contain a similar intriguing knot-like structure as in leptin and discovered 11 structurally homologous proteins in the PDB. We call this new helical family class the Pierced Lasso Bundle (PLB) and the knot-like threaded structural motif a Pierced Lasso (PL). In the current study, we use structure-based simulation to investigate the threading/folding mechanisms for all the PLBs along with three unthreaded homologs as the covalent loop (or lasso) in leptin is important in folding dynamics and activity. We find that the presence of a small covalent loop leads to a mechanism where structural elements slipknot to thread through the covalent loop. Larger loops use a piercing mechanism where the free terminal plugs through the covalent loop. Remarkably, the position of the loop as well as its size influences the native state dynamics, which can impact receptor binding and biological activity. This previously unrecognized complexity of knot-like proteins within the helical bundle family comprises a completely new class within the knot family, and the hidden complexity we unraveled in the PLBs is expected to be found in other protein structures outside the four-helix bundles. The insights gained here provide critical new elements for future investigation of this emerging class of proteins, where function and the energetic landscape can be controlled by hidden topology, and should be take into account in ab initio predictions of newly identified protein targets. PMID:24945798

  4. Particulate behavior in a controlled-profile pulverized coal-fired reactor: A study of coupled turbulent particle dispersion and thermal radiation transport. Final technical progress report

    SciTech Connect

    Queiroz, M.; Webb, B.W.

    1996-06-01

    To aid in the evaluation and development of advanced coal-combustion models, comprehensive experimental data sets are needed containing information on both the condensed and gas phases. To address this need a series of test were initiated on a 300 kW laboratory-scale, coal-fired reactor at a single test condition using several types of instrumentation. Data collected on the reactor during the course of the test includes: gas, particle, and wall temperature profiles; radiant, total, and convective heat fluxes to the walls; particle size and velocity profiles; transmission measurements; and gas species concentrations. Solid sampling was also performed to determine carbon and total burnout. Along with the extensive experimental measurements, the particle dispersion and radiation submodels in the ACERC comprehensive 2D code were studied in detail and compared to past experimental measurements taken in the CPR. In addition to the presentation and discussion of the experimental data set, a detailed description of the measurement techniques used in collecting the data, including a discussion of the error associated with each type of measurement, is given.

  5. Ion-exchange reactions on clay minerals coupled with advection/dispersion processes. Application to Na+/Ca2+ exchange on vermiculite: Reactive-transport modeling, batch and stirred flow-through reactor experiments

    NASA Astrophysics Data System (ADS)

    Tertre, E.; Hubert, F.; Bruzac, S.; Pacreau, M.; Ferrage, E.; Prêt, D.

    2013-07-01

    The present study aims at testing the validity of using an Na+/Ca2+ ion-exchange model, derived from batch data to interpret experimental Ca2+-for-Na+ exchange breakthrough curves obtained on vermiculite (a common swelling clay mineral in surface environments). The ion-exchange model was constructed considering the multi-site nature of the vermiculite surface as well as the exchange of all aqueous species (Mg2+ derived from the dissolution of the solid and H+). The proposed ion-exchange model was then coupled with a transport model, and the predicted breakthrough curves were compared with the experimental ones obtained using a well stirred flow-through reactor. For a given solute residence time in the reactor (typically 50 min), our thermodynamic model based on instantaneous equilibrium was found to accurately reproduce several of the experimental breakthrough curves, depending on the Na+ and Ca2+ concentrations of the influents pumped through the reactor. However the model failed to reproduce experimental breakthrough curves obtained at high flow rates and low chemical gradient between the exchanger phase and the solution. An alternative model based on a hybrid equilibrium/kinetic approach was thus used and allowed predicting experimental data. Based on these results, we show that a simple parameter can be used to differentiate between thermodynamic and kinetic control of the exchange reaction with water flow. The results of this study are relevant for natural systems where two aquatic environments having contrasted chemistries interact. Indeed, the question regarding the attainment of a full equilibrium in such a system during the contact time of the aqueous phase with the particle/colloid remains most often open. In this context, we show that when a river (a flow of fresh water) encounters marine colloids, a systematic full equilibrium can be assumed (i.e., the absence of kinetic effects) when the residence time of the solute in 1 m3 of the system is ⩾6200 h.

  6. NEUTRONIC REACTOR

    DOEpatents

    Fermi, E.; Zinn, W.H.; Anderson, H.L.

    1958-09-16

    Means are presenied for increasing the reproduction ratio of a gaphite- moderated neutronic reactor by diminishing the neutron loss due to absorption or capture by gaseous impurities within the reactor. This means comprised of a fluid-tight casing or envelope completely enclosing the reactor and provided with a valve through which the casing, and thereby the reactor, may be evacuated of atmospheric air.

  7. Optical and infrared observations of the Crab Pulsar and its nearby knot

    NASA Astrophysics Data System (ADS)

    Sandberg, A.; Sollerman, J.

    2009-09-01

    Aims: We study the spectral energy distribution (SED) of the Crab Pulsar and its nearby knot in the optical and in the infrared (IR) regime. We want to investigate how the contribution from the knot affects the pulsar SED in that regime, and examine the evidence for synchrotron self-absorption in the IR. We also draw the attention to the predicted secular decrease in luminosity of the Crab Pulsar, and attempt to investigate this with CCD observations. Methods: We present high-quality UBVRIz, as well as adaptive optics JHK_sL' photometry, achieved under excellent conditions with the FORS1 and NAOS/CONICA instruments at the VLT. We combine these data with re-analyzed archival Spitzer Space Telescope data to construct a SED for the pulsar, and quantify the contamination from the knot. We have also gathered optical imaging data from 1988 to 2008 from several telescopes in order to examine the predicted secular decrease in luminosity. Results: For the Crab Pulsar SED we find a spectral slope of α_ν = 0.27 ± 0.03 in the optical/near-IR regime, when we exclude the contribution from the knot. For the knot itself, we find a much redder slope of α_ν = -1.3 ± 0.1. Our best estimate of the average decrease in luminosity for the pulsar is 2.9 ± 1.6 mmag per year. Conclusions: We have demonstrated the importance of the nearby knot in precision measurements of the Crab Pulsar SED, in particular in the near-IR. We have scrutinized the evidence for the traditional view of a synchrotron self-absorption roll-over in the infrared, and find that these claims are unfounded. We also find evidence for a secular decrease in the optical light for the Crab Pulsar, in agreement with current pulsar spin-down models. However, although our measurements of the decrease significantly improve on previous investigations, the detection is still tentative. We finally point to future observations that can improve the situation significantly. Based on observations made with ESO Telescopes under

  8. Accomplishments of a 10-year initiative to develop host plant resistance to root-knot and reniform nematodes in cotton

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In 2003 Cotton Incorporated initiated a Beltwide research program to develop host plant resistance against root-knot (Meloidogyne incognita) and reniform (Rotylenchulus reniformis) nematodes. Objectives formulated at a coordinating meeting in 2003 that included participants from public institutions...

  9. X-Wing RSRA - 80 Knot Taxi Test

    NASA Technical Reports Server (NTRS)

    1987-01-01

    The Rotor Systems Research Aircraft/X-Wing, a vehicle that was used to demonstrate an advanced rotor/fixed wing concept called X-Wing, is shown here during high-speed taxi tests at NASA's Ames-Dryden Flight Research Facility (later redesignated Dryden Flight Research Center), Edwards, California, on 4 November 1987. During these tests, the vehicle made three taxi tests at speeds of up to 138 knots. On the third run, the RSRA/X-Wing lifted off the runway to a 25-foot height for about 16 seconds. This liftoff maneuver was pre-planned as an aid to evaluations for first flight. At the controls were NASA pilot G. Warren Hall and Sikorsky pilot W. Faull. The unusual aircraft that resulted from the Ames Research Center/Army X-Wing Project was flown at the Ames-Dryden Flight Research Facility (now Dryden Flight Research Center), Edwards, California, beginning in the spring of 1984, with a follow-on program beginning in 1986. The program, was conceived to provide an efficient combination of the vertical lift characteristic of conventional helicopters and the high cruise speed of fixed-wing aircraft. It consisted of a hybrid vehicle called the NASA/Army Rotor Systems Research Aircraft (RSRA), which was equipped with advanced X-wing rotor systems. The program began in the early 1970s to investigate ways to increase the speed of rotor aircraft, as well as their performance, reliability, and safety . It also sought to reduce the noise, vibration, and maintenance costs of helicopters. Sikorsky Aircraft Division of United Technologies Laboratories built two RSRA aircraft. NASA's Langley Research Center, Hampton, Virginia, did some initial testing and transferred the program to Ames Research Center, Mountain View, California, for an extensive flight research program conducted by Ames and the Army. The purpose of the 1984 tests was to demonstrate the fixed-wing capability of the helicopter/airplane hybrid research vehicle and explore its flight envelope and flying qualities. These

  10. Scanning tunneling microscope assembly, reactor, and system

    DOEpatents

    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.

  11. The olive knot disease as a model to study the role of interspecies bacterial communities in plant disease

    PubMed Central

    Buonaurio, Roberto; Moretti, Chiaraluce; da Silva, Daniel Passos; Cortese, Chiara; Ramos, Cayo; Venturi, Vittorio

    2015-01-01

    There is an increasing interest in studying interspecies bacterial interactions in diseases of animals and plants as it is believed that the great majority of bacteria found in nature live in complex communities. Plant pathologists have thus far mainly focused on studies involving single species or on their interactions with antagonistic competitors. A bacterial disease used as model to study multispecies interactions is the olive knot disease, caused by Pseudomonas savastanoi pv. savastanoi (Psv). Knots caused by Psv in branches and other aerial parts of the olive trees are an ideal niche not only for the pathogen but also for many other plant-associated bacterial species, mainly belonging to the genera Pantoea, Pectobacterium, Erwinia, and Curtobacterium. The non-pathogenic bacterial species Erwinia toletana, Pantoea agglomerans, and Erwinia oleae, which are frequently isolated inside the olive knots, cooperate with Psv in modulating the disease severity. Co-inoculations of these species with Psv result in bigger knots and better bacterial colonization when compared to single inoculations. Moreover, harmless bacteria co-localize with the pathogen inside the knots, indicating the formation of stable bacterial consortia that may facilitate the exchange of quorum sensing signals and metabolites. Here we discuss the possible role of bacterial communities in the establishment and development of olive knot disease, which we believe could be taking place in many other bacterial plant diseases. PMID:26113855

  12. The olive knot disease as a model to study the role of interspecies bacterial communities in plant disease.

    PubMed

    Buonaurio, Roberto; Moretti, Chiaraluce; da Silva, Daniel Passos; Cortese, Chiara; Ramos, Cayo; Venturi, Vittorio

    2015-01-01

    There is an increasing interest in studying interspecies bacterial interactions in diseases of animals and plants as it is believed that the great majority of bacteria found in nature live in complex communities. Plant pathologists have thus far mainly focused on studies involving single species or on their interactions with antagonistic competitors. A bacterial disease used as model to study multispecies interactions is the olive knot disease, caused by Pseudomonas savastanoi pv. savastanoi (Psv). Knots caused by Psv in branches and other aerial parts of the olive trees are an ideal niche not only for the pathogen but also for many other plant-associated bacterial species, mainly belonging to the genera Pantoea, Pectobacterium, Erwinia, and Curtobacterium. The non-pathogenic bacterial species Erwinia toletana, Pantoea agglomerans, and Erwinia oleae, which are frequently isolated inside the olive knots, cooperate with Psv in modulating the disease severity. Co-inoculations of these species with Psv result in bigger knots and better bacterial colonization when compared to single inoculations. Moreover, harmless bacteria co-localize with the pathogen inside the knots, indicating the formation of stable bacterial consortia that may facilitate the exchange of quorum sensing signals and metabolites. Here we discuss the possible role of bacterial communities in the establishment and development of olive knot disease, which we believe could be taking place in many other bacterial plant diseases. PMID:26113855

  13. Determination of Noncovalent Binding Using a Continuous Stirred Tank Reactor as a Flow Injection Device Coupled to Electrospray Ionization Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Santos, Inês C.; Waybright, Veronica B.; Fan, Hui; Ramirez, Sabra; Mesquita, Raquel B. R.; Rangel, António O. S. S.; Fryčák, Petr; Schug, Kevin A.

    2015-07-01

    Described is a new method based on the concept of controlled band dispersion, achieved by hyphenating flow injection analysis with ESI-MS for noncovalent binding determinations. A continuous stirred tank reactor (CSTR) was used as a FIA device for exponential dilution of an equimolar host-guest solution over time. The data obtained was treated for the noncovalent binding determination using an equimolar binding model. Dissociation constants between vancomycin and Ac-Lys(Ac)-Ala-Ala-OH peptide stereoisomers were determined using both the positive and negative ionization modes. The results obtained for Ac- L-Lys(Ac)- D-Ala- D-Ala (a model for a Gram-positive bacterial cell wall) binding were in reasonable agreement with literature values made by other mass spectrometry binding determination techniques. Also, the developed method allowed the determination of dissociation constants for vancomycin with Ac- L-Lys(Ac)- D-Ala- L-Ala, Ac- L-Lys(Ac)- L-Ala- D-Ala, and Ac- L-Lys(Ac)- L-Ala- L-Ala. Although some differences in measured binding affinities were noted using different ionization modes, the results of each determination were generally consistent. Differences are likely attributable to the influence of a pseudo-physiological ammonium acetate buffer solution on the formation of positively- and negatively-charged ionic complexes.

  14. Determination of Noncovalent Binding Using a Continuous Stirred Tank Reactor as a Flow Injection Device Coupled to Electrospray Ionization Mass Spectrometry.

    PubMed

    Santos, Inês C; Waybright, Veronica B; Fan, Hui; Ramirez, Sabra; Mesquita, Raquel B R; Rangel, António O S S; Fryčák, Petr; Schug, Kevin A

    2015-07-01

    Described is a new method based on the concept of controlled band dispersion, achieved by hyphenating flow injection analysis with ESI-MS for noncovalent binding determinations. A continuous stirred tank reactor (CSTR) was used as a FIA device for exponential dilution of an equimolar host-guest solution over time. The data obtained was treated for the noncovalent binding determination using an equimolar binding model. Dissociation constants between vancomycin and Ac-Lys(Ac)-Ala-Ala-OH peptide stereoisomers were determined using both the positive and negative ionization modes. The results obtained for Ac-L-Lys(Ac)-D-Ala-D-Ala (a model for a Gram-positive bacterial cell wall) binding were in reasonable agreement with literature values made by other mass spectrometry binding determination techniques. Also, the developed method allowed the determination of dissociation constants for vancomycin with Ac-L-Lys(Ac)-D-Ala-L-Ala, Ac-L-Lys(Ac)-L-Ala-D-Ala, and Ac-L-Lys(Ac)-L-Ala-L-Ala. Although some differences in measured binding affinities were noted using different ionization modes, the results of each determination were generally consistent. Differences are likely attributable to the influence of a pseudo-physiological ammonium acetate buffer solution on the formation of positively- and negatively-charged ionic complexes. PMID:25832030

  15. Sensitivity of Bedding Plants to Southern Root-knot Nematode, Meloidogyne incognita Race 3.

    PubMed

    Walker, J T; Melin, J B; Davis, J

    1994-12-01

    Thirty-two cultivars of 10 commonly-grown bedding plants, representing eight families, were evaluated for their response to infection by the root-knot nematode, Meloidogyne incognita race 3, under greenhouse conditions. Four ageratum cultivars, two marigold, and two salvia cultivars were rated resistant after exposure for 8 weeks. Four begonia, four celosia, one dianthus, one verbena, one vinca, and three pansy cultivars were susceptible. Three salvia, one begonia, one gerber, one verbena, and three vinca cultivars were slightly susceptible with an average of knot nematode. PMID:19279964

  16. Engineered cystine knot miniproteins as potent inhibitors of human mast cell tryptase beta.

    PubMed

    Sommerhoff, Christian P; Avrutina, Olga; Schmoldt, Hans-Ulrich; Gabrijelcic-Geiger, Dusica; Diederichsen, Ulf; Kolmar, Harald

    2010-01-01

    Here we report the design, chemical and recombinant synthesis, and functional properties of a series of novel inhibitors of human mast cell tryptase beta, a protease of considerable interest as a therapeutic target for the treatment of allergic asthma and inflammatory disorders. These inhibitors are derived from a linear variant of the cyclic cystine knot miniprotein MCoTI-II, originally isolated from the seeds of Momordica cochinchinensis. A synthetic cyclic miniprotein that bears additional positive charge in the loop connecting the N- and C-termini inhibits all monomers of the tryptase beta tetramer with an overall equilibrium dissociation constant K(i) of 1 nM and thus is one of the most potent proteinaceous inhibitors of tryptase beta described to date. These cystine knot miniproteins may therefore become valuable scaffolds for the design of a new generation of tryptase inhibitors. PMID:19852971

  17. Transcriptomics: a sword to cut the Gordian knot of traditional Chinese medicine.

    PubMed

    Liu, Yufeng; Ai, Ni; Liao, Jie; Fan, Xiaohui

    2015-01-01

    The systemic effects of traditional Chinese medicine (TCM) seem to be a Gordian knot, impossible to untie for decades. With the advent of transcriptomics, a useful sword is provided to cut the knot and shed some light on complex bioprocesses and intrinsic connections among them. Here, we revisit studies on TCM ZHENGs using this approach, highlight its applications on elucidating the potential scientific basis of ZHENG and investigating mechanisms of action for the TCM formula, and demonstrating its unique role in novel TCM drug design and discovery through active ingredient detection from TCM and compatibility theory study of TCM. The limitations and future perspectives of transcriptomics approaches to TCM study are also discussed. PMID:26501686

  18. An easy technique for removal of knotted catheter in the bladder: percutaneous suprapubic cystoscopic intervention

    PubMed Central

    Özkan, Aybars; Okur, Mesut; Kaya, Murat; Büyükkaya, Ramazan; Katranci, Ali Osman; Kucuk, Adem

    2013-01-01

    Uncontaminated urine samples are indispensable to precisely diagnose urinary tract infections in new-borns or infants. Among many clinical interventions for urine collection are described, the most common noninvasive practice is using sterile bags, associated with significant contamination of samples. In children, however, invasive methods i.e. catheterization, are generally needed for reliable urine specimens. Almost always all the inserted catheters are easily drawn back, nevertheless, might not work as expected, and lead to considerable problems that cannot be overcome. Herein, a case of a female newborn treated with a successful percutaneous suprapubic cystoscopic procedure for extracting knotted urinary catheter in the bladder is presented. The least invasive and easiest technic is suggested to be used when catheter is knotted in the bladder, as elaborately stated. PMID:23936602

  19. Optical knots and contact geometry I. From Arnol'd inequality to Ranada's dyons

    NASA Astrophysics Data System (ADS)

    Kholodenko, Arkady L.

    2016-06-01

    Recently there had been a great deal of activity associated with various schemes of designing both analytic and experimental methods describing knotted structures in electrodynamics and in hydrodynamics. The majority of works in electrodynamics were inspired by the influential paper by Ranada (Lett Math Phys 18:97-106, 1989) and its subsequent refinements. In this work and in its companion we analyze Ranada's results using methods of contact geometry and topology. Not only our analysis allows us to reproduce his major results but in addition, it provides opportunities for considerably extending the catalog of the known/obtained knot types. In addition, it allows to reinterpret both the electric and magnetic charges purely geometrically thus opening the possibility of treatment of masses and charges in Yang-Mills and gravitational fields purely geometrically.

  20. Oxidative folding of peptides with cystine-knot architectures: kinetic studies and optimization of folding conditions.

    PubMed

    Reinwarth, Michael; Glotzbach, Bernhard; Tomaszowski, Michael; Fabritz, Sebastian; Avrutina, Olga; Kolmar, Harald

    2013-01-01

    Bioactive peptides often contain several disulfide bonds that provide the main contribution to conformational rigidity and structural, thermal, or biological stability. Among them, cystine-knot peptides-commonly named "knottins"-make up a subclass with several thousand natural members. Hence, they are considered promising frameworks for peptide-based pharmaceuticals. Although cystine-knot peptides are available through chemical and recombinant synthetic routes, oxidative folding to afford the bioactive isomers still remains a crucial step. We therefore investigated the oxidative folding of ten protease-inhibiting peptides from two knottin families, as well as that of an HIV entry inhibitor and of aprotinin, under two conventional sets of folding conditions and by a newly developed procedure. Kinetic studies identified folding conditions that resulted in correctly folded miniproteins with high rates of conversion even for highly hydrophobic and aggregation-prone peptides in concentrated solutions. PMID:23229141