WorldWideScience

Sample records for atomic interaction networks

  1. Interacting single atoms with nanophotonics for chip-integrated quantum networks

    Science.gov (United States)

    Alton, Daniel James

    Underlying matter and light are their building blocks of tiny atoms and photons. The ability to control and utilize matter-light interactions down to the elementary single atom and photon level at the nano-scale opens up exciting studies at the frontiers of science with applications in medicine, energy, and information technology. Of these, an intriguing front is the development of quantum networks where N ≫ 1 single-atom nodes are coherently linked by single photons, forming a collective quantum entity potentially capable of performing quantum computations and simulations. Here, a promising approach is to use optical cavities within the setting of cavity quantum electrodynamics (QED). However, since its first realization in 1992 by Kimble et al., current proof-of-principle experiments have involved just one or two conventional cavities. To move beyond to N ≫ 1 nodes, in this thesis we investigate a platform born from the marriage of cavity QED and nanophotonics, where single atoms at ˜100 nm near the surfaces of lithographically fabricated dielectric photonic devices can strongly interact with single photons, on a chip. Particularly, we experimentally investigate three main types of devices: microtoroidal optical cavities, optical nanofibers, and nanophotonic crystal based structures. With a microtoroidal cavity, we realized a robust and efficient photon router where single photons are extracted from an incident coherent state of light and redirected to a separate output with high efficiency. We achieved strong single atom-photon coupling with atoms located ~100 nm near the surface of a microtoroid, which revealed important aspects in the atom dynamics and QED of these systems including atom-surface interaction effects. We present a method to achieve state-insensitive atom trapping near optical nanofibers, critical in nanophotonic systems where electromagnetic fields are tightly confined. We developed a system that fabricates high quality nanofibers with high

  2. Atomic and Molecular Interactions

    International Nuclear Information System (INIS)

    The Gordon Research Conference (GRC) on Atomic and Molecular Interactions was held at Roger Williams University, Bristol, RI. Emphasis was placed on current unpublished research and discussion of the future target areas in this field

  3. Neuromorphic atomic switch networks.

    Directory of Open Access Journals (Sweden)

    Audrius V Avizienis

    Full Text Available Efforts to emulate the formidable information processing capabilities of the brain through neuromorphic engineering have been bolstered by recent progress in the fabrication of nonlinear, nanoscale circuit elements that exhibit synapse-like operational characteristics. However, conventional fabrication techniques are unable to efficiently generate structures with the highly complex interconnectivity found in biological neuronal networks. Here we demonstrate the physical realization of a self-assembled neuromorphic device which implements basic concepts of systems neuroscience through a hardware-based platform comprised of over a billion interconnected atomic-switch inorganic synapses embedded in a complex network of silver nanowires. Observations of network activation and passive harmonic generation demonstrate a collective response to input stimulus in agreement with recent theoretical predictions. Further, emergent behaviors unique to the complex network of atomic switches and akin to brain function are observed, namely spatially distributed memory, recurrent dynamics and the activation of feedforward subnetworks. These devices display the functional characteristics required for implementing unconventional, biologically and neurally inspired computational methodologies in a synthetic experimental system.

  4. Interacting atoms in optical lattices

    OpenAIRE

    Mentink, Johan; Kokkelmans, Servaas

    2008-01-01

    We propose an easy to use model to solve for interacting atoms in an optical lattice. This model allows for the whole range of weakly to strongly interacting atoms, and it includes the coupling between relative and center-of-mass motion via anharmonic lattice terms. We apply this model to a high-precision spin dynamics experiment, and we discuss the corrections due to atomic interactions and the anharmonic coupling. Under suitable experimental conditions, energy can be transferred between the...

  5. Mapping Out Atom-Wall Interaction with Atomic Clocks

    International Nuclear Information System (INIS)

    We explore the feasibility of probing atom-wall interaction with atomic clocks based on atoms trapped in engineered optical lattices. Optical lattice is normal to the wall. By monitoring the wall-induced clock shift at individual wells of the lattice, one would measure the dependence of the atom-wall interaction on the atom-wall separation. We find that the induced clock shifts are large and observable at already experimentally demonstrated levels of accuracy. We show that this scheme may uniquely probe the long-range atom-wall interaction in all three qualitatively distinct regimes of the interaction: van der Waals (image-charge interaction), Casimir-Polder (QED vacuum fluctuations), and Lifshitz (thermal-bath fluctuations) regimes.

  6. Quantum Network of Atom Clocks: A Possible Implementation with Neutral Atoms

    Science.gov (United States)

    Kómár, P.; Topcu, T.; Kessler, E. M.; Derevianko, A.; Vuletić, V.; Ye, J.; Lukin, M. D.

    2016-08-01

    We propose a protocol for creating a fully entangled Greenberger-Horne-Zeilinger-type state of neutral atoms in spatially separated optical atomic clocks. In our scheme, local operations make use of the strong dipole-dipole interaction between Rydberg excitations, which give rise to fast and reliable quantum operations involving all atoms in the ensemble. The necessary entanglement between distant ensembles is mediated by single-photon quantum channels and collectively enhanced light-matter couplings. These techniques can be used to create the recently proposed quantum clock network based on neutral atom optical clocks. We specifically analyze a possible realization of this scheme using neutral Yb ensembles.

  7. Optically polarized atoms understanding light-atom interactions

    CERN Document Server

    Auzinsh, Marcis; Rochester, Simon M

    2010-01-01

    This book is addressed at upper-level undergraduate and graduate students involved in research in atomic, molecular, and optical Physics. It will also be useful to researchers practising in this field. It gives an intuitive, yet sufficiently detailed and rigorous introduction to light-atom interactions with a particular emphasis on the symmetry aspects of the interaction, especially those associated with the angular momentum of atoms and light. The book will enable readers to carryout practical calculations on their own, and is richly illustrated with examples drawn from current research topic

  8. Manipulating nanoscale atom-atom interactions with cavity QED

    CERN Document Server

    Pal, Arpita; Deb, Bimalendu

    2016-01-01

    We theoretically explore manipulation of interactions between excited and ground state atoms at nanoscale separations by cavity quantum electrodynamics (CQED). We develop an adiabatic molecular dressed state formalism and show that it is possible to generate Fano-Feshbach resonances between ground and long-lived excited-state atoms inside a cavity. The resonances are shown to arise due to non-adiabatic coupling near a pseudo-crossing between the dressed state potentials. We illustrate our results with a model study using fermionic $^{171}$Yb atoms in a two-modal cavity. Our study is important for manipulation of interatomic interactions at low energy by cavity field.

  9. Entanglement Swapping: Entangling Atoms That Never Interacted

    CERN Document Server

    Guerra, E S

    2005-01-01

    In this paper we discuss four different proposals of entangling atomic states of particles which have never interacted. The experimental realization proposed makes use of the interaction of Rydberg atoms with a micromaser cavity prepared in either a coherent state or in a superposition of the zero and one field Fock states. We consider atoms in either a three-level cascade or lambda configuration

  10. Interaction, Relationships And Networks

    OpenAIRE

    Benson-Rea, M

    1999-01-01

    This paper presents four case studies which have been selected to represent different insights into the strategic evaluation of relationships within one industry. From an analysis of how each of the case study firms has formed its networks of relationships, within its overall approach to industry strategy, we discuss how the interactions are evaluated, with a particular emergent focus on social or actor bonds. The strategy literature models strategy formation processes and content. The networ...

  11. Interacting neural networks.

    Science.gov (United States)

    Metzler, R; Kinzel, W; Kanter, I

    2000-08-01

    Several scenarios of interacting neural networks which are trained either in an identical or in a competitive way are solved analytically. In the case of identical training each perceptron receives the output of its neighbor. The symmetry of the stationary state as well as the sensitivity to the used training algorithm are investigated. Two competitive perceptrons trained on mutually exclusive learning aims and a perceptron which is trained on the opposite of its own output are examined analytically. An ensemble of competitive perceptrons is used as decision-making algorithms in a model of a closed market (El Farol Bar problem or the Minority Game. In this game, a set of agents who have to make a binary decision is considered.); each network is trained on the history of minority decisions. This ensemble of perceptrons relaxes to a stationary state whose performance can be better than random. PMID:11088736

  12. Design of atomic energy information network system

    International Nuclear Information System (INIS)

    As the 21st century is expected to induce a Knowledge based society, responding to this kind of change on our own initiative could be achieved by establishing networks among atomic energy agencies with the Atomic Energy Portal Site in a pivotal role. Thus, enabling the knowledge information from each agency to be easily shared and utilized. Furthermore, it can contribute to further researches by providing accumulated knowledge in the atomic energy, such as research output and past achievements, and by avoiding the repetition of researches on the same subjects. It could also provide remote educational data to researchers and industrial experts in atomic energy, as well as atomic energy information for general public consistently, so that we can promote our confidence in atomic energy

  13. Super-Coulombic atom-atom interactions in hyperbolic media

    CERN Document Server

    Cortes, Cristian L

    2016-01-01

    Dipole-dipole interactions which govern phenomena like cooperative Lamb shifts, superradiant decay rates, Van der Waals forces, as well as resonance energy transfer rates are conventionally limited to the Coulombic near-field. Here, we reveal a class of real-photon and virtual-photon long-range quantum electrodynamic (QED) interactions that have a singularity in media with hyperbolic dispersion. The singularity in the dipole-dipole coupling, referred to as a Super-Coulombic interaction, is a result of an effective interaction distance that goes to zero in the ideal limit irrespective of the physical distance. We investigate the entire landscape of atom-atom interactions in hyperbolic media and propose practical implementations with phonon-polaritonic hexagonal boron nitride in the infrared spectral range and plasmonic super-lattice structures in the visible range. Our work paves the way for the control of cold atoms in hyperbolic media and the study of many-body atomic states where optical phonons mediate qua...

  14. Atoms of multistationarity in chemical reaction networks

    CERN Document Server

    Joshi, Badal

    2011-01-01

    Chemical reaction networks taken with mass-action kinetics are dynamical systems that arise in chemical engineering and systems biology. Deciding whether a chemical reaction network admits multiple positive steady states is to determine existence of multiple positive solutions to a system of polynomials with unknown coefficients. In this work, we consider the question of whether the minimal (in a precise sense) networks, which we propose to call `atoms of multistationarity,' characterize the entire set of multistationary networks. We show that if a subnetwork admits multiple nondegenerate positive steady states, then these steady states can be extended to establish multistationarity of a larger network, provided that the two networks share the same stoichiometric subspace. Our result provides the mathematical foundation for a technique used by Siegal-Gaskins et al. of establishing bistability by way of `network ancestry.' Here, our main application is for enumerating small multistationary continuous-flow stir...

  15. Social Interaction in Learning Networks

    NARCIS (Netherlands)

    Sloep, Peter

    2009-01-01

    The original publication is available from www.springerlink.com. Sloep, P. (2009). Social Interaction in Learning Networks. In R. Koper (Ed.), Learning Network Services for Professional Development (pp 13-15). Berlin, Germany: Springer Verlag.

  16. Strong Interactions in Strange Exotic Atoms

    Science.gov (United States)

    Mareš, J.

    2003-08-01

    Strong interaction level shifts and widths in - and K- atoms have been analyzed. The phenomenological density dependent approach as well as the relativistic mean field (RMF) model yield nucleus optical potentials with a repulsive real part in the nuclear interior. This has important consequences for the spectroscopy of hypernuclei. The study of K- atoms cannot resolve the depth of the K- nucleus potential. The fits to the kaonic atom data are satisfactory for both the relatively shallow potentials derived from chiral models and for the deep potentials based on the phenomenological and RMF analyses.

  17. Long-range interactions between Rydberg atoms

    Science.gov (United States)

    Deiglmayr, Johannes

    2016-10-01

    We present an overview over theoretical models to describe adiabatic potential-energy curves, experimental excitation spectra, and electronic and nuclear dynamics in interacting Rydberg-atom pairs at large internuclear separations. The potential-energy curves and molecular wavefunctions are determined from the multipole expansion of the static Coulomb interaction which is evaluated numerically in a product basis of atomic orbitals. The convergence of this approach both in the truncation of the multipole expansion as well as in the size of the product basis is discussed, and the comparison of simulated excitation spectra is established as a useful criterium to test the convergence of the calculation. We finally discuss the dynamics of electronic and nuclear motions of pairs of Rydberg atoms, focusing on the stability of ultralong range Rydberg molecules with respect to autoionization.

  18. Biomolecular Interactions Measured by Atomic Force Microscopy

    NARCIS (Netherlands)

    Willemsen, Oscar H.; Snel, Margot M.E.; Cambi, Alessandra; Greve, Jan; Grooth, de Bart G.; Figdor, Carl G.

    2000-01-01

    Atomic force microscopy (AFM) is nowadays frequently applied to determine interaction forces between biological molecules. Starting with the detection of the first discrete unbinding forces between ligands and receptors by AFM only several years ago, measurements have become more and more quantitati

  19. Atomic hydrogen interaction with Ru(1010).

    Science.gov (United States)

    Vesselli, E; Comelli, G; Rosei, R

    2004-05-01

    The interaction of atomic hydrogen with clean and deuterium precovered Ru(1010) was studied by means of temperature-programmed desorption (TPD) spectroscopy. Compared to molecular hydrogen experiments, after exposure of the clean surface to gas-phase atomic hydrogen at 90 K, two additional peaks grow in the desorption spectra at 115 and 150 K. The surface saturation coverage, determined by equilibrium between abstraction and adsorption reactions, is 2.5 monolayers. Preadsorbed deuterium abstraction experiments with gas-phase atomic hydrogen show that a pure Eley-Rideal mechanism is not involved in the process, while a hot atom (HA) kinetics describes well the reaction. By least-squares fitting of the experimental data, a simplified HA kinetic model yields an abstraction cross section value of 0.5 +/- 0.2 angstroms2. The atomic hydrogen interaction with an oxygen precovered surface was also studied by means of both TPD and x-ray photoelectron spectroscopy: oxygen hydrogenation and water production take place already at very low temperature (90 K).

  20. Atoms and Molecules Interacting with Light

    Science.gov (United States)

    van der Straten, Peter; Metcalf, Harold

    2016-02-01

    Part I. Atom-Light Interaction: 1. The classical physics pathway; Appendix 1.A. Damping force on an accelerating charge; Appendix 1.B. Hanle effect; Appendix 1.C. Optical tweezers; 2. Interaction of two-level atoms and light; Appendix 2.A. Pauli matrices for motion of the bloch vector; Appendix 2.B. The Ramsey method; Appendix 2.C. Echoes and interferometry; Appendix 2.D. Adiabatic rapid passage; Appendix 2.E Superposition and entanglement; 3. The atom-light interaction; Appendix 3.A. Proof of the oscillator strength theorem; Appendix 3.B. Electromagnetic fields; Appendix 3.C. The dipole approximation; Appendix 3.D. Time resolved fluorescence from multi-level atoms; 4. 'Forbidden' transitions; Appendix 4.A. Higher order approximations; 5. Spontaneous emission; Appendix 5.A. The quantum mechanical harmonic oscillator; Appendix 5.B. Field quantization; Appendix 5.C. Alternative theories to QED; 6. The density matrix; Appendix 6.A. The Liouville-von Neumann equation; Part II. Internal Structure: 7. The hydrogen atom; Appendix 7.A. Center-of-mass motion; Appendix 7.B. Coordinate systems; Appendix 7.C. Commuting operators; Appendix 7.D. Matrix elements of the radial wavefunctions; 8. Fine structure; Appendix 8.A. The Sommerfeld fine-structure constant; Appendix 8.B. Measurements of the fine structure 9. Effects of the nucleus; Appendix 9.A. Interacting magnetic dipoles; Appendix 9.B. Hyperfine structure for two spin =2 particles; Appendix 9.C. The hydrogen maser; 10. The alkali-metal atoms; Appendix 10.A. Quantum defects for the alkalis; Appendix 10.B. Numerov method; 11. Atoms in magnetic fields; Appendix 11.A. The ground state of atomic hydrogen; Appendix 11.B. Positronium; Appendix 11.C. The non-crossing theorem; Appendix 11.D. Passage through an anticrossing: Landau-Zener transitions; 12. Atoms in electric fields; 13. Rydberg atoms; 14. The helium atom; Appendix 14.A. Variational calculations; Appendix 14.B. Detail on the variational calculations of the ground state

  1. Bright Solitons in an Atomic Tunnel Array with Either Attractive or Repulsive Atom-Atom Interactions

    Institute of Scientific and Technical Information of China (English)

    YANG Xiao-Xue; YOU Jun; WU Ying

    2004-01-01

    @@ Taking a coherent state representation, we derive the nonlinear Schrodinger-type differential-difference equations from the quantized model of an array of traps containing Bose-Einstein condensates and linked by the tunnelling process among the adjacent traps. It is shown that no matter whether two-body interactions among atoms are repulsive or attractive, a nearly uniform atom distribution can evolve into a bright soliton-type localized ensemble of atoms and a lump of atom distribution can also be smeared out by redistributing atoms among traps under appropriate initial phase differences of atoms in adjacent traps. These two important features originate from the tailoring effect of the initial phase conditions in coherent tunnelling processes, which differs crucially from the previous tailoring effect coming mainly from the periodicity of optical lattices.

  2. ATOMS INTERACTING WITH ELECTROMAGNETIC FIELDS, MULTIPHOTON IONIZATION

    OpenAIRE

    Mainfray, G

    1982-01-01

    The non linear interaction between an intense laser radiation and atoms leads to ionization through the absorption of N photons from the laser radiation via laser-induced virtual states. The multiphoton ionization rate varies as a function of the laser intensity I as IN. We discuss the two most important effects which govern multiphoton ionization processes : resonance effects and laser-coherence effects. In a moderate laser intensity range (107 - 109 W cm-2) corresponding to the two, three o...

  3. Networks and Interactivity

    DEFF Research Database (Denmark)

    Considine, Mark; Lewis, Jenny

    2012-01-01

    The systemic reform of employment services in OECD countries was driven by New Public Management (NPM) and then post-NPM reforms, when first-phase changes such as privatization were amended with `joined up' processes to help manage fragmentation. This article examines the networking strategies...

  4. Interactive Network Exploration with Orange

    Directory of Open Access Journals (Sweden)

    Miha Štajdohar

    2013-04-01

    Full Text Available Network analysis is one of the most widely used techniques in many areas of modern science. Most existing tools for that purpose are limited to drawing networks and computing their basic general characteristics. The user is not able to interactively and graphically manipulate the networks, select and explore subgraphs using other statistical and data mining techniques, add and plot various other data within the graph, and so on. In this paper we present a tool that addresses these challenges, an add-on for exploration of networks within the general component-based environment Orange.

  5. Effective potentials for atom-atom interaction at low temperatures

    OpenAIRE

    Gao, Bo

    2002-01-01

    We discuss the concept and design of effective atom-atom potentials that accurately describe any physical processes involving only states around the threshold. The existence of such potentials gives hope to a quantitative, and systematic, understanding of quantum few-atom and quantum many-atom systems at relatively low temperatures.

  6. Nanoarchitectonic atomic switch networks for unconventional computing

    Science.gov (United States)

    Demis, Eleanor C.; Aguilera, Renato; Scharnhorst, Kelsey; Aono, Masakazu; Stieg, Adam Z.; Gimzewski, James K.

    2016-11-01

    Developments in computing hardware are constrained by the operating principles of complementary metal oxide semiconductor (CMOS) technology, fabrication limits of nanometer scaled features, and difficulties in effective utilization of high density interconnects. This set of obstacles has promulgated a search for alternative, energy efficient approaches to computing inspired by natural systems including the mammalian brain. Atomic switch network (ASN) devices are a unique platform specifically developed to overcome these current barriers to realize adaptive neuromorphic technology. ASNs are composed of a massively interconnected network of atomic switches with a density of ∼109 units/cm2 and are structurally reminiscent of the neocortex of the brain. ASNs possess both the intrinsic capabilities of individual memristive switches, such as memory capacity and multi-state switching, and the characteristics of large-scale complex systems, such as power-law dynamics and non-linear transformations of input signals. Here we describe the successful nanoarchitectonic fabrication of next-generation ASN devices using combined top-down and bottom-up processing and experimentally demonstrate their utility as reservoir computing hardware. Leveraging their intrinsic dynamics and transformative input/output (I/O) behavior enabled waveform regression of periodic signals in the absence of embedded algorithms, further supporting the potential utility of ASN technology as a platform for unconventional approaches to computing.

  7. Strong interaction studies with kaonic atoms

    CERN Document Server

    Marton, J; Beer, G; Berucci, C; Bosnar, D; Bragadireanu, A M; Cargnelli, M; Clozza, A; Curceanu, C; d'Uffizi, A; Fiorini, C; Ghio, F; Guaraldo, C; Hayano, R; Iliescu, M; Ishiwatari, T; Iwasaki, M; Sandri, P Levi; Okada, S; Pietreanu, D; Piscicchia, K; Ponta, T; Quaglia, R; Vidal, A Romero; Sbardella, E; Scordo, A; Shi, H; Sirghi, D L; Sirghi, F; Tatsuno, H; Doce, O Vazquez; Widmann, E; Zmeskal, J

    2015-01-01

    The strong interaction of antikaons (K-) with nucleons and nuclei in the low energy regime represents an active research field connected intrinsically with few-body physics. There are important open questions like the question of antikaon nuclear bound states - the prototype system being K-pp. A unique and rather direct experimental access to the antikaon-nucleon scattering lengths is provided by precision X-ray spectroscopy of transitions in low-lying states of light kaonic atoms like kaonic hydrogen isotopes. In the SIDDHARTA experiment at the electron-positron collider DA?NE of LNF-INFN we measured the most precise values of the strong interaction observables, i.e. the strong interaction on the 1s ground state of the electromagnetically bound K-p atom leading to a hadronic shift and a hadronic broadening of the 1s state. The SIDDHARTA result triggered new theoretical work which achieved major progress in the understanding of the low-energy strong interaction with strangeness. Antikaon-nucleon scattering le...

  8. Strong interaction studies with kaonic atoms

    CERN Document Server

    Marton, J; Beer, G; Berucci, C; Bosnar, D; Bragadireanu, A M; Cargnelli, M; Clozza, A; Curceanu, C; d'Uffizi, A; Fiorini, C; Ghio, F; Guaraldo, C; Hayano, R; Iliescu, M; Ishiwatari, T; Iwasaki, M; Sandri, P Levi; Okada, S; Pietreanu, D; Piscicchia, K; Ponta, T; Quaglia, R; Vidal, A Romero; Sbardella, E; Scordo, A; Shi, H; Sirghi, D L; Sirghi, F; Tatsuno, H; Doce, O Vazquez; Widmann, E; Zmeskal, J

    2016-01-01

    The strong interaction of antikaons with nucleons and nuclei in the low-energy regime represents an active research field connected intrinsically with few-body physics. There are important open questions like the question of antikaon nuclear bound states. A unique and rather direct experimental access to the antikaon-nucleon scattering lengths is provided by precision X-ray spectroscopy of transitions in low-lying states of light kaonic atoms like kaonic hydrogen isotopes. In the SIDDHARTA experiment at the electron-positron collider DAFNE of LNF-INFN we measured the most precise values of the strong interaction observables, i.e. the strong interaction on the 1s ground state of the electromagnetically bound kaonic hydrogen atom leading to a hadronic shift and a hadronic broadening of the 1s state. The SIDDHARTA result triggered new theoretical work which achieved major progress in the understanding of the low-energy strong interaction with strangeness. Antikaon-nucleon scattering lengths have been calculated ...

  9. Friction Effects in Atom-Surface Interactions

    Science.gov (United States)

    Jentschura, Ulrich D.

    2016-05-01

    Atom-surface interactions both have a conservative as well as a dissipative component. A treatment of the dissipative terms requires the use of the fluctuation-dissipation theorem, and the calculation of the imaginary part of the polarizability of an atom is required. The paper will review the recent resolution of a long-standing question regarding the low-frequency asymptotics of the imaginary part, as summarized in and, together with K. Pachucki, G. Lach and M. De Kieviet. The surprising conclusion is that the precise form of the imaginary part for low driving frequency is dominated by a so-called quantum electrodynamic loop correction, where ``correction'' here is not to be taken literally. The one-loop QED term dominates over the tree-level contribution! The findings drastically alter theoretical predictions for non-contact friction, and blackbody friction (due to the atom's interaction with a bath of thermal photons). The basic principle behind the calculation and the methods of nonrelativistic quantum electrodynamics will be discussed. Supported by the NSF (Grant PHY-1403973).

  10. Strong interaction studies with kaonic atoms

    Directory of Open Access Journals (Sweden)

    Marton J.

    2016-01-01

    Full Text Available The strong interaction of antikaons (K− with nucleons and nuclei in the low-energy regime represents an active research field connected intrinsically with few-body physics. There are important open questions like the question of antikaon nuclear bound states - the prototype system being K−pp. A unique and rather direct experimental access to the antikaon-nucleon scattering lengths is provided by precision X-ray spectroscopy of transitions in low-lying states of light kaonic atoms like kaonic hydrogen isotopes. In the SIDDHARTA experiment at the electron-positron collider DAΦNE of LNF-INFN we measured the most precise values of the strong interaction observables, i.e. the strong interaction on the 1s ground state of the electromagnetically bound K−p atom leading to a hadronic shift ϵ1s and a hadronic broadening Γ1s of the 1s state. The SIDDHARTA result triggered new theoretical work which achieved major progress in the understanding of the low-energy strong interaction with strangeness. Antikaon-nucleon scattering lengths have been calculated constrained by the SIDDHARTA data on kaonic hydrogen. For the extraction of the isospin-dependent scattering lengths a measurement of the hadronic shift and width of kaonic deuterium is necessary. Therefore, new X-ray studies with the focus on kaonic deuterium are in preparation (SIDDHARTA2. Many improvements in the experimental setup will allow to measure kaonic deuterium which is challenging due to the anticipated low X-ray yield. Especially important are the data on the X-ray yields of kaonic deuterium extracted from a exploratory experiment within SIDDHARTA.

  11. Atom-atom interactions around the band edge of a photonic crystal waveguide.

    Science.gov (United States)

    Hood, Jonathan D; Goban, Akihisa; Asenjo-Garcia, Ana; Lu, Mingwu; Yu, Su-Peng; Chang, Darrick E; Kimble, H J

    2016-09-20

    Tailoring the interactions between quantum emitters and single photons constitutes one of the cornerstones of quantum optics. Coupling a quantum emitter to the band edge of a photonic crystal waveguide (PCW) provides a unique platform for tuning these interactions. In particular, the cross-over from propagating fields [Formula: see text] outside the bandgap to localized fields [Formula: see text] within the bandgap should be accompanied by a transition from largely dissipative atom-atom interactions to a regime where dispersive atom-atom interactions are dominant. Here, we experimentally observe this transition by shifting the band edge frequency of the PCW relative to the [Formula: see text] line of atomic cesium for [Formula: see text] atoms trapped along the PCW. Our results are the initial demonstration of this paradigm for coherent atom-atom interactions with low dissipation into the guided mode.

  12. A Network Synthesis Model for Generating Protein Interaction Network Families

    OpenAIRE

    Sayed Mohammad Ebrahim Sahraeian; Byung-Jun Yoon

    2012-01-01

    In this work, we introduce a novel network synthesis model that can generate families of evolutionarily related synthetic protein-protein interaction (PPI) networks. Given an ancestral network, the proposed model generates the network family according to a hypothetical phylogenetic tree, where the descendant networks are obtained through duplication and divergence of their ancestors, followed by network growth using network evolution models. We demonstrate that this network synthesis model ca...

  13. Interaction of a slow monopole with a hydrogen atom

    OpenAIRE

    Shnir, Ya. M.

    1996-01-01

    The electric dipole moment of the hydrogen-like atom induced by a monopole moving outside the electron shell is calculated. The correction to the energy of the ground state of the hydrogen atom due to this interaction is calculated.

  14. Long range interactions between alkali and alkaline-earth atoms

    CERN Document Server

    Jiang, Jun; Mitroy, J

    2013-01-01

    Dispersion coefficients between the alkali metal atoms (Li-Rb) and alkaline-earth metal atoms (Be-Sr) are evaluated using matrix elements computed from frozen core configuration interaction calculations. Besides dispersion coefficients with both atoms in their respective ground states, dispersion coefficients are also given for the case where one atom is in its ground state and the other atom is in a low lying excited state.

  15. Effects of a uniform acceleration on atom-field interactions

    CERN Document Server

    Marino, Jamir; Passante, Roberto; Rizzuto, Lucia; Spagnolo, Salvatore

    2014-01-01

    We review some quantum electrodynamical effects related to the uniform acceleration of atoms in vacuum. After discussing the energy level shifts of a uniformly accelerated atom in vacuum, we investigate the atom-wall Casimir-Polder force for accelerated atoms, and the van der Waals/Casimir-Polder interaction between two accelerated atoms. The possibility of detecting the Unruh effect through these phenomena is also discussed in detail.

  16. Manipulating Higher Partial-Wave Atom-Atom Interaction by Strong Photoassoiative Coupling

    OpenAIRE

    Deb, Bimalendu; Hazra, Jisha

    2009-01-01

    We show that it is possible to change not only s-wave but also higher partial wave atom-atom interactions in cold collision in the presence of relatively intense laser fields tuned near a photoassociative transition.

  17. Interaction-Free Measurements, Atom Localisation and Complementarity

    OpenAIRE

    Karlsson, Anders; Bjork, Gunnar; Forsberg, Erik

    1997-01-01

    We analyse interaction-free measurements on classical and quantum objects. We show the transition from a classical interaction free measurement to a quantum non-demolition measurement of atom number, and discuss the mechanism of the enforcement of complementarity in atom interferometric interaction-free measurements.

  18. Preparation of Entangled Atomic States Through Resonant Atom-Field Interaction

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    A scheme is proposed for the generation of two-atom maximally entangled states and multi-atom maximally entangled states of W class. The scheme is based on the simultaneous resonant interaction of atoms with a single-mode cavity field. It does not require accurate adjustment of the interaction time. The time needed to complete the generation does not increase with the number of the atom.

  19. Entanglement properties between two atoms in the binomial optical field interacting with two entangled atoms

    Institute of Scientific and Technical Information of China (English)

    刘堂昆; 张康隆; 陶宇; 单传家; 刘继兵

    2016-01-01

    The temporal evolution of the degree of entanglement between two atoms in a system of the binomial optical field interacting with two arbitrary entangled atoms is investigated. The influence of the strength of the dipole–dipole interaction between two atoms, probabilities of the Bernoulli trial, and particle number of the binomial optical field on the temporal evolution of the atomic entanglement are discussed. The result shows that the two atoms are always in the entanglement state. Moreover, if and only if the two atoms are initially in the maximally entangled state, the entanglement evolution is not affected by the parameters, and the degree of entanglement is always kept as 1.

  20. Positron Interactions with Atoms and Ions

    Science.gov (United States)

    Bhatia, Anand K.

    2012-01-01

    Dirac, in 1928, combining the ideas of quantum mechanics and the ideas of relativity invented the well-known relativistic wave equation. In his formulation, he predicted an antiparticle of the electron of spin n-bar/2. He thought that this particle must be a proton. Dirac published his interpretation in a paper 'A theory of electrons and protons.' It was shown later by the mathematician Hermann Weyl that the Dirac theory was completely symmetric between negative and positive particles and the positive particle must have the same mass as that of the electron. In his J. Robert Oppenheimer Memorial Prize Acceptance Speech, Dirac notes that 'Blackett was really the first person to obtain hard evidence for the existence of a positron but he was afraid to publish it. He wanted confirmation, he was really over cautious.' Positron, produced by the collision of cosmic rays in a cloud chamber, was detected experimentally by Anderson in 1932. His paper was published in Physical Review in 1933. The concept of the positron and its detection were the important discoveries of the 20th century. I have tried to discuss various processes involving interactions of positrons with atoms and ions. This includes scattering, bound states and resonances. It has not been possible to include the enormous work which has been carried out during the last 40 or 50 years in theory and measurements.

  1. Protein interaction networks from literature mining

    Science.gov (United States)

    Ihara, Sigeo

    2005-03-01

    The ability to accurately predict and understand physiological changes in the biological network system in response to disease or drug therapeutics is of crucial importance in life science. The extensive amount of gene expression data generated from even a single microarray experiment often proves difficult to fully interpret and comprehend the biological significance. An increasing knowledge of protein interactions stored in the PubMed database, as well as the advancement of natural language processing, however, makes it possible to construct protein interaction networks from the gene expression information that are essential for understanding the biological meaning. From the in house literature mining system we have developed, the protein interaction network for humans was constructed. By analysis based on the graph-theoretical characterization of the total interaction network in literature, we found that the network is scale-free and semantic long-ranged interactions (i.e. inhibit, induce) between proteins dominate in the total interaction network, reducing the degree exponent. Interaction networks generated based on scientific text in which the interaction event is ambiguously described result in disconnected networks. In contrast interaction networks based on text in which the interaction events are clearly stated result in strongly connected networks. The results of protein-protein interaction networks obtained in real applications from microarray experiments are discussed: For example, comparisons of the gene expression data indicative of either a good or a poor prognosis for acute lymphoblastic leukemia with MLL rearrangements, using our system, showed newly discovered signaling cross-talk.

  2. Depletion interaction measured by colloidal probe atomic force microscopy

    NARCIS (Netherlands)

    Wijting, W.K.; Knoben, W.; Besseling, N.A.M.; Leermakers, F.A.M.; Cohen Stuart, M.A.

    2004-01-01

    We investigated the depletion interaction between stearylated silica surfaces in cyclohexane in the presence of dissolved polydimethylsiloxane by means of colloidal probe atomic force microscopy. We found that the range of the depletion interaction decreases with increasing concentration. Furthermor

  3. Effective oscillator strength distributions of spherically symmetric atoms for calculating polarizabilities and long-range atom-atom interactions

    CERN Document Server

    Jiang, Jun; Cheng, Yongjun; Bromley, M W J

    2014-01-01

    Effective oscillator strength distributions are systematically generated and tabulated for the alkali atoms, the alkaline-earth atoms, the alkaline-earth ions, the rare gases and some miscellaneous atoms. These effective distributions are used to compute the dipole, quadrupole and octupole static polarizabilities, and are then applied to the calculation of the dynamic polarizabilities at imaginary frequencies. These polarizabilities can be used to determine the long-range $C_6$, $C_8$ and $C_{10}$ atom-atom interactions for the dimers formed from any of these atoms and ions, and we present tables covering all of these combinations.

  4. Coherent and incoherent dipole-dipole interactions between atoms

    Science.gov (United States)

    Robicheaux, Francis

    2016-05-01

    Results will be presented on the collective interaction between atoms due to the electric dipole-dipole coupling between states of different parity on two different atoms. A canonical example of this effect is when the electronic state of one atom has S-character and the state of another atom has P-character. The energy difference between the two states plays an important role in the interaction since the change in energy determines the wave number of a photon that would cause a transition between the states. If the atoms are much closer than the wave length of this photon, then the dipole-dipole interaction is in the near field and has a 1 /r3 dependence on atomic separation. If the atoms are farther apart than the wave length, then the interaction is in the far field and has a 1 / r dependence. When many atoms interact, collective effects can dominate the system with the character of the collective effect depending on whether the atomic separation leads to near field or far field coupling. As an example of the case where the atoms are in the far field, the line broadening of transitions and strong deviations from the Beer-Lambert law in a diffuse gas will be presented. As an example of near field collective behavior, the radiative properties of a Rydberg gas will be presented. Based upon work supported by the National Science Foundation under Grant No. 1404419-PHY in collaboration with R.T. Sutherland.

  5. Spectroscopic detection of atom-surface interactions in an atomic vapour layer with nanoscale thickness

    CERN Document Server

    Whittaker, K A; Hughes, I G; Sargsyan, A; Sarkisyan, D; Adams, C S

    2015-01-01

    We measure the resonance line shape of atomic vapor layers with nanoscale thickness confined between two sapphire windows. The measurement is performed by scanning a probe laser through resonance and collecting the scattered light. The line shape is dominated by the effects of Dicke narrowing, self-broadening, and atom-surface interactions. By fitting the measured line shape to a simple model we discuss the possibility to extract information about the atom-surface interaction.

  6. Entanglement Preparation and Quantum Information Processing with Atoms Trapped in Separated Cavities Through a Single Resonant Atom-Field Interaction

    Science.gov (United States)

    Lin, Li-Hua

    2014-01-01

    In this paper, a scheme is presented for generation of W-type entangled states for n atoms trapped in separated cavities connected by optical fibers. The scheme only requires a single atom-cavity-fiber interaction and no classical field is needed. Due to these features, the scheme is simpler and more robust against decoherence than the previous ones. The scheme can also be used to realize quantum state transfer and controlled phase gates between qubits located at distant nodes of a quantum network.

  7. Interaction-Free Effects Between Distant Atoms

    CERN Document Server

    Aharonov, Yakir; Elitzur, Avshalom C; Smolin, Lee

    2016-01-01

    A gedankenexperiment is presented where an excited and a ground-state atom are positioned such that, within the former's half-life time, they exchange a photon with 50% probability. A measurement of their energy state will therefore indicate in 50% of the cases that no photon was exchanged. Yet other measurements would reveal that, by the mere possibility of exchange, the two atoms become entangled. Consequently, the "no exchange" result, apparently precluding entanglement, is non-locally established between the atoms by this very entanglement. When densely repeated several times, this result gives rise to the Quantum Zeno effect as well, again exerted between distant atoms without photon exchange. We discuss these experiments as variants of IFM, now generalized for both spatial and temporal uncertainties. We next employ weak measurements for a sharper and simpler elucidation of the paradox. Interpretational issues are discussed in the conclusion, and a resolution is offered within the Two-State Vector Formal...

  8. Spontaneous emission of two interacting atoms near an interface

    Institute of Scientific and Technical Information of China (English)

    Dehua Wang

    2009-01-01

    The spontaneous emission rate of two interacting excited atoms near a dielectric interface is studied using the photon closed-orbit theory and the dipole image method.The total emission rate of one atom during the emission process is calculated as a function of the distance between the atom and the interface.The results suggest that the spontaneous emission rate depends not only on the atomic-interface distances,but also on the orientation of the two atomic dipoles and the initial distance between the two atoms.The oscillation in the spontaneous emission rate is caused by the interference between the outgoing electromagnetic wave emitted from one atom and other waves arriving at this atom after traveling along various classical orbits.Each peak in the Fourier transformed spontaneous emission rate corresponds with one action of photon classical orbit.

  9. Controlling interaction of ultracold atoms in an optical superlattice

    Science.gov (United States)

    Duan, Luming

    2008-05-01

    First, I will briefly review the methods to control spin- exchange interaction for ultracold atoms in an optical lattice [1], and the recent experimental techniques to demonstrate the second-order tunneling responsible for the spin exchange interaction with a superlattice [2]. Then, I will discuss the interaction for strongly interacting atoms in a lattice near a wide Feshbach resonance. The strong interaction brings in a number of new features such as multi-band populations and direct neighboring interaction. Under certain circumstances, this complicated system can be described by an effective single- band model (the general Hubbard model) which has particle assisted tunneling for the atoms [3]. The particle assisted tunneling means that the effective atomic tunneling rate from the site i to j depends on whether there is another atom on these two sites. The particle assisted tunneling brings in new feature for quantum many-body physics. I will describe an experimental scheme to test the prediction of the particle assisted tunneling for strongly interacting atoms based on the use of the optical superlattice technique [4]. [1] L.-M. Duan, E. Demler, M. D. Lukin, Controlling Spin Exchange Interactions of Ultracold Atoms in Optical Lattices, Phys. Rev. Lett. 91, 090402 (2003). [2] S. F"olling, S. Trotzky, P. Cheinet, M. Feld, R. Saers, A. Widera, T. M"uller, I. Bloch, Direct Observation of Second Order Atom Tunnelling, Nature 448, 1029 (2007). [3] L.-M. Duan, Effective Hamiltonian for fermions in an optical lattice across a Feshbach resonance, cond-mat/0508745, Phys. Rev. Lett. 95, 243202 (2005); L.-M. Duan General Hubbard model for strongly interacting fermions in an optical lattice and its phase detection, arXiv:0706.2161, Europhys. Lett. 81, 20001 (2008). [4] T. Goodman, L.-M. Duan, Test of particle assisted tunneling with strongly interacting atoms in an opticla superlattice, in preparation.

  10. Atomic processes in matter-antimatter interactions

    International Nuclear Information System (INIS)

    Atomic processes dominate antiproton stopping in matter at nearly all energies of interest. They significantly influence or determine the antiproton annihilation rate at all energies around or below several MeV. This article reviews what is known about these atomic processes. For stopping above about 10 eV the processes are antiproton-electron collisions, effective at medium keV through high MeV energies, and elastic collisions with atoms and adiabatic ionization of atoms, effective from medium eV through low keB energies. For annihilation above about 10 eV is the enhancement of the antiproton annihilation rate due to the antiproton-nucleus coulomb attraction, effective around and below a few tens of MeV. At about 10 eV and below, the atomic rearrangement/annihilation process determines both the stopping and annihilation rates. Although a fair amount of theoretical and some experimental work relevant to these processes exist, there are a number of energy ranges and material types for which experimental data does not exist and for which the theoretical information is not as well grounded or as accurate as desired. Additional experimental and theoretical work is required for accurate prediction of antiproton stopping and annihilation for energies and material relevant to antiproton experimentation and application

  11. Observation of atom wave phase shifts induced by van der Waals atom-surface interactions

    OpenAIRE

    Perreault, John D.; Cronin, Alexander D.

    2005-01-01

    The development of nanotechnology and atom optics relies on understanding how atoms behave and interact with their environment. Isolated atoms can exhibit wave-like (coherent) behaviour with a corresponding de Broglie wavelength and phase which can be affected by nearby surfaces. Here an atom interferometer is used to measure the phase shift of Na atom waves induced by the walls of a 50 nm wide cavity. To our knowledge this is the first direct measurement of the de Broglie wave phase shift ca...

  12. Rydberg atom interactions from 300 K to 300 K

    Science.gov (United States)

    Pillet, P.; Gallagher, T. F.

    2016-09-01

    Cold Rydberg atoms provide novel approaches to many-body problems and quantum simulation. To introduce the recent work presented in this special issue, we present here a quick history of a half-century research activity in the Rydberg-atom field, focusing our attention on the giant interactions between Rydberg atoms and other atoms. These interactions are the origin of many effects observed with Rydberg atoms: pressure shifts, dipole–dipole energy transfer, and avalanche-ionization. These effects have led to evidence of new bound chemical states, such as trilobites states, many-body effects in frozen Rydberg gases, and the spontaneous formation of ultra-cold plasmas. They open exciting new prospects at the intersection of atomic physics, condensed matter physics, and plasma physics.

  13. Atom-atom interactions around the band edge of a photonic crystal waveguide

    Science.gov (United States)

    Hood, Jonathan D.; Goban, Akihisa; Asenjo-Garcia, Ana; Lu, Mingwu; Yu, Su-Peng; Chang, Darrick E.; Kimble, H. J.

    2016-09-01

    Tailoring the interactions between quantum emitters and single photons constitutes one of the cornerstones of quantum optics. Coupling a quantum emitter to the band edge of a photonic crystal waveguide (PCW) provides a unique platform for tuning these interactions. In particular, the cross-over from propagating fields E(x)∝e±ikxxE(x)∝e±ikxx outside the bandgap to localized fields E(x)∝e-κx|x|E(x)∝e-κx|x| within the bandgap should be accompanied by a transition from largely dissipative atom-atom interactions to a regime where dispersive atom-atom interactions are dominant. Here, we experimentally observe this transition by shifting the band edge frequency of the PCW relative to the D1D1 line of atomic cesium for N¯=3.0±0.5N¯=3.0±0.5 atoms trapped along the PCW. Our results are the initial demonstration of this paradigm for coherent atom-atom interactions with low dissipation into the guided mode.

  14. Exotic atoms and the kaon-nucleon interaction

    International Nuclear Information System (INIS)

    Recent progress in the study of p-bar-p and p-bar-nucleus atoms is briefly reviewed before moving on to a discussion of the kaon-nucleon interaction at low energies. The need for new definitive X-ray measurements for K-p atoms is emphasised. Finally some comments are made about K-bar-nucleus and Σ-, Ξ- and Ω- atoms. (author)

  15. Study on the fine control of atoms by coherent interaction

    Energy Technology Data Exchange (ETDEWEB)

    Han, Jae Min; Rho, S. P.; Park, H. M.; Lee, K. S.; Rhee, Y. J.; Yi, J. H.; Jeong, D. Y.; Jung, E. C.; Choe, A. S.; Lee, J. M

    1998-01-01

    The basic research on the control of atoms using the coherent interaction, such as the development of the generator of the thermal atomic beam with high directionality, the photodeflection of atomic beam and the coherent excitation of atoms, has been performed. Yb atomic beam with small divergence was generated and the deflection mechanism of the atomic beam was studied by using a broad band dye laser and a narrow band laser. It has been proved that the single mode dye laser with narrow bandwidth was suitable for deflection of atoms but the frequency locking system was indispensable. And the apparatus for intermodulated optogalvanic (IMOG) experiment was developed and the high resolution optogalvanic spectroscopy was studied for laser frequency stabilization. (author). 74 refs., 1 tab., 26 figs

  16. Atoms and molecules interacting with light atomic physics for the laser era

    CERN Document Server

    Straten, Peter van der

    2016-01-01

    This in-depth textbook with a focus on atom-light interactions prepares students for research in a fast-growing and dynamic field. Intended to accompany the laser-induced revolution in atomic physics, it is a comprehensive text for the emerging era in atomic, molecular and optical science. Utilising an intuitive and physical approach, the text describes two-level atom transitions, including appendices on Ramsey spectroscopy, adiabatic rapid passage and entanglement. With a unique focus on optical interactions, the authors present multi-level atomic transitions with dipole selection rules, and M1/E2 and multiphoton transitions. Conventional structure topics are discussed in some detail, beginning with the hydrogen atom and these are interspersed with material rarely found in textbooks such as intuitive descriptions of quantum defects. The final chapters examine modern applications and include many references to current research literature. The numerous exercises and multiple appendices throughout enable advanc...

  17. Experimental investigations of the dipolar interactions between single Rydberg atoms

    CERN Document Server

    Browaeys, Antoine; Lahaye, Thierry

    2016-01-01

    This review summarizes experimental works performed over the last decade by several groups on the manipulation of a few individual interacting Rydberg atoms. These studies establish arrays of single Rydberg atoms as a promising platform for quantum state engineering, with potential applications to quantum metrology, quantum simulation and quantum information.

  18. Study on the fine control of atoms by coherent interaction

    Energy Technology Data Exchange (ETDEWEB)

    Han, Jae Min; Rho, S. P.; Park, H. M.; Lee, K. S.; Rhee, Y. J.; Yi, J. H.; Jeong, D. Y.; Ko, K. H.; Lee, J. M.; Kim, M.K

    2000-01-01

    Study on one dimensional atom cooling and trapping process which is basic to the development of atom manipulation technology has been performed. A Zeeman slower has been designed and manufactured for efficient cooling of atoms. The speed of atoms finally achieved is as slow as 15 m/s with proper cooling conditions. By six circularly-polarized laser beams and quadrupole magnetic field, the atoms which have been slowed down by zeeman slower have been trapped in a small spatial region inside MOT. The higher the intensity of the slowing laser is the more is the number of atoms slowed and the maximum number of atoms trapped has been 10{sup 8}. The atoms of several tens of {mu}K degree have been trapped by controlling the intensity of trapping laser and intensity gradient of magnetic field. EIT phenomena caused by atomic coherent interaction has been studied for the development of atom optical elements. For the investigation of the focusing phenomena induced by the coherent interaction, experimental measurements and theoretical analysis have been performed. Spatial dependency of spectrum and double distribution signal of coupling laser have been obtained. The deflection of laser beams utilizing the EIT effects has also been considered. (author)

  19. Study on the fine control of atoms by coherent interaction

    International Nuclear Information System (INIS)

    Study on one dimensional atom cooling and trapping process which is basic to the development of atom manipulation technology has been performed. A Zeeman slower has been designed and manufactured for efficient cooling of atoms. The speed of atoms finally achieved is as slow as 15 m/s with proper cooling conditions. By six circularly-polarized laser beams and quadrupole magnetic field, the atoms which have been slowed down by zeeman slower have been trapped in a small spatial region inside MOT. The higher the intensity of the slowing laser is the more is the number of atoms slowed and the maximum number of atoms trapped has been 108. The atoms of several tens of μK degree have been trapped by controlling the intensity of trapping laser and intensity gradient of magnetic field. EIT phenomena caused by atomic coherent interaction has been studied for the development of atom optical elements. For the investigation of the focusing phenomena induced by the coherent interaction, experimental measurements and theoretical analysis have been performed. Spatial dependency of spectrum and double distribution signal of coupling laser have been obtained. The deflection of laser beams utilizing the EIT effects has also been considered. (author)

  20. Magnetic monopole interactions in simple atoms

    International Nuclear Information System (INIS)

    The excitation of simple atoms by slow moving massive monopoles is discussed. Previously presented results for a monopole of Dirac strength on hydrogen and helium are reviewed, and current efforts to refine the helium result are described. Helium proportional counters currently in operation which exploit this effect are briefly discussed. It is concluded that such counters are reliable and effective detectors for monopoles of arbitrary strength, and for negatively charged ions. (author)

  1. Preparation of entangled atomic states through simultaneous nonresonant atom-field interaction

    Institute of Scientific and Technical Information of China (English)

    Chen Mei-Feng

    2006-01-01

    A scheme is proposed for generating a three-atom maximal entanglement W state. It is based on the simultaneous nonresonant interaction of atoms with a single-mode cavity field. Our scheme is insensitive to the cavity field, so the cavity field in our scheme can be initially in thermal states.

  2. Explorers of the Universe: Interactive Electronic Network

    Science.gov (United States)

    Alvarez, Marino C.; Burks, Geoffrey; Busby, Michael R.; Cannon, Tiffani; Sotoohi, Goli; Wade, Montanez

    2000-01-01

    This paper details how the Interactive Electronic Network is being utilized by secondary and postsecondary students, and their teachers and professors, to facilitate learning and understanding. The Interactive Electronic Network is couched within the Explorers of the Universe web site in a restricted portion entitled Gateway.

  3. Collisional interaction between metastable neon atoms

    Energy Technology Data Exchange (ETDEWEB)

    Drunen, Wouter Johannes van

    2008-07-07

    In this thesis, the study of cold gases of neon atoms in different metastable states is described. It contains measurements of the collisional parameters for both the 3s[3/2]{sub 2} and the 3s'[1/2]{sub 0} metastable state and the dependence of the inelastic loss on external fields. Furthermore, the investigation of frequency dependent laser-induced collisions, and the possibility to excite photoassociation resonances is presented. For the measurements described here, neon atoms have been confined in a magnetooptical trap, in a magnetostatic trap, or in an optical dipole trap, respectively. By laser cooling inside the magnetic trap, atomic samples with more than 95 percent occupation of the magnetic substate m{sub J} = +2 could be prepared. They have a typical temperature of 0.5 mK, central densities up to 10{sup 11} cm{sup -3}, and a central phase-space density of up to 2.2.10{sup -7}. After loading the optical dipole trap from the magnetic trap, 2.5.10{sup 6} atoms with typical temperatures of 0.1 mK, and central densities up to 5.10{sup 10} cm{sup -3} were trapped. By evaporative cooling of the atoms in the magnetic trap we could increase the phase-space density by a factor of 200 to 5.10{sup -5}. Investigating the frequency dependence of laser-induced collisions did not reveal an experimental signature for the excitation of photoassociation resonances. For the {sup 3}D{sub 3} line a frequency dependence of laser enhanced Penning ionization was observed. Measurement of the two-body loss coefficient as function of the magnetic field showed a field dependence of the inelastic loss. These losses increase towards both small and large offset fields. The implementation of an optical dipole trap allowed us to trap the {sup 3}P{sub 0} metastable state. From the trap loss measurements we determined the two-body loss coefficient of the {sup 3}P{sub 0} metastable state for both bosonic isotopes {sup 20}Ne and {sup 22}Ne. For {sup 20}Ne we obtained {beta}=6{sup +5}{sub

  4. Collisional interaction between metastable neon atoms

    International Nuclear Information System (INIS)

    In this thesis, the study of cold gases of neon atoms in different metastable states is described. It contains measurements of the collisional parameters for both the 3s[3/2]2 and the 3s'[1/2]0 metastable state and the dependence of the inelastic loss on external fields. Furthermore, the investigation of frequency dependent laser-induced collisions, and the possibility to excite photoassociation resonances is presented. For the measurements described here, neon atoms have been confined in a magnetooptical trap, in a magnetostatic trap, or in an optical dipole trap, respectively. By laser cooling inside the magnetic trap, atomic samples with more than 95 percent occupation of the magnetic substate mJ = +2 could be prepared. They have a typical temperature of 0.5 mK, central densities up to 1011 cm-3, and a central phase-space density of up to 2.2.10-7. After loading the optical dipole trap from the magnetic trap, 2.5.106 atoms with typical temperatures of 0.1 mK, and central densities up to 5.1010 cm-3 were trapped. By evaporative cooling of the atoms in the magnetic trap we could increase the phase-space density by a factor of 200 to 5.10-5. Investigating the frequency dependence of laser-induced collisions did not reveal an experimental signature for the excitation of photoassociation resonances. For the 3D3 line a frequency dependence of laser enhanced Penning ionization was observed. Measurement of the two-body loss coefficient as function of the magnetic field showed a field dependence of the inelastic loss. These losses increase towards both small and large offset fields. The implementation of an optical dipole trap allowed us to trap the 3P0 metastable state. From the trap loss measurements we determined the two-body loss coefficient of the 3P0 metastable state for both bosonic isotopes 20Ne and 22Ne. For 20Ne we obtained β=6+5-4.10-10 cm3/s and for 22Ne β = 11+7-6.10-10 cm3/s. (orig.)

  5. A quantum network with atoms and photons (QNET-AP)

    Science.gov (United States)

    Meyers, Ronald E.; Lee, Patricia; Deacon, Keith S.; Tunick, Arnold; Quraishi, Qudsia; Stack, Daniel

    2012-10-01

    Enabling secure communication, unparalleled computing capabilities, and fundamental nonlocality physics exploration, the development of quantum repeaters is the key quantum information processing technology advance needed for implementing real world quantum networks beyond the laboratory environment. Currently, components exist for intra-laboratory quantum networks but no system exists for connecting distant ( 1 km ) quantum memories in the real world. We present a physics analysis of quantum repeater network designs for intracity optical fiber connections between nodes based on atomic memories and linear optics. Long distances will necessitate the use of (1) two-photon Hong-Ou-Mandel style interference between atomic ensembles for entanglement swapping, and (2) photonic qubit wavelength conversion between atomic emissions and photons at telecommunication wavelengths in fiber. We report on our experimental progress towards implementing A Quantum Network with Atoms and Photons (QNET-AP), a quantum repeater network test-bed, between the US Army Research Laboratory (ARL) and the Joint Quantum Institute (JQI) of the National Institute of Standards and Technology (NIST) and the University of Maryland (UMD).

  6. Controlled long-range interactions between Rydberg atoms and ions

    Science.gov (United States)

    Secker, T.; Gerritsma, R.; Glaetzle, A. W.; Negretti, A.

    2016-07-01

    We theoretically investigate trapped ions interacting with atoms that are coupled to Rydberg states. The strong polarizabilities of the Rydberg levels increase the interaction strength between atoms and ions by many orders of magnitude, as compared to the case of ground-state atoms, and may be mediated over micrometers. We calculate that such interactions can be used to generate entanglement between an atom and the motion or internal state of an ion. Furthermore, the ion could be used as a bus for mediating spin-spin interactions between atomic spins in analogy to much employed techniques in ion-trap quantum simulation. The proposed scheme comes with attractive features as it maps the benefits of the trapped-ion quantum system onto the atomic one without obviously impeding its intrinsic scalability. No ground-state cooling of the ion or atom is required and the setup allows for full dynamical control. Moreover, the scheme is to a large extent immune to the micromotion of the ion. Our findings are of interest for developing hybrid quantum information platforms and for implementing quantum simulations of solid-state physics.

  7. Controlled long-range interactions between Rydberg atoms and ions

    CERN Document Server

    Secker, Thomas; Glaetzle, Alexander W; Negretti, Antonio

    2016-01-01

    We theoretically investigate trapped ions interacting with atoms that are coupled to Rydberg states. The strong polarizabilities of the Rydberg levels increases the interaction strength between atoms and ions by many orders of magnitude, as compared to the case of ground state atoms, and may be mediated over micrometers. We calculate that such interactions can be used to generate entanglement between an atom and the motion or internal state of an ion. Furthermore, the ion could be used as a bus for mediating spin-spin interactions between atomic spins in analogy to much employed techniques in ion trap quantum simulation. The proposed scheme comes with attractive features as it maps the benefits of the trapped ion quantum system onto the atomic one without obviously impeding its intrinsic scalability. No ground state cooling of the ion or atom is required and the setup allows for full dynamical control. Moreover, the scheme is to a large extent immune to the micromotion of the ion. Our findings are of interest...

  8. Data Mining on Social Interaction Networks

    OpenAIRE

    Atzmueller, Martin

    2013-01-01

    Social media and social networks have already woven themselves into the very fabric of everyday life. This results in a dramatic increase of social data capturing various relations between the users and their associated artifacts, both in online networks and the real world using ubiquitous devices. In this work, we consider social interaction networks from a data mining perspective - also with a special focus on real-world face-to-face contact networks: We combine data mining and social netwo...

  9. Electrostatic interaction in atomic force microscopy

    OpenAIRE

    Butt, Hans-Jüurgen

    1991-01-01

    In atomic force microscopy, the stylus experiences an electrostatic force when imaging in aqueous medium above a charged surface. This force has been calculated numerically with continuum theory for a silicon nitrite or silicon oxide stylus. For comparison, the Van der Waals force was also calculated. In contrast to the Van der Waals attraction, the electrostatic force is repulsive. At a distance of 0.5 nm the electrostatic force is typically 10-12-10-10 N and thus comparable in strength to t...

  10. Calibrating dipolar interaction in an atomic condensate

    OpenAIRE

    Yi, S; You, L.

    2004-01-01

    We revisit the topic of a dipolar condensate with the recently derived more rigorous pseudo-potential for dipole-dipole interaction [A. Derevianko, Phys. Rev. A {\\bf 67}, 033607 (2003)]. Based on the highly successful variational technique, we find that all dipolar effects estimated before (using the bare dipole-dipole interaction) become significantly larger, i.e. are amplified by the new velocity-dependent pseudo-potential, especially in the limit of large or small trap aspect ratios. This ...

  11. Dynamics of deceptive interactions in social networks

    CERN Document Server

    Barrio, Rafael A; Dunbar, Robin; Iñiguez, Gerardo; Kaski, Kimmo

    2015-01-01

    In this paper we examine the role of lies in human social relations by implementing some salient characteristics of deceptive interactions into an opinion formation model, so as to describe the dynamical behaviour of a social network more realistically. In this model we take into account such basic properties of social networks as the dynamics of the intensity of interactions, the influence of public opinion, and the fact that in every human interaction it might be convenient to deceive or withhold information depending on the instantaneous situation of each individual in the network. We find that lies shape the topology of social networks, especially the formation of tightly linked, small communities with loose connections between them. We also find that agents with a larger proportion of deceptive interactions are the ones that connect communities of different opinion, and in this sense they have substantial centrality in the network. We then discuss the consequences of these results for the social behaviou...

  12. Interaction-induced decoherence of atomic BLOCH oscillations.

    Science.gov (United States)

    Buchleitner, Andreas; Kolovsky, Andrey R

    2003-12-19

    We show that the energy spectrum of the Bose-Hubbard model amended by a static field exhibits Wigner-Dyson level statistics. In itself a characteristic signature of quantum chaos, this induces the irreversible decay of Bloch oscillations of cold, interacting atoms loaded into an optical lattice, and provides a Hamiltonian model for interaction-induced decoherence.

  13. Engineered Rydberg Atom-Surface Interactions Using Metamaterials

    Science.gov (United States)

    Chao, Yuanxi; Sheng, Jiteng; Sedlacek, Jonathan; Shaffer, James

    2016-05-01

    We report on studies of Rydberg atom-surface interactions aimed at engineering Rydberg atom coupling to metamaterials. Rydberg atoms posses large electric dipole moments that can be strongly coupled to the tightly confined electromagnetic fields of surface phonon polariton (SPhP) modes of a properly constructed piezoelectric superlattice (PSL). Coupling of Rb87 Rydberg atoms, typically in microwave range, to real SPhP resonances on a periodically poled lithium niobate surface is studied theoretically for different periodic domain and surface orientations. Coupling constants, much larger than the dissipation of the atom-surface system, are calculated for atom-surface separations in the near field. This remarkable result opens up a simple way to design and conduct experiments to study the atom-surface interactions in the strong coupling regime which is usually hard to reach in other systems. The light-matter interaction described can be used for a quantum hybrid system that has potential applications for quantum photonic devices. Experimental studies of surfaces showing the efficacy of our calculations are also presented. This work is supported by AFOSR.

  14. Exact wave functions for atomic electron interacting with photon fields

    Institute of Scientific and Technical Information of China (English)

    Dong-Sheng Guo

    2013-01-01

    Many nonlinear quantum optical physics phenomena need more accurate wave functions and corresponding energy or quasienergy levels to account for. An analytic expression of wave functions with corresponding energy levels for an atomic electron interacting with a photon field is presented as an exact solution to the SchrSdinger-like equation involved with both atomic Coulomb interaction and electron-photon interaction. The solution is a natural generalization of the quantum-field Volkov states for an otherwise free electron interacting with a photon field. The solution shows that an N- level atom in light form stationary states without extra energy splitting in addition to the Floquet mechanism. The treatment developed here with computing codes can be conveniently transferred to quantum optics in classical-field version as research tools to benefit the whole physics community.

  15. Cavity-based quantum networks with single atoms and optical photons

    Science.gov (United States)

    Reiserer, Andreas; Rempe, Gerhard

    2015-10-01

    Distributed quantum networks will allow users to perform tasks and to interact in ways which are not possible with present-day technology. Their implementation is a key challenge for quantum science and requires the development of stationary quantum nodes that can send and receive as well as store and process quantum information locally. The nodes are connected by quantum channels for flying information carriers, i.e., photons. These channels serve both to directly exchange quantum information between nodes and to distribute entanglement over the whole network. In order to scale such networks to many particles and long distances, an efficient interface between the nodes and the channels is required. This article describes the cavity-based approach to this goal, with an emphasis on experimental systems in which single atoms are trapped in and coupled to optical resonators. Besides being conceptually appealing, this approach is promising for quantum networks on larger scales, as it gives access to long qubit coherence times and high light-matter coupling efficiencies. Thus, it allows one to generate entangled photons on the push of a button, to reversibly map the quantum state of a photon onto an atom, to transfer and teleport quantum states between remote atoms, to entangle distant atoms, to detect optical photons nondestructively, to perform entangling quantum gates between an atom and one or several photons, and even provides a route toward efficient heralded quantum memories for future repeaters. The presented general protocols and the identification of key parameters are applicable to other experimental systems.

  16. Atom-Pair Kinetics with Strong Electric-Dipole Interactions.

    Science.gov (United States)

    Thaicharoen, N; Gonçalves, L F; Raithel, G

    2016-05-27

    Rydberg-atom ensembles are switched from a weakly to a strongly interacting regime via adiabatic transformation of the atoms from an approximately nonpolar into a highly dipolar quantum state. The resultant electric dipole-dipole forces are probed using a device akin to a field ion microscope. Ion imaging and pair-correlation analysis reveal the kinetics of the interacting atoms. Dumbbell-shaped pair-correlation images demonstrate the anisotropy of the binary dipolar force. The dipolar C_{3} coefficient, derived from the time dependence of the images, agrees with the value calculated from the permanent electric-dipole moment of the atoms. The results indicate many-body dynamics akin to disorder-induced heating in strongly coupled particle systems. PMID:27284655

  17. Entropy of Field Interacting With Two Atoms in Bell State

    Institute of Scientific and Technical Information of China (English)

    JIAO Zhi-Yong; MA Jun-Mao; LI Ning; FU Xia

    2009-01-01

    In this paper, we investigate entropy properties of the single-mode coherent optical field interacting with the two two-level atoms initially in one of the four Bell states. It is found that the different initial states of the two atoms lead to different evolutions of field entropy and the intensity of the field plays an important role for the evolution properties of field entropy.

  18. The Casimir-Polder interaction an atom with spherical shell

    OpenAIRE

    Khusnutdinov, Nail

    2014-01-01

    The Casimir-Polder and van der Waals interaction energy of an atom with infinitely thin sphere with finite conductivity is investigated in the framework of the hydrodynamic approach. We put the sphere into spherical cavity inside the infinite dielectric media, then calculate the energy of vacuum fluctuations in the context of the zeta-function approach. The energy for a single atom is obtained by rarefying media. The Casimir-Polder expression for an atom and plate is recovered in the limit of...

  19. Resolved atomic interaction sidebands in an optical clock transition

    CERN Document Server

    Bishof, Michael; Swallows, Matthew D; Gorshkov, Alexey V; Ye, Jun; Rey, Ana Maria

    2011-01-01

    We report the observation of resolved atomic interaction sidebands (ISB) in the ${}^{87}$Sr optical clock transition when atoms at microkelvin temperatures are confined in a two-dimensional (2D) optical lattice. The ISB are a manifestation of the strong interactions that occur between atoms confined in a quasi-one-dimensional geometry and disappear when the confinement is relaxed along one dimension. The emergence of ISB is linked to the recently observed suppression of collisional frequency shifts in [1]. At the current temperatures, the ISB can be resolved but are broad. At lower temperatures, ISB are predicted to be substantially narrower and usable as powerful spectroscopic tools in strongly interacting alkaline-earth gases.

  20. Interactivity vs. fairness in networked linux systems

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Wenji; Crawford, Matt; /Fermilab

    2007-01-01

    In general, the Linux 2.6 scheduler can ensure fairness and provide excellent interactive performance at the same time. However, our experiments and mathematical analysis have shown that the current Linux interactivity mechanism tends to incorrectly categorize non-interactive network applications as interactive, which can lead to serious fairness or starvation issues. In the extreme, a single process can unjustifiably obtain up to 95% of the CPU! The root cause is due to the facts that: (1) network packets arrive at the receiver independently and discretely, and the 'relatively fast' non-interactive network process might frequently sleep to wait for packet arrival. Though each sleep lasts for a very short period of time, the wait-for-packet sleeps occur so frequently that they lead to interactive status for the process. (2) The current Linux interactivity mechanism provides the possibility that a non-interactive network process could receive a high CPU share, and at the same time be incorrectly categorized as 'interactive.' In this paper, we propose and test a possible solution to address the interactivity vs. fairness problems. Experiment results have proved the effectiveness of the proposed solution.

  1. Mutually-antagonistic interactions in baseball networks

    Science.gov (United States)

    Saavedra, Serguei; Powers, Scott; McCotter, Trent; Porter, Mason A.; Mucha, Peter J.

    2010-03-01

    We formulate the head-to-head matchups between Major League Baseball pitchers and batters from 1954 to 2008 as a bipartite network of mutually-antagonistic interactions. We consider both the full network and single-season networks, which exhibit structural changes over time. We find interesting structure in the networks and examine their sensitivity to baseball’s rule changes. We then study a biased random walk on the matchup networks as a simple and transparent way to (1) compare the performance of players who competed under different conditions and (2) include information about which particular players a given player has faced. We find that a player’s position in the network does not correlate with his placement in the random walker ranking. However, network position does have a substantial effect on the robustness of ranking placement to changes in head-to-head matchups.

  2. Mutually-Antagonistic Interactions in Baseball Networks

    CERN Document Server

    Saavedra, Serguei; McCotter, Trent; Porter, Mason A; Mucha, Peter J

    2009-01-01

    We formulate the head-to-head matchups between Major League Baseball pitchers and batters from 1954 to 2008 as a bipartite network of mutually-antagonistic interactions. We consider both the full network and single-season networks, which exhibit interesting structural changes over time. We also find that these networks exhibit a significant network structure that is sensitive to baseball's rule changes. We then study a biased random walk on the matchup networks as a simple and transparent way to compare the performance of players who competed under different conditions. We find that a player's position in the network does not correlate with his success in the random walker ranking but instead has a substantial effect on its sensitivity to changes in his own aggregate performance.

  3. Multiple complex networks emerging from individual interactions

    CERN Document Server

    da Rocha, Luis Enrique Correa

    2007-01-01

    Systems composed of distinct complex networks are present in many real-world environments, from society to ecological systems. In the present paper, we propose a network model obtained as a consequence of interactions between two species (e.g. predator and prey). Fields are produced and sensed by the individuals, defining spatio-temporal patterns which are strongly affected by the attraction intensity between individuals from the same species. The dynamical evolution of the system, including the change of individuals between different clusters, is investigated by building two complex networks having the individuals as nodes. In the first network, the edge weight is given by the Euclidean distance between every two individuals and, in the case of the second network, by the amount of time two individuals stay close one another. A third network is obtained from the two previous networks whose nodes correspond to the spatially congruent groups. The system evolves to an organized state where Gaussian and scale-fre...

  4. Synchronization in interacting Scale Free Networks

    CERN Document Server

    Torres, M F; La Rocca, C E; Braunstein, L A

    2015-01-01

    We study the fluctuations of the interface, in the steady state, of the Surface Relaxation Model (SRM) in two Scale Free interacting Networks where a fraction $q$ of nodes in both networks interact one to one through external connections. We find that as $q$ increases the fluctuations on both networks decrease and thus the synchronization is better than in isolated networks. As a consequence the system is optimal synchronized for $q=1$. The decrease of the fluctuations in both networks is due mainly to the diffusion through external connections which allows to reducing the load in nodes by sending the excess of load mostly to low degree nodes. This effect enhances the matching of the heights of low and high degree nodes as $q$ increases reducing the fluctuations.

  5. Identifying hubs in protein interaction networks.

    Directory of Open Access Journals (Sweden)

    Ravishankar R Vallabhajosyula

    Full Text Available BACKGROUND: In spite of the scale-free degree distribution that characterizes most protein interaction networks (PINs, it is common to define an ad hoc degree scale that defines "hub" proteins having special topological and functional significance. This raises the concern that some conclusions on the functional significance of proteins based on network properties may not be robust. METHODOLOGY: In this paper we present three objective methods to define hub proteins in PINs: one is a purely topological method and two others are based on gene expression and function. By applying these methods to four distinct PINs, we examine the extent of agreement among these methods and implications of these results on network construction. CONCLUSIONS: We find that the methods agree well for networks that contain a balance between error-free and unbiased interactions, indicating that the hub concept is meaningful for such networks.

  6. Theory of noncontact friction for atom-surface interactions

    Science.gov (United States)

    Jentschura, U. D.; Janke, M.; DeKieviet, M.

    2016-08-01

    The noncontact (van der Waals) friction is an interesting physical effect, which has been the subject of controversial scientific discussion. The direct friction term due to the thermal fluctuations of the electromagnetic field leads to a friction force proportional to 1 /Z5 (where Z is the atom-wall distance). The backaction friction term takes into account the feedback of thermal fluctuations of the atomic dipole moment onto the motion of the atom and scales as 1 /Z8 . We investigate noncontact friction effects for the interactions of hydrogen, ground-state helium, and metastable helium atoms with α -quartz (SiO2), gold (Au), and calcium difluorite (CaF2). We find that the backaction term dominates over the direct term induced by the thermal electromagnetic fluctuations inside the material, over wide distance ranges. The friction coefficients obtained for gold are smaller than those for SiO2 and CaF2 by several orders of magnitude.

  7. Trigger and control entanglement by atoms with different interaction times

    Institute of Scientific and Technical Information of China (English)

    Ren Jie; Hao Xiang; Zhu Shi-Qun

    2007-01-01

    The generation of the entanglement between two two-level atoms interacting with the third atom driven by white noise is investigated when the coupling between atoms is modulated by a pulse function.This paper finds that the initial triggering time and the width of the pulse call generate a peak in the entanglement.There is an optimal width of the pulse for which the entanglement can reach a maximum.The asymmetry of the coupling between atoms can generate different entanglement in the system.The multiple triggers can generate multiple peaks in the entanglement.The separation between two peaks is increased as the width of the pulse is increased.

  8. Non—conservation of energy arising from atomic dipole interactions and its effects on light field and coupled atoms

    Institute of Scientific and Technical Information of China (English)

    DongChuan-Hua

    2003-01-01

    The interactions between coulpled atoms and a single mode of a quantized electromagnetic field, which involve the terms originating from the dipole interactions, are discussed. In the usual Jaynes-Cummings model for coupled atoms, the terms of non-conservation of energy originating from dipole interactions are neglected, however, we take them into consideration in this paper. The effects of these terms on the evolutions of quantum statistic properties and squeezing of the field, the squeezing of atomic dipole moments and atomic population inversion are investigated. It has been shown that the coupling between atoms modulates these evolutions of fields and atoms. The terms of non-conservation of energy affect these evolutions of field and atoms slightly. They also have effects on the squeezing of the field, the squeezing of atomic dipole and atomic population inversions. The initial states of atoms also affect these properties.

  9. Non-conservation of energy arising from atomic dipole interactions and its effects on light field and coupled atoms

    Institute of Scientific and Technical Information of China (English)

    董传华

    2003-01-01

    The interactions between coupled atoms and a single mode of a quantized electromagnetic field, which involve the terms originating from the dipole interactions, are discussed. In the usual Jaynes Cummings model for coupled atoms,the terms of non-conservation of energy originating from dipole interactions are neglected, however, we take them into consideration in this paper. The effects of these terms on the evolutions of quantum statistic properties and squeezing of the field, the squeezing of atomic dipole moments and atomic population inversion are investigated. It has been shown that the coupling between atoms modulates these evolutions of fields and atoms. The terms of non-conservation of energy affect these evolutions of fields and atoms slightly. They also have effects on the squeezing of the field, the squeezing of atomic dipole and atomic population inversions. The initial states of atoms also affect these properties.

  10. 2004 Atomic and Molecular Interactions Gordon Research Conference

    International Nuclear Information System (INIS)

    The 2004 Gordon Research Conference on Atomic and Molecular Interactions was held July 11-16 at Colby-Sawyer College, New London, New Hampshire. This latest edition in a long-standing conference series featured invited talks and contributed poster papers on dynamics and intermolecular interactions in a variety of environments, ranging from the gas phase through surfaces and condensed media. A total of 90 conferees participated in the conference

  11. Spin diffusion in trapped clouds of strongly interacting cold atoms

    OpenAIRE

    Bruun, G. M.; Pethick, C.J.

    2011-01-01

    We show that puzzling recent experimental results on spin diffusion in a strongly interacting atomic gas may be understood in terms of the predicted spin diffusion coefficient for a generic strongly interacting system. Three important features play a central role: a) Fick's law for diffusion must be modified to allow for the trapping potential, b) the diffusion coefficient is inhomogeneous, due to the density variations in the cloud and c) the diffusion approximation fails in the outer parts ...

  12. 2004 Atomic and Molecular Interactions Gordon Research Conference

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Paul J. Dagdigian

    2004-10-25

    The 2004 Gordon Research Conference on Atomic and Molecular Interactions was held July 11-16 at Colby-Sawyer College, New London, New Hampshire. This latest edition in a long-standing conference series featured invited talks and contributed poster papers on dynamics and intermolecular interactions in a variety of environments, ranging from the gas phase through surfaces and condensed media. A total of 90 conferees participated in the conference.

  13. Interaction of Hg Atom with Bare Si(111) Surface

    Institute of Scientific and Technical Information of China (English)

    LIU Yong-Jun; LIU Ying

    2006-01-01

    To evaluate the interaction between Hg atom and bare Si(111) surface, three types of silicon cluster models of Si4H7, Si7H10 and Si16H20 together with their Hg complexes were studied by using hybrid (U)B3LYP density functional theory method. Optimized geometries and energies for Hg atom on different adsorption sites indicate that: 1) the binding energies at different adsorption sites are small (ranging from ~3 to 8 kJ/mol dependent on the adsorption sites), suggesting a weak interaction between Hg atom and silicon surface; 2) the most favorable adsorption site is the on top (T) site. By analyzing their natural bonding orbitals, the possible reason of this difference is suggested.

  14. Dynamics of interacting information waves in networks

    CERN Document Server

    Mirshahvalad, Atieh; Lizana, Ludvig; Rosvall, Martin

    2013-01-01

    To better understand the inner workings of information spreading, network researchers often use simple models to capture the spreading dynamics. But most models only highlight the effect of local interactions on the global spreading of a single information wave, and ignore the effects of interactions between multiple waves. Here we take into account the effect of multiple interacting waves by using an agent-based model in which the interaction between information waves is based on their novelty. We analyzed the global effects of such interactions and found that information that actually reaches nodes reaches them faster. This effect is caused by selection between information waves: slow waves die out and only fast waves survive. As a result, and in contrast to models with non-interacting information dynamics, the access to information decays with the distance from the source. Moreover, when we analyzed the model on various synthetic and real spatial road networks, we found that the decay rate also depends on ...

  15. Tailoring the chiral magnetic interaction between two individual atoms

    Science.gov (United States)

    Wiebe, J.; Khajetoorians, A. A.; Steinbrecher, M.; Ternes, M.; Bouhassoune, M.; Dos Santos Dias, M.; Lounis, S.; Wiesendanger, R.

    Chiral magnets are a promising route toward dense magnetic storage technology due to their inherent nano-scale dimensions and energy efficient properties. Engineering chiral magnets requires atomic-level control of the magnetic exchange interactions, including the Dzyaloshinskii-Moriya interaction, which defines a rotational sense for the magnetization of two coupled magnetic moments. Here we show that the indirect conduction electron mediated Dzyaloshinskii-Moriya interaction between two individual magnetic atoms on a metallic surface can be manipulated by changing the interatomic distance with the tip of a scanning tunneling microscope. We quantify this interaction by comparing our measurements to a quantum magnetic model and ab-initio calculations yielding a map of the chiral ground states of pairs of atoms depending on the interatomic separation. The map enables tailoring the chirality of the magnetization in dilute atomic-scale magnets. Acknowledgements: SFB668, GrK1286, SFB767, LO 1659 5-1, Emmy Noether Program of the DFG, FOM of NWO, VH-NG-717.

  16. Nonrelativistic atom-photon interaction beyond the multipole approximation

    NARCIS (Netherlands)

    Boers, D.J.; Wijers, C.M.J.

    2003-01-01

    We investigate the interaction between the hydrogen atomic orbitals and the quantized modes of the electromagnetic field within the domain of nonrelativistic quantum electrodynamics in the Coulomb gauge. Contrary to the conventional dipole approximation and higher-order multipole approximations, whi

  17. A Waveguide Platform for Collective Light-Atom Interaction

    DEFF Research Database (Denmark)

    Sørensen, Heidi Lundgaard

    In this work a tapered optical fiber is studied as a waveguide platform for efficient collective light-atom interaction. We present an allcomputer controlled heat-and-pull setup with which a standard optical fiber can reproducible be tapered down to sub-micron waist size. The resulting fiber shape...

  18. Electronic interaction anisotropy between atoms in arbitrary angular momentum states

    NARCIS (Netherlands)

    Krems, R.V.; Groenenboom, G.C.; Dalgarno, A.

    2004-01-01

    A general tensorial expansion for the interaction potential between two atoms in arbitrary angular momentum states is derived and the relations between the expansion coefficients and the Born-Oppenheimer potentials of the diatomic molecule are obtained. It is demonstrated that a complete expansion o

  19. On atom–atom `short contact' bonding interactions in crystals

    OpenAIRE

    Claude Lecomte; Enrique Espinosa; Cherif F. Matta

    2015-01-01

    Professor Dunitz questions the usefulness of ascribing crystalline structural stability to individual atom–atom intermolecular interactions viewed as bonding (hence stabilizing) whenever linked by a bond path. An alternative view is expressed in the present essay that articulates the validity and usefulness of the bond path concept in a crystallographic and crystal engineering context.

  20. Two interacting atoms in a cavity: Entanglement vs decoherence

    CERN Document Server

    Torres, J M; Seligman, T H

    2009-01-01

    We address the problem of two interacting atoms of different species inside a cavity and find the explicit solutions of the corresponding eigenvalue problem. Closed expressions for concurrence and purity as a function of time when the cavity is prepared in a number state are found. The behavior in the concurrence-purity plane is discussed.

  1. Unraveling Spurious Properties of Interaction Networks with Tailored Random Networks

    CERN Document Server

    Bialonski, Stephan; Lehnertz, Klaus; 10.1371/journal.pone.0022826

    2012-01-01

    We investigate interaction networks that we derive from multivariate time series with methods frequently employed in diverse scientific fields such as biology, quantitative finance, physics, earth and climate sciences, and the neurosciences. Mimicking experimental situations, we generate time series with finite length and varying frequency content but from independent stochastic processes. Using the correlation coefficient and the maximum cross-correlation, we estimate interdependencies between these time series. With clustering coefficient and average shortest path length, we observe unweighted interaction networks, derived via thresholding the values of interdependence, to possess non-trivial topologies as compared to Erd\\H{o}s-R\\'{e}nyi networks, which would indicate small-world characteristics. These topologies reflect the mostly unavoidable finiteness of the data, which limits the reliability of typically used estimators of signal interdependence. We propose random networks that are tailored to the way i...

  2. Retardation effects in induced atomic dipole-dipole interactions

    CERN Document Server

    Graham, S D

    2016-01-01

    We present mean-field calculations of azimuthally averaged retarded dipole-dipole interactions in a Bose-Einstein condensate induced by a laser, at both long and short wavelengths. Our calculations demonstrate that dipole-dipole interactions become significantly stronger at shorter wavelengths, by as much as 30-fold, due to retardation effects. This enhancement, along with inclusion of the dynamic polarizability, indicate a method of inducing long-range interatomic interactions in neutral atom condensates at significantly lower intensities than previously realized.

  3. Collective Dipole-Dipole Interactions in an Atomic Array

    CERN Document Server

    Sutherland, R T

    2016-01-01

    The coherent dipole-dipole interactions of atoms in an atomic array are studied. It is found that the excitation probability of an atom in an array parallel to the direction of laser propagation ($\\boldsymbol{\\hat{k}}$) will either grow or decay logarithmically along $\\boldsymbol{\\hat{k}}$, depending on the detuning of the laser. The symmetry of the system for atomic separations of $\\delta r = j\\lambda/2$, where $j$ is an integer, causes the excitation distribution and scattered radiation to abruptly become symmetric about the center of the array. For atomic separations of $\\delta r < \\lambda/2$, the appearance of a collection of extremely subradiant states ($\\Gamma\\sim 0$), disrupts the described trend. In order to interpret the results from a finite array of atoms, a band structure calculation in the $N\\rightarrow \\infty$ limit is conducted where the decay rates and the Collective Lamb Shifts of the eigenmodes along the Brillouin zone are shown. Finally, the band structure of an array strongly affects it...

  4. Dispersion interaction between an atom and a corrugated mirror plate

    International Nuclear Information System (INIS)

    Full text. In this work we make use of the general expressions for level shifts obtained from the master equation for a small system (an atom or molecule) interacting with a large one considered as a reservoir (the quantized electromagnetic field) in order to calculate the dispersive potentials between an atom and a corrugated mirror plate. Taking the dipole approximation, the level shifts are computed as an incoherent superposition of all field modes coupled to radiation reaction and fluctuating induced atom and field polarizations. The dispersion forces are then obtained as the gradient of the level shifts, which geometric behavior comes from the boundary conditions imposed to the field modes. In order to obtain the appropriate field modes to perform the calculations of dispersion forces between the atom and the corrugated wall, we use the scattering approach. In this approach, the total field mode is taken as a sum of the incident and reflected waves (specular and non-specular reflections) from the wall, resulting in a mixing of TE and TM polarizations. It applies to small amplitudes h of the corrugation profile compared to atom-wall distance z and to the corrugation length λc (spatial corrugation period). From the normalization condition for the fields, we then was able to obtain the quantized field modes for an arbitrary corrugation profile up to first order in h. From these modes, we then perform the calculation of dispersion potentials between a generic atom and a sinusoidal corrugated mirror plate. Considering the atom in its ground state as well as the field in its vacuum state, we obtain the atom-corrugated mirror van der Waals interaction, which besides the leading atom-mirror term, presents a contribution of the corrugation partner proportional to corrugation amplitude and which provides a lateral dispersion force (lateral Casimir-Polder force). We show that for small kλc, where λ = 2π/k is a dominant wavelength of the atomic spectrum, the lateral

  5. Broadband networks for interactive telemedical applications

    Science.gov (United States)

    Graschew, Georgi; Roelofs, Theo A.; Rakowsky, Stefan; Schlag, Peter M.

    2002-08-01

    Using off-the-shelf hardware components and a specially developed high-end software communication system (WinVicos) satellite networks for interactive telemedicine have been designed and developed. These networks allow for various telemedical applications, like intraoperative teleconsultation, second opinioning, teleteaching, telementoring, etc.. Based on the successful GALENOS network, several projects are currently being realized: MEDASHIP (Medical Assistance for Ships); DELTASS (Disaster Emergency Logistic Telemedicine Advanced Satellites Systems) and EMISPHER (Euro-Mediterranean Internet-Satellite Platform for Health, medical Education and Research).

  6. String order via Floquet interactions in atomic systems

    Science.gov (United States)

    Lee, Tony E.; Joglekar, Yogesh N.; Richerme, Philip

    2016-08-01

    We study the transverse-field Ising model with interactions that are modulated in time. In a rotating frame, the system is described by a time-independent Hamiltonian with many-body interactions, similar to the cluster Hamiltonians of measurement-based quantum computing. In one dimension, there is a three-body interaction, which leads to string order instead of conventional magnetic order. We show that the string order is robust to power-law interactions that decay with the cube of distance. In two and three dimensions, there are five- and seven-body interactions. We discuss adiabatic preparation of the ground state as well as experimental implementation with trapped ions, Rydberg atoms, and polar molecules.

  7. Propagation of light through small clouds of cold interacting atoms

    CERN Document Server

    Jennewein, S; Greffet, J -J; Browaeys, A

    2015-01-01

    We demonstrate experimentally that a cloud of cold atoms with a size comparable to the wavelength of light can induce large group delays on a laser pulse when the laser is tightly focused on it and is close to an atomic resonance. Delays as large as -10 ns are observed, corresponding to "superluminal" propagation with negative group velocities as low as -300 m/s. Strikingly, this large delay is associated with a moderate extinction owing to the very small size of the cloud and to the light-induced interactions between atoms. It implies that a large phase shift is imprinted on the continuous laser beam, and opens interesting perspectives for applications to quantum technologies.

  8. Atom depth analysis delineates mechanisms of protein intermolecular interactions

    Energy Technology Data Exchange (ETDEWEB)

    Alocci, Davide, E-mail: alodavide@gmail.com [Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via A. Fiorentina 1, 53100 Siena (Italy); Bernini, Andrea, E-mail: andrea.bernini@unisi.it [Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via A. Fiorentina 1, 53100 Siena (Italy); Niccolai, Neri, E-mail: neri.niccolai@unisi.it [Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via A. Fiorentina 1, 53100 Siena (Italy); SienaBioGrafix Srl, via A. Fiorentina 1, 53100 Siena (Italy)

    2013-07-12

    Highlights: •3D atom depth analysis is proposed to identify different layers in protein structures. •Amino acid contents for each layers have been analyzed for a large protein dataset. •Charged amino acids in the most external layer are present at very different extents. •Atom depth indexes of K residues reflect their side chains flexibility. •Mobile surface charges can be responsible for long range protein–protein recognition. -- Abstract: The systematic analysis of amino acid distribution, performed inside a large set of resolved protein structures, sheds light on possible mechanisms driving non random protein–protein approaches. Protein Data Bank entries have been selected using as filters a series of restrictions ensuring that the shape of protein surface is not modified by interactions with large or small ligands. 3D atom depth has been evaluated for all the atoms of the 2,410 selected structures. The amino acid relative population in each of the structural layers formed by grouping atoms on the basis of their calculated depths, has been evaluated. We have identified seven structural layers, the inner ones reproducing the core of proteins and the outer one incorporating their most protruding moieties. Quantitative analysis of amino acid contents of structural layers identified, as expected, different behaviors. Atoms of Q, R, K, N, D residues are increasingly more abundant in going from core to surfaces. An opposite trend is observed for V, I, L, A, C, and G. An intermediate behavior is exhibited by P, S, T, M, W, H, F and Y. The outer structural layer hosts predominantly E and K residues whose charged moieties, protruding from outer regions of the protein surface, reorient free from steric hindrances, determining specific electrodynamics maps. This feature may represent a protein signature for long distance effects, driving the formation of encounter complexes and the eventual short distance approaches that are required for protein

  9. Nature of intramolecular interactions of vitamin C in view of interacting quantum atoms: the role of hydrogen bond cooperativity on geometry.

    Science.gov (United States)

    Ebrahimi, Saeid; Dabbagh, Hossein A; Eskandari, Kiamars

    2016-07-21

    The conformational analysis of six dihedral angles was calculated by second-order Moller-Plesset perturbation theory (MP2) with the correlation-consistent aug-cc-pVDZ basis set. The quantum theory of atoms in molecules (QTAIM) was applied to gain a description of the atoms and chemical bonds. A high content of hydroxyl groups in vitamin C's (VC) structure leads to a wide range of intramolecular interactions. The nature of these interactions within the selected VC conformers was studied in view of the interacting quantum atom (IQA) approach. Complete IQA analysis of the atomic and interatomic interaction energies indicated hydrogen bond formation was responsible for the stability of most of the local minima in the potential energy surface. In these conformers, the tandem participation of interactions was operating by way of two- or three-centered (bifurcated) cooperative networks. For the intramolecular hydrogen bond interplay in cooperativity, changes of the IQA atomic and interatomic interaction energies of the participant interactions were monitored during the formation of cooperative networks. The results of the intramolecular cooperativity were evaluated with changes of the delocalization index and bond distances. PMID:27332782

  10. Atomic size zone interaction potential between two ground-state cold atoms

    CERN Document Server

    Wang, Zhaoying; Wu, Yunhan

    2016-01-01

    The complex-source-point model are already used in the exact solution for the urtrashort pulse and nonparaxial beam. In this letter we have used the complex-source-point model to deduce the interaction potential equation for the separation R between two atoms which is comparable with the size of the atoms. We show the result and the characteristics of the numerical calculation. Since the singular point around R=0 is removed by using the complex-source-point model, so that we can obtain the result force around R=0. With the decreasing of the distance between two atoms, the force switches from the electromagnetic force to the strong force by use our equation.

  11. From networks of protein interactions to networks of functional dependencies

    Directory of Open Access Journals (Sweden)

    Luciani Davide

    2012-05-01

    Full Text Available Abstract Background As protein-protein interactions connect proteins that participate in either the same or different functions, networks of interacting and functionally annotated proteins can be converted into process graphs of inter-dependent function nodes (each node corresponding to interacting proteins with the same functional annotation. However, as proteins have multiple annotations, the process graph is non-redundant, if only proteins participating directly in a given function are included in the related function node. Results Reasoning that topological features (e.g., clusters of highly inter-connected proteins might help approaching structured and non-redundant understanding of molecular function, an algorithm was developed that prioritizes inclusion of proteins into the function nodes that best overlap protein clusters. Specifically, the algorithm identifies function nodes (and their mutual relations, based on the topological analysis of a protein interaction network, which can be related to various biological domains, such as cellular components (e.g., peroxisome and cellular bud or biological processes (e.g., cell budding of the model organism S. cerevisiae. Conclusions The method we have described allows converting a protein interaction network into a non-redundant process graph of inter-dependent function nodes. The examples we have described show that the resulting graph allows researchers to formulate testable hypotheses about dependencies among functions and the underlying mechanisms.

  12. Network compression as a quality measure for protein interaction networks.

    Directory of Open Access Journals (Sweden)

    Loic Royer

    Full Text Available With the advent of large-scale protein interaction studies, there is much debate about data quality. Can different noise levels in the measurements be assessed by analyzing network structure? Because proteomic regulation is inherently co-operative, modular and redundant, it is inherently compressible when represented as a network. Here we propose that network compression can be used to compare false positive and false negative noise levels in protein interaction networks. We validate this hypothesis by first confirming the detrimental effect of false positives and false negatives. Second, we show that gold standard networks are more compressible. Third, we show that compressibility correlates with co-expression, co-localization, and shared function. Fourth, we also observe correlation with better protein tagging methods, physiological expression in contrast to over-expression of tagged proteins, and smart pooling approaches for yeast two-hybrid screens. Overall, this new measure is a proxy for both sensitivity and specificity and gives complementary information to standard measures such as average degree and clustering coefficients.

  13. Long-distance quantum networks using ultra-cold atoms

    Science.gov (United States)

    Solmeyer, Neal; Li, Xiao; Quraishi, Qudsia

    2016-05-01

    The generation of entanglement between distantly located quantum memories via frequency converted single photons could enable many applications in quantum networking, including quantum teleportation, distributed quantum computing and potentially distributed precision timing. A quantum network with three or more nodes has yet to be demonstrated and moreover hybrid networks leverage advantages of different platforms. With an existing memory at the Army Research Laboratory (ARL), based on weak Raman scattering in a Rb magneto-optical trap, we are building a second node at the Joint Quantum Institute (JQI), connected to ARL by a 13 km optical fiber. The second node will be a higher photon-rate node based on Rydberg excitations of a Rb ensemble in an optical dipole trap (N. Solmeyer et al., arXiv:1511.00025) and the first node will be upgraded to a Rydberg system soon. In the near term, we plan to generate entanglement between the second and a third node, based on a similar experimental setup, 100 m away at the JQI. For the ARL-JQI link we are presently working on quantum frequency conversion from IR photons to telecom wavelengths. Separately, we are pursuing frequency conversion from 493 nm photons to 780 nm to be used in a hybrid quantum network between ions and neutral atoms.

  14. Theory of noncontact friction for atom-surface interactions

    CERN Document Server

    Jentschura, U D; DeKieviet, M

    2016-01-01

    The noncontact (van der Waals) friction is an interesting physical effect which has been the subject of controversial scientific discussion. The "direct" friction term due to the thermal fluctuations of the electromagnetic field leads to a friction force proportional to 1/Z^5 where Z is the atom-wall distance). The "backaction" friction term takes into account the feedback of thermal fluctuations of the atomic dipole moment onto the motion of the atom and scales as 1/Z^8. We investigate noncontact friction effects for the interactions of hydrogen, ground-state helium and metastable helium atoms with alpha-quartz (SiO_2), gold (Au) and calcium difluorite (CaF_2). We find that the backaction term dominates over the direct term induced by the thermal electromagnetic fluctuations inside the material, over wide distance ranges. The friction coefficients obtained for gold are smaller than those for SiO_2 and CaF_2 by several orders of magnitude.

  15. Interaction of atomic hydrogen with charcoal at 77 K

    International Nuclear Information System (INIS)

    Full text: When the inner surface of the ITER pumping duct is covered with a thin αN-tilde:H film, the hydrogen recombination coefficient can be reduced. In this case, atomic hydrogen can reach the cryopump region and interact with charcoal cryosorbent. The interaction of thermal hydrogen molecules and atoms with charcoal has been analyzed by sorption measurements and TDS at 77 K. A stream quartz reactor with H2 RF discharge was used for the production of H atoms. The ratio of H and H2 in mixture in the afterglow zone was 1/10000. After exposure in H/H2 mixture the tube section with charcoal was warmed up to 300 K. In reference experiments the same sample of charcoal was exposed successively in H2 and CH4. After sample exposure in H/H2 mixture, the TD peak shifted to higher temperatures from 125 K (peak temperature after exposure in H2) to 150 K. The high temperature shoulder of this peak coincided with the temperature of methane release. The wide spectrum of heavy hydrocarbons formed at 77 K was registered by mass-spectrometry at charcoal heating up to 700 K. The specific adsorption volume of charcoal measured by N2 adsorption at 77 K decreased by 10-15%. (author)

  16. Evolutionarily conserved herpesviral protein interaction networks.

    Directory of Open Access Journals (Sweden)

    Even Fossum

    2009-09-01

    Full Text Available Herpesviruses constitute a family of large DNA viruses widely spread in vertebrates and causing a variety of different diseases. They possess dsDNA genomes ranging from 120 to 240 kbp encoding between 70 to 170 open reading frames. We previously reported the protein interaction networks of two herpesviruses, varicella-zoster virus (VZV and Kaposi's sarcoma-associated herpesvirus (KSHV. In this study, we systematically tested three additional herpesvirus species, herpes simplex virus 1 (HSV-1, murine cytomegalovirus and Epstein-Barr virus, for protein interactions in order to be able to perform a comparative analysis of all three herpesvirus subfamilies. We identified 735 interactions by genome-wide yeast-two-hybrid screens (Y2H, and, together with the interactomes of VZV and KSHV, included a total of 1,007 intraviral protein interactions in the analysis. Whereas a large number of interactions have not been reported previously, we were able to identify a core set of highly conserved protein interactions, like the interaction between HSV-1 UL33 with the nuclear egress proteins UL31/UL34. Interactions were conserved between orthologous proteins despite generally low sequence similarity, suggesting that function may be more conserved than sequence. By combining interactomes of different species we were able to systematically address the low coverage of the Y2H system and to extract biologically relevant interactions which were not evident from single species.

  17. Study on the fine control of atoms by coherent interaction

    Energy Technology Data Exchange (ETDEWEB)

    Min, Han Jae; Rho, S. P.; Park, H. M.; Lee, K. S.; Rhee, Y. J.; Yi, J. H.; Jeong, D. Y.; Jung, E. C.; Choe, A. S.; Lee, J. M

    1999-01-01

    The doppler-free saturation spectroscopy of Na atoms has been performed and the proper conditions for the frequency stabilization of narrow band cw dye lasers, which was used as laser sources for the laser cooling and trapping, have been obtained as follows : a) optimum pressure of a Na vapor cell: 10 mTorr b) intensity of a pump laser : a few {mu}W c) intensity of a probe laser : 1/10 of that of a pump laser. EIT (Electromagnetically Induced Transparency) generated by coherent laser-atom interactions was investigated experimentally and analyzed theoretically. The absorption of a probe laser could be remarkably reduced more than 90 % due to EIT effect. The EIT spectrum as narrow as 6 MHz which is even narrower than the natural linewidth of an excited state could be obtained under proper conditions.

  18. Study on the fine control of atoms by coherent interaction

    International Nuclear Information System (INIS)

    The doppler-free saturation spectroscopy of Na atoms has been performed and the proper conditions for the frequency stabilization of narrow band cw dye lasers, which was used as laser sources for the laser cooling and trapping, have been obtained as follows : a) optimum pressure of a Na vapor cell: 10 mTorr b) intensity of a pump laser : a few μW c) intensity of a probe laser : 1/10 of that of a pump laser. EIT (Electromagnetically Induced Transparency) generated by coherent laser-atom interactions was investigated experimentally and analyzed theoretically. The absorption of a probe laser could be remarkably reduced more than 90 % due to EIT effect. The EIT spectrum as narrow as 6 MHz which is even narrower than the natural linewidth of an excited state could be obtained under proper conditions

  19. Cooperative Tertiary Interaction Network Guides RNA Folding

    Energy Technology Data Exchange (ETDEWEB)

    Behrouzi, Reza; Roh, Joon Ho; Kilburn, Duncan; Briber, R.M.; Woodson, Sarah A. (JHU); (Maryland)

    2013-04-08

    Noncoding RNAs form unique 3D structures, which perform many regulatory functions. To understand how RNAs fold uniquely despite a small number of tertiary interaction motifs, we mutated the major tertiary interactions in a group I ribozyme by single-base substitutions. The resulting perturbations to the folding energy landscape were measured using SAXS, ribozyme activity, hydroxyl radical footprinting, and native PAGE. Double- and triple-mutant cycles show that most tertiary interactions have a small effect on the stability of the native state. Instead, the formation of core and peripheral structural motifs is cooperatively linked in near-native folding intermediates, and this cooperativity depends on the native helix orientation. The emergence of a cooperative interaction network at an early stage of folding suppresses nonnative structures and guides the search for the native state. We suggest that cooperativity in noncoding RNAs arose from natural selection of architectures conducive to forming a unique, stable fold.

  20. Data management of protein interaction networks

    CERN Document Server

    Cannataro, Mario

    2012-01-01

    Interactomics: a complete survey from data generation to knowledge extraction With the increasing use of high-throughput experimental assays, more and more protein interaction databases are becoming available. As a result, computational analysis of protein-to-protein interaction (PPI) data and networks, now known as interactomics, has become an essential tool to determine functionally associated proteins. From wet lab technologies to data management to knowledge extraction, this timely book guides readers through the new science of interactomics, giving them the tools needed to: Generate

  1. Interactive network graphs of Biblical Hebrew data.

    OpenAIRE

    J. H. Kroeze; Theo J.D. Bothma; Matthee, Machdel C; Kruger, Ockert C; Kroeze, Jan C W

    2009-01-01

    Knowledge workers, including Biblical Hebrew computational linguists, should look into the possibilities offered by graphical visualisation techniques to allow explorative investigation of available linguistic data, since this may prompt new hypotheses, which may then be examined in more traditional, empirical ways. This article experiments with two-dimensional and three-dimensional implementations of interactive network graphs to enable dynamic, "what-if" investigations, using semantic-ro...

  2. Hylleraas-Configuration Interaction calculations on helium atom

    CERN Document Server

    Ruiz, Maria Belen

    2012-01-01

    Hylleraas-Configuration Interaction (Hy-CI) calculations on the ground 1S state of helium atom are presented using s-, p-, and d-Slater orbitals of both real and complex type. Techniques of construction of adapted configurations, optimization of the orbital exponents, structure of the wave function expansion are explored. A new method to evaluate the two-electron kinetic energy integrals occurring in the Hy-CI method is presented. The calculations show that nanohartree accuracy, about 0.0002 cm-1 is achieved.

  3. Effect of pairwise dipole–dipole interaction among three-atom systems

    Indian Academy of Sciences (India)

    P Anantha Lakshmi; Ashoka Vudayagiri; Shaik Ahmed

    2014-08-01

    We present an analysis of a system of three two-level atoms interacting with one another through dipole–dipole interaction. The interaction manifests between the excited state of one of the atoms and the ground state of its nearest neighbour. Steady-state populations of the density matrix elements are presented and are compared with a situation when only two atoms are present. It can be noticed that the third atom modifies the behaviour of the three atoms. Two configurations are analysed, one in which the three atoms are in a line, with no interaction between atoms at the end points and the other in which the atoms form a closed loop with one atom interacting with both its neighbours.

  4. Light interacting with atomic ensembles: collective, cooperative and mesoscopic effects

    CERN Document Server

    Guerin, W; Kaiser, R

    2016-01-01

    Cooperative scattering has been the subject of intense research in the last years. In this article, we discuss the concept of cooperative scattering from a broad perspective. We briefly review the various collective effects that occur when light interacts with an ensemble of atoms. We show that some effects that have been recently discussed in the context of "single-photon superradiance", or cooperative scattering in the linear-optics regime, can also be explained by "standard optics", i.e., using macroscopic quantities such as the susceptibility or the diffusion coefficient. We explain why some collective effects depend on the atomic density, and others on the optical depth. In particular, we show that, for a large and dilute atomic sample driven by a far-detuned laser, the decay of the fluorescence, which exhibits superradiant and subradiant dynamics, depends only on the on-resonance optical depth. We also discuss the link between concepts that are independently studied in the quantum-optics community and i...

  5. Revealing the fast atomic motion of network glasses.

    Science.gov (United States)

    Ruta, B; Baldi, G; Chushkin, Y; Rufflé, B; Cristofolini, L; Fontana, A; Zanatta, M; Nazzani, F

    2014-01-01

    Still very little is known on the relaxation dynamics of glasses at the microscopic level due to the lack of experiments and theories. It is commonly believed that glasses are in a dynamical arrested state, with relaxation times too large to be observed on human time scales. Here we provide the experimental evidence that glasses display fast atomic rearrangements within a few minutes, even in the deep glassy state. Following the evolution of the structural relaxation in a sodium silicate glass, we find that this fast dynamics is accompanied by the absence of any detectable aging, suggesting a decoupling of the relaxation time and the viscosity in the glass. The relaxation time is strongly affected by the network structure with a marked increase at the mesoscopic scale associated with the ion-conducting pathways. Our results modify the conception of the glassy state and asks for a new microscopic theory. PMID:24835825

  6. The interaction of atoms with LiF(001) revisited

    CERN Document Server

    Miraglia, J E

    2016-01-01

    Pairwise additive potentials for multielectronic atoms interacting with a LiF(001) surface are revisited by including an improved description of the electron density associated with the different lattice sites, as well as non-local electron density contributions. Within this model, the electron distribution around each ionic site of the crystal is described by means of an onion approach that accounts for the influence of the Madelung potential. From such densities, binary interatomic potentials are then derived by using well-known non-local functionals for the kinetic, exchange and correlation terms. Rumpling and long-range contributions due to projectile polarization and van der Waals forces are also included in an analogous fashion. We apply this pairwise additive approximation to evaluate the interaction potential between closed-shell - He, Ne, Ar, Kr, and Xe - and open-shell - N, S, and Cl - atoms and the LiF surface, analyzing the relative importance of the different contributions. The performance of the...

  7. Thermal Casimir-Polder interaction of different atoms with graphene

    CERN Document Server

    Chaichian, M; Mostepanenko, V M; Tureanu, A

    2012-01-01

    The thermal correction to the energy of Casimir-Polder interaction of atoms with a suspended graphene membrane described by the Dirac model is investigated. We show that a major impact on the thermal correction is made by the size of the gap in the energy spectrum of graphene quasiparticles. Specifically, if the temperature is much smaller than the gap parameter (alternatively, larger or of the order of the gap parameter), the thermal correction is shown to be relatively small (alternatively, large). We have calculated the free energy of the thermal Casimir-Polder interaction of atoms of He, Na, Rb, and Cs with graphene described by both the hydrodynamic and Dirac models. It is shown that in exact computations using the Dirac model, one should use the polarization operator at nonzero temperature. The computational results for the Casimir-Polder free energy obtained in the framework of hydrodynamic model of graphene are several times larger than in the Dirac model within the separation region below 2$\\mu$m. We...

  8. Entanglement between two atoms in the system of Schr(o)dinger cat state interacting with two entangled atoms

    Institute of Scientific and Technical Information of China (English)

    Liu Tang-Kun

    2007-01-01

    By the negative eigenvalues of partial transposition of density matrix, this paper investigates the time evolution of entanglement of the two entangled atoms in the system of two atoms interacting with Schr(o)dinger cat state. The result shows that the two atoms are always in the entanglement state, and the degree of entanglement between the two atoms exhibits ordinary collapses and revivals at 0.2 degree of entanglement, when the light field is large enough. On the other hand, the reinforcement of three different light fields on the degree of entanglement between two atoms is not evident.

  9. Atom-Resonant Heralded Single Photons by Interaction-Free Measurement

    CERN Document Server

    Wolfgramm, Florian; Beduini, Federica A; Cere, Alessandro; Mitchell, Morgan W; 10.1103/PhysRevLett.106.053602

    2011-01-01

    We demonstrate the generation of rubidium-resonant heralded single photons for quantum memories. Photon pairs are created by cavity-enhanced down-conversion and narrowed in bandwidth to 7 MHz with a novel atom-based filter operating by "interaction-free measurement" principles. At least 94% of the heralded photons are atom-resonant as demonstrated by a direct absorption measurement with rubidium vapor. A heralded auto-correlation measurement shows $g_c^{(2)}(0)=0.040 \\pm 0.012$, i.e., suppression of multi-photon contributions by a factor of 25 relative to a coherent state. The generated heralded photons can readily be used in quantum memories and quantum networks.

  10. Amino Acid Interaction Network Prediction Using Multi-Objective Optimization

    Directory of Open Access Journals (Sweden)

    Md. Shiplu Hawlader

    2014-01-01

    Full Text Available Protein can be represented by amino acid interaction network. This network is a graph whose vertices are the proteins amino acids and whose edges are the interactions between them. This interaction network is the first step of proteins three-dimensional structure prediction. In this paper we present a multi-objective evolutionary algorithm for interaction prediction and ant colony probabilistic optimization algorithm is used to confirm the interaction.

  11. Entropy evolution properties in a system of two entangled atoms interacting with light field

    Institute of Scientific and Technical Information of China (English)

    Liu Tang-Kun; Wang Ji-Suo; Feng Jian; Zhan Ming-Sheng

    2005-01-01

    In the paper, we use the field entropy as a measurement of the degree of entanglement between the light field and the atoms of the system which is composed of two dipole-dipole interacting two-level atoms initially in an entangled state interacting with the single mode coherent field in a Kerr medium. The influence of the coupling constant of dipole-dipole interaction between atoms and the coupling strength of the kerr medium with the light field and the intensity of the atoms with the light field becomes weaker. The degree of entanglement only changes slightly with the change of the coupling constant of dipole-dipole interaction between atoms.

  12. On an Interactive Network Security Measure

    Institute of Scientific and Technical Information of China (English)

    LUO Huiqiong; WANG Jiahao; ZHAO Qiang

    2004-01-01

    An interactive network security measure and a description of its function as well as its principle are presented.Based on the existing security loopholes and bugsin operating systems,this measure focuses on the restrictive condition of security and the establishment of configuration files.Under the control and administration of the secure management of configuration files,each system module brings much fiexibility,adaptability and high-level security.The security detecting and managing software used in UNIX based on this measure has obtained good results,achieving the goal of automatically detecting and handling inner and outer system-violation and system abuse.

  13. Random matrix analysis for gene interaction networks in cancer cells

    CERN Document Server

    Kikkawa, Ayumi

    2016-01-01

    Motivation: The investigation of topological modifications of the gene interaction networks in cancer cells is essential for understanding the desease. We study gene interaction networks in various human cancer cells with the random matrix theory. This study is based on the Cancer Network Galaxy (TCNG) database which is the repository of huge gene interactions inferred by Bayesian network algorithms from 256 microarray experimental data downloaded from NCBI GEO. The original GEO data are provided by the high-throughput microarray expression experiments on various human cancer cells. We apply the random matrix theory to the computationally inferred gene interaction networks in TCNG in order to detect the universality in the topology of the gene interaction networks in cancer cells. Results: We found the universal behavior in almost one half of the 256 gene interaction networks in TCNG. The distribution of nearest neighbor level spacing of the gene interaction matrix becomes the Wigner distribution when the net...

  14. Study of the interaction of atoms with strong laser fields

    International Nuclear Information System (INIS)

    Three aspects of the interactions of atoms with high intensity laser fields were treated. All three were motivated by experiment. The first investigation was prompted by a recent experiment (Kruit et al. 1983) involving multiphoton ionization of Xe. In this experiment it was found that the photoelectron energy spectrum contained peaks that corresponded to the absorption of more than the minimum number of photons required to ionize the atom. A model approximation here showed good qualitative agreement with experiment. An experiment (Grove et al. 1977) designed to test a theoretical calculation of the dynamical Stark effect stimulated the second part of this thesis, namely: a study of how an adiabatically and near-adiabatically changing field intensity affects the resonance fluorescence spectrum of a two-level atom. It was found that there is an asymmetry in the spectrum for off-resonance excitation produced because the field turn-on repopulates the dressed state that is depopulated by spontaneous emission. The third part of this thesis was based on an experiment (Granneman and Van der Wiel 1976) that attempted to verify a perturbation calculation of the two-photon ionization cross section of Cs. A discrepancy of four orders of magnitude near a minimum in the cross section was found between theory and experiment. To explain this discrepancy it was suggested (Armstrong and Beers 1977) that the effective order of nonlinearity (k) for this process varied significantly around the minimum. This study involves a perturbation calculation of k. It was found that k varies rapidly around the minimum, and that this variation should be experimentally observable for laser intensities of the order of tens of GW cm-2

  15. Interaction of laser-cooled $^{87}$Rb atoms with higher order modes of an optical nanofiber

    CERN Document Server

    Kumar, Ravi; Maimaiti, Aili; Deasy, Kieran; Frawley, Mary C; Chormaic, Síle Nic

    2013-01-01

    Optical nanofibers can be used to confine light to submicron regions and are very promising for the realization of optical fiber-based quantum networks using cold, neutral atoms. Light propagating in the higher order modes of a nanofiber has a greater evanescent field extension around the waist in comparison with the fundamental mode, leading to a stronger interaction with the surrounding environment. In this work, we report on the integration of a few-mode, optical nanofiber, with a waist diameter of ~700 nm, into a magneto-optical trap for $^{87}$Rb atoms. The nanofiber is fabricated from 80 $\\mu$m diameter fiber using a brushed hydrogen-oxygen flame pulling rig. We show that absorption by laser-cooled atoms around the waist of the nanofiber is stronger when probe light is guided in the higher order modes than in the fundamental mode. As predicted by Masalov and Minogin*, fluorescent light from the atoms coupling in to the nanofiber through the waist has a higher pumping rate (5.8 times) for the higher-orde...

  16. Collective dynamics of dislocations interacting with mobile solute atoms

    Science.gov (United States)

    Ovaska, Markus; Paananen, Topi; Laurson, Lasse; Alava, Mikko J.

    2016-04-01

    We study the effect of diffusing solute atoms on the collective dynamics of dislocations in plastically deforming crystals, by simulating a two-dimensional discrete dislocation dynamics model with solute atoms included. We employ various protocols to apply the external stress, including constant, oscillatory and quasistatically increasing stress, and study the resulting dynamics for various values of the solute mobility, temperature, and interaction strength with the dislocations. The values of these parameters dictate if Cottrell clouds are formed around the dislocations, and whether the dislocations are able to drag them along as they move. The relevant solute-induced processes include a temporally increasing average Cottrell cloud size due to cloud merging during the evolution of the dislocation structures subject to constant stresses, and a crossover between a solute-free ‘phase’ and a regime where solute drag is important for cyclic stresses, controlled by the solute mobility and temperature. Statistics of deformation bursts under quasistatic loading exhibit atypical scaling where the average burst size is directly proportional to its duration, and are also affected by solute-induced strain hardening in the high-stress regime.

  17. Atom-scale molecular interactions in lipid raft mixtures

    DEFF Research Database (Denmark)

    Niemelä, Perttu S; Hyvönen, Marja T; Vattulainen, Ilpo

    2009-01-01

    We review the relationship between molecular interactions and the properties of lipid environments. A specific focus is given on bilayers which contain sphingomyelin (SM) and sterols due to their essential role for the formation of lipid rafts. The discussion is based on recent atom-scale molecular....... As a particularly intriguing example of this, the lateral pressure profiles of raft-like and non-raft systems indicate that the lipid composition of membrane domains may have a major impact on membrane protein activation....... another, thus acting as nucleation sites for the formation of highly ordered nanosized domains. Finally, the fourth part discusses the large-scale properties of raft-like membrane environments and compares them to the properties of non-raft membranes. The differences turn out to be substantial...

  18. Interaction between polystyrene spheres by atomic force microscopy

    CERN Document Server

    Looi, L

    2002-01-01

    The interaction between a single polystyrene particle and a polystyrene substrate has been previously reported by a number of investigators. However, the effects of relative humidity, applied load and contact time on the adhesion of polystyrene surfaces have not been investigated and these effects are poorly understood. It is the primary aim of the current work to characterise the effect of the aforementioned parameters on the adhesion of polystyrene surfaces using atomic force microscopy. The polystyrene used in this study contained 1% of di-vinyl benzene as a cross-linking agent. From the work conducted using the custom-built instrument, the dependency of adhesion forces on the relative humidity is greatest at relative humidities above 60% where capillary forces cause a sharp increase in adhesion with increasing relative humidity. Hysteresis was observed in the solid-solid contact gradient of the accompanying force curves, suggesting non-elastic behaviour at the contact area of the surfaces

  19. Unlocking higher harmonics in atomic force microscopy with gentle interactions

    Directory of Open Access Journals (Sweden)

    Sergio Santos

    2014-03-01

    Full Text Available In dynamic atomic force microscopy, nanoscale properties are encoded in the higher harmonics. Nevertheless, when gentle interactions and minimal invasiveness are required, these harmonics are typically undetectable. Here, we propose to externally drive an arbitrary number of exact higher harmonics above the noise level. In this way, multiple contrast channels that are sensitive to compositional variations are made accessible. Numerical integration of the equation of motion shows that the external introduction of exact harmonic frequencies does not compromise the fundamental frequency. Thermal fluctuations are also considered within the detection bandwidth of interest and discussed in terms of higher-harmonic phase contrast in the presence and absence of an external excitation of higher harmonics. Higher harmonic phase shifts further provide the means to directly decouple the true topography from that induced by compositional heterogeneity.

  20. Modularity in the evolution of yeast protein interaction network

    OpenAIRE

    Ogishima, Soichi; Tanaka, Hiroshi; Nakaya, Jun

    2015-01-01

    Protein interaction networks are known to exhibit remarkable structures: scale-free and small-world and modular structures. To explain the evolutionary processes of protein interaction networks possessing scale-free and small-world structures, preferential attachment and duplication-divergence models have been proposed as mathematical models. Protein interaction networks are also known to exhibit another remarkable structural characteristic, modular structure. How the protein interaction netw...

  1. Competing dynamical processes on two interacting networks

    CERN Document Server

    Alvarez-Zuzek, L G; Braunstein, L A; Vazquez, F

    2016-01-01

    We propose and study a model for the competition between two different dynamical processes, one for opinion formation and the other for decision making, on two interconnected networks. The networks represent two interacting social groups, the society and the Congress. An opinion formation process takes place on the society, where the opinion S of each individual can take one of four possible values (S=-2,-1,1,2), describing its level of agreement on a given issue, from totally against (S=-2) to totally in favor (S=2). The dynamics is controlled by a reinforcement parameter r, which measures the ratio between the likelihood to become an extremist or a moderate. The dynamics of the Congress is akin to that of the Abrams-Strogatz model, where congressmen can adopt one of two possible positions, to be either in favor (+) or against (-) the issue. The probability that a congressman changes his decision is proportional to the fraction of interacting neighbors that hold the opposite opinion raised to a power $\\beta$...

  2. Long-range interactions of excited He atoms with ground-state noble-gas atoms

    KAUST Repository

    Zhang, J.-Y.

    2013-10-09

    The dispersion coefficients C6, C8, and C10 for long-range interactions of He(n1,3S) and He(n1,3P), 2≤n≤10, with the ground-state noble-gas atoms Ne, Ar, Kr, and Xe are calculated by summing over the reduced matrix elements of multipole transition operators. The large-n expansions for the sums over the He oscillator strength divided by the corresponding transition energy are presented for these series. Using the expansions, the C6 coefficients for the systems involving He(131,3S) and He(131,3P) are calculated and found to be in good agreement with directly calculated values.

  3. Entanglement Swapping and Disentanglement via an Entangled State of Atoms Interacting with a Cavity Field

    Institute of Scientific and Technical Information of China (English)

    刘堂昆; 王继锁; 冯健; 詹明生

    2002-01-01

    We consider entanglement swapping and disentanglement schemes via an entangled state of three two-level atoms interacting with a coherent field. When a two-level atom C, entangled with two other two-level atoms A and B,is injected into a high-Q cavity and atoms A and B are far away from the cavity, the entanglement swapping or disentanglement can be realized by carrying out the measurement on the atom C and by selecting an appropriate interaction time of atom C with the coherent field.

  4. Nonadiabatic effects on population transfer of two Bose-Einstein condensates induced by atomic interaction

    Institute of Scientific and Technical Information of China (English)

    胡正峰; 杜春光; 李师群

    2003-01-01

    We investigate the stimulated Raman adiabatic passage for Bose-Einstein condensate (BEG) states which are trapped in different potential wells or two ground states of BEG in the same trap. We consider that lasers are nearly resonant with the atomic transitions. The difference of population transfer processes between BEG atoms and usual atoms is that the atomic interaction of the BEG atoms can cause some nonadiabatic effects, which may degrade the process. But with suitable detunings of laser pulses, the effects can be remedied to some extent according to different atomic interactions.

  5. Dependences of the Casimir-Polder interaction between an atom and a cavity wall on atomic and material properties

    CERN Document Server

    Mostepanenko, V M; Caride, A O; Klimchitskaya, G L; Zanette, S I

    2006-01-01

    The Casimir-Polder and van der Waals interactions between an atom and a flat cavity wall are investigated under the influence of real conditions including the dynamic polarizability of the atom, actual conductivity of the wall material and nonzero temperature of the wall. The cases of different atoms near metal and dielectric walls are considered. It is shown that to obtain accurate results for the atom-wall interaction at short separations, one should use the complete tabulated optical data for the complex refractive index of the wall material and the accurate dynamic polarizability of an atom. At relatively large separations in the case of a metal wall, one may use the plasma model dielectric function to describe the dielectric properties of wall material. The obtained results are important for the theoretical interpretation of experiments on quantum reflection and Bose-Einstein condensation.

  6. Investigating physics learning with layered student interaction networks

    DEFF Research Database (Denmark)

    Bruun, Jesper; Traxler, Adrienne

    Centrality in student interaction networks (SINs) can be linked to variables like grades [1], persistence [2], and participation [3]. Recent efforts in the field of network science have been done to investigate layered - or multiplex - networks as mathematical objects [4]. These networks can...

  7. Resonance interaction energy between two accelerated identical atoms in a coaccelerated frame and the Unruh effect

    CERN Document Server

    Zhou, Wenting; Rizzuto, Lucia

    2016-01-01

    We investigate the resonance interaction energy between two uniformly accelerated identical atoms, interacting with the scalar field or the electromagnetic field in the vacuum state, in the reference frame coaccelerating with the atoms. We assume that one atom is excited and the other in the ground state, and that they are prepared in their correlated symmetric or antisymmetric state. Using perturbation theory, we separate, at the second order in the atom-field coupling, the contributions of vacuum fluctuations and radiation reaction field to the energy shift of the interacting system. We show that only the radiation reaction term contributes to the resonance interaction between the two atoms, while Unruh thermal fluctuations, related to the vacuum fluctuations contribution, do not affect the resonance interatomic interaction. We also show that the resonance interaction between two uniformly accelerated atoms, recently investigated in the comoving (locally inertial) frame, can be recovered in the coaccelerate...

  8. All-atom Molecular Dynamic Simulations and NMR Spectra Study on Intermolecular Interactions of N,N-dimethylacetamide-Water System

    Institute of Scientific and Technical Information of China (English)

    Rong Zhang; Zai-you Tan; San-lai Luo

    2008-01-01

    N,N-dimethylacetamide (DMA) has been investigated extensively in studying models of peptide bonds. An all-atom MD simulation and the NMR spectra were performed to investigate the interactions in the DMA- water system. The radial distribution functions (RDFs) and the hydrogen-bonding network were used in MD simulations. There are strong hydrogen bonds and weak C-H…O contacts in the mixtures, as shown by the analysis of the RDFs. The insight structures in the DMA-water mixtures can be classified into different regions by the analysis of the hydrogen-bonding network. Chemical shifts of the hydrogen atom of water molecule with concentration and temperatures are adopted to study the interactions in the mixtures. The results of NMR spectra show good agreement with the statistical results of hydrogen bonds in MD simulations.

  9. Ant Colony Approach to Predict Amino Acid Interaction Networks

    OpenAIRE

    Gaci, Omar; Balev, Stefan

    2009-01-01

    In this paper we introduce the notion of protein interaction network. This is a graph whose vertices are the proteins amino acids and whose edges are the interactions between them. We consider the problem of reconstructing protein's interaction network from its amino acid sequence. An ant colony approach is used to solve this problem.

  10. Introduction to the theory of laser-atom interactions

    CERN Document Server

    Mittleman, Marvin H

    1993-01-01

    In response to the explosion of theories and experiments since the appearance of the first edition, the author has revised and expanded his basic text New sections include up-to-date discussions of multiphoton ionization, and electron-atom and atom-atom scattering in laser fields, reaffirming the work's position as the standard introduction to the field

  11. Noble gas, alkali and alkaline atoms interacting with a gold surface

    CERN Document Server

    Łach, Grzegorz; Jentschura, Ulrich D; 10.1142/S0217751X1004961X

    2013-01-01

    The attractive branch of the interaction potentials with the surface of gold have been computed for a large variety of atomic systems: the hydrogen atom, noble gases (He, Ne, Ar, Kr, Xe), alkali atoms (Li, Na, K, Rb, Cs) and alkaline atoms (Be, Mg, Ca, Sr, Ba). The results include highly accurate dynamic polarizabilities for the helium atom calculated using a variational method and explicitly correlated wavefunctions. For other atoms considered we used the data available in the literature. The interaction potentials include both the effects of retardation of the electromagnetic interactions and a realistic representation of the optical response function of gold (beyond the approximation of a perfect conductor). An explicit comparison of our result to the interaction between an atom and a perfect conductor is given.

  12. Deducing topology of protein-protein interaction networks from experimentally measured sub-networks

    Directory of Open Access Journals (Sweden)

    MacLellan W Robb

    2008-07-01

    Full Text Available Abstract Background Protein-protein interaction networks are commonly sampled using yeast two hybrid approaches. However, whether topological information reaped from these experimentally-measured sub-networks can be extrapolated to complete protein-protein interaction networks is unclear. Results By analyzing various experimental protein-protein interaction datasets, we found that they are not random samples of the parent networks. Based on the experimental bait-prey behaviors, our computer simulations show that these non-random sampling features may affect the topological information. We tested the hypothesis that a core sub-network exists within the experimentally sampled network that better maintains the topological characteristics of the parent protein-protein interaction network. We developed a method to filter the experimentally sampled network to result in a core sub-network that more accurately reflects the topology of the parent network. These findings have fundamental implications for large-scale protein interaction studies and for our understanding of the behavior of cellular networks. Conclusion The topological information from experimental measured networks network as is may not be the correct source for topological information about the parent protein-protein interaction network. We define a core sub-network that more accurately reflects the topology of the parent network.

  13. Photon-Mediated Interactions: A Scalable Tool to Create and Sustain Entangled States of N Atoms

    Science.gov (United States)

    Aron, Camille; Kulkarni, Manas; Türeci, Hakan E.

    2016-01-01

    We propose and study the use of photon-mediated interactions for the generation of long-range steady-state entanglement between N atoms. Through the judicious use of coherent drives and the placement of the atoms in a network of cavity QED systems, a balance between their unitary and dissipative dynamics can be precisely engineered to stabilize a long-range correlated state of qubits in the steady state. We discuss the general theory behind such a scheme and present an example of how it can be used to drive a register of N atoms to a generalized W state and how the entanglement can be sustained indefinitely. The achievable steady-state fidelities for entanglement and its scaling with the number of qubits are discussed for presently existing superconducting quantum circuits. While the protocol is primarily discussed for a superconducting circuit architecture, it is ideally realized in any cavity QED platform that permits controllable delivery of coherent electromagnetic radiation to specified locations.

  14. Game theory in communication networks cooperative resolution of interactive networking scenarios

    CERN Document Server

    Antoniou, Josephina

    2012-01-01

    A mathematical tool for scientists and researchers who work with computer and communication networks, Game Theory in Communication Networks: Cooperative Resolution of Interactive Networking Scenarios addresses the question of how to promote cooperative behavior in interactive situations between heterogeneous entities in communication networking scenarios. It explores network design and management from a theoretical perspective, using game theory and graph theory to analyze strategic situations and demonstrate profitable behaviors of the cooperative entities. The book promotes the use of Game T

  15. Effect of Virtual Photon Exchange on the Interaction of Light Field with N Atoms

    Institute of Scientific and Technical Information of China (English)

    LIANG Mai-Lin; ZHAO Lin

    2003-01-01

    Under no rotating wave approximation and including the effect of dipole-dipole interaction between the atoms, exact squeezing properties for the output optical field and the atomic field are obtained. It is shown that an atom laser keeping squeezed all the time can be generated, though the input optical field is at the coherent state or vacuum state.

  16. Multiple Tipping Points and Optimal Repairing in Interacting Networks

    CERN Document Server

    Majdandzic, Antonio; Curme, Chester; Vodenska, Irena; Levy-Carciente, Sary; Stanley, H Eugene; Havlin, Shlomo

    2015-01-01

    Systems that comprise many interacting dynamical networks, such as the human body with its biological networks or the global economic network consisting of regional clusters, often exhibit complicated collective dynamics. To understand the collective behavior of these systems, we investigate a model of interacting networks exhibiting the fundamental processes of failure, damage spread, and recovery. We find a very rich phase diagram that becomes exponentially more complex as the number of networks is increased. In the simplest example of $n=2$ interacting networks we find two critical points, 4 triple points, 10 allowed transitions, and two "forbidden" transitions, as well as a manifold of metastable regions represented by complex hysteresis. Knowing and understanding the phase diagram have an immediate practical implication; it enables us to find the optimal strategy for repairing partially or fully damaged interconnected networks. To support our model, we analyze an example of real interacting financial net...

  17. Non-thermal effects of acceleration in the resonance interaction between two uniformly accelerated identical atoms

    CERN Document Server

    Rizzuto, Lucia; Marino, Jamir; Noto, Antonio; Spagnolo, Salvatore; Passante, Roberto

    2016-01-01

    We study the resonance interaction between two uniformly accelerated identical atoms, one excited and the other in the ground state, prepared in a correlated (symmetric or antisymmetric) state and interacting with the scalar field in the vacuum state. Because the two atoms are in a correlated state, the interaction is a second-order effect in the atom-field coupling. We separate the contributions of vacuum fluctuations and radiation reaction to the resonance energy shift of the system, and show that only radiation reaction contributes, while Unruh thermal fluctuations do not affect the resonant interatomic interaction. We also find that beyond a characteristic length scale associated to the breakdown of a local inertial description of the two-atom system, non-thermal effects in the radiation reaction correction change the distance-dependence of the resonance interaction. Finally, we generalize our model to the case of atoms interacting with the electromagnetic field, and shown that new features appear in the ...

  18. Multiple tipping points and optimal repairing in interacting networks

    Science.gov (United States)

    Majdandzic, Antonio; Braunstein, Lidia A.; Curme, Chester; Vodenska, Irena; Levy-Carciente, Sary; Eugene Stanley, H.; Havlin, Shlomo

    2016-03-01

    Systems composed of many interacting dynamical networks--such as the human body with its biological networks or the global economic network consisting of regional clusters--often exhibit complicated collective dynamics. Three fundamental processes that are typically present are failure, damage spread and recovery. Here we develop a model for such systems and find a very rich phase diagram that becomes increasingly more complex as the number of interacting networks increases. In the simplest example of two interacting networks we find two critical points, four triple points, ten allowed transitions and two `forbidden' transitions, as well as complex hysteresis loops. Remarkably, we find that triple points play the dominant role in constructing the optimal repairing strategy in damaged interacting systems. To test our model, we analyse an example of real interacting financial networks and find evidence of rapid dynamical transitions between well-defined states, in agreement with the predictions of our model.

  19. Preparation of Multicomponent Schr(o)dinger Cat States Through Resonant Atom-Field Interaction

    Institute of Scientific and Technical Information of China (English)

    ZHENG Shi-Biao

    2005-01-01

    A simple method is presented for generating multicomponent Schrodinger cat states through resonant atom-field interactions. In the scheme n two-level atoms, initially in ground states, are sent through a resonant cavity filled with a strong coherent field sequentially. Then state-selective measurements are performed on the atoms. The detections of the atoms in ground states collapse the cavity field onto a superposition of 2n coherent states. This is the first way for producing superpositions of many coherent states through resonant atom-field interaction.

  20. Controlling interactions between highly-magnetic atoms with Feshbach resonances

    CERN Document Server

    Kotochigova, Svetlana

    2014-01-01

    This paper reviews current experimental and theoretical progress in the study of dipolar quantum gases of ground and meta-stable atoms with a large magnetic moment. We emphasize the anisotropic nature of Feshbach resonances due to coupling to fast-rotating resonant molecular states in ultracold s-wave collisions between magnetic atoms in external magnetic fields. The dramatic differences in the distribution of resonances of magnetic $^7$S$_3$ chromium and magnetic lanthanide atoms with a submerged 4f shell and non-zero electron angular momentum is analyzed. We focus on Dysprosium and Erbium as important experimental advances have been recently made to cool and create quantum-degenerate gases for these atoms. Finally, we describe progress in locating resonances in collisions of meta-stable magnetic atoms in electronic P states with ground-state atoms, where an interplay between collisional anisotropies and spin-orbit coupling exists.

  1. Van der Waals Interactions among Alkali Rydberg Atoms with Excitonic States

    CERN Document Server

    Zoubi, Hashem

    2015-01-01

    We investigate the influence of the appearance of excitonic states on van der Waals interactions among two Rydberg atoms. The atoms are assumed to be in different Rydberg states, e.g., in the $|ns\\rangle$ and $|np\\rangle$ states. The resonant dipole-dipole interactions yield symmetric and antisymmetric excitons, with energy splitting that give rise to new resonances as the atoms approach each other. Only far from these resonances the van der Waals coefficients, $C_6^{sp}$, can be defined. We calculate the $C_6$ coefficients for alkali atoms and present the results for lithium by applying perturbation theory. At short interatomic distances of several $\\mu m$, we show that the widely used simple model of two-level systems for excitons in Rydberg atoms breaks down, and the correct representation implies multi-level atoms. Even though, at larger distances one can keep the two-level systems but in including van der Waals interactions among the atoms.

  2. Enhancing the functional content of eukaryotic protein interaction networks.

    Directory of Open Access Journals (Sweden)

    Gaurav Pandey

    Full Text Available Protein interaction networks are a promising type of data for studying complex biological systems. However, despite the rich information embedded in these networks, these networks face important data quality challenges of noise and incompleteness that adversely affect the results obtained from their analysis. Here, we apply a robust measure of local network structure called common neighborhood similarity (CNS to address these challenges. Although several CNS measures have been proposed in the literature, an understanding of their relative efficacies for the analysis of interaction networks has been lacking. We follow the framework of graph transformation to convert the given interaction network into a transformed network corresponding to a variety of CNS measures evaluated. The effectiveness of each measure is then estimated by comparing the quality of protein function predictions obtained from its corresponding transformed network with those from the original network. Using a large set of human and fly protein interactions, and a set of over 100 GO terms for both, we find that several of the transformed networks produce more accurate predictions than those obtained from the original network. In particular, the HC.cont measure and other continuous CNS measures perform well this task, especially for large networks. Further investigation reveals that the two major factors contributing to this improvement are the abilities of CNS measures to prune out noisy edges and enhance functional coherence in the transformed networks.

  3. Teleportation of an unknown two-atom state using simultaneous interaction of two two-level atoms with cavity field

    Institute of Scientific and Technical Information of China (English)

    Shaohua Xiang(向少华); Kehui Song(宋克慧)

    2003-01-01

    Proposal for the teleportation of two-atom state is presented. It is based on the simultaneous interaction of two two-level atoms with a single-mode cavity with a filed of n photons. In the proposed scheme, two pairs of EPR state are used as quantum channel to teleport an unknown two-atom state. The completed time is greatly reduced and cavity field is not required to be detected are shown to be the distinct features of the presented scheme.

  4. Reconstructing Amino Acid Interaction Networks by an Ant Colony Approach

    OpenAIRE

    Gaci, Omar; Balev, Stefan

    2009-01-01

    In this paper we introduce the notion of protein interaction network. This is a graph whose vertices are the proteins amino acids and whose edges are the interactions between them. We consider the problem of reconstructing protein's interaction network from its amino acid sequence. We rely on a probability that two amino acids interact as a function of their physico-chemical properties coupled to an ant colony system to solve this problem.

  5. Many-body interaction and deformation of the atomic electron shells in the lattice dynamics of compressed atomic cryocrystals

    Science.gov (United States)

    Troitskaya, E. P.; Gorbenko, Ie. Ie.; Pilipenko, E. A.

    2016-05-01

    The lattice dynamics of compressed atomic cryocrystals are based on ab initio quantum-mechanical theories of deformable and polarizable atoms (Tolpygo model), while taking into account the many-body interaction. The parameters of the three-particle interaction and deformation of the atomic electron shells, which are calculated in terms of the overlap integrals of atomic orbitals and their derivatives, have the same order of magnitude thus demonstrating that they must be considered in tandem. Accounting for the deformation effects of the electron shells in the dipole approximation when calculating phonon frequencies leads to a "softening" of the longitudinal modes at points L and X, for an entire series of Ne-Xe crystals, and of the transverse modes in the directions Σ and Λ for Xe, under high compression. It is shown that it impossible to adequately reproduce the observed deviation from the Cauchi relation δ(p) for compressed atomic cryocrystals, without accounting for the deformation of electron shells of atoms in a quadrupole approximation. The inputs from a three-particle and quadrupole interaction for Ne, Kr, and Xe crystals are mutually compensated, which provides a weak dependence on pressure for δ(p). We found a good agreement between the calculated phonon frequencies, Birch and Fuchs elastic moduli, the deviation from the Cauchi relation for the total number of Ne-Xe crystals in a wide range of pressures, and existing experiments.

  6. Reconstructing direct and indirect interactions in networked public goods game

    Science.gov (United States)

    Han, Xiao; Shen, Zhesi; Wang, Wen-Xu; Lai, Ying-Cheng; Grebogi, Celso

    2016-07-01

    Network reconstruction is a fundamental problem for understanding many complex systems with unknown interaction structures. In many complex systems, there are indirect interactions between two individuals without immediate connection but with common neighbors. Despite recent advances in network reconstruction, we continue to lack an approach for reconstructing complex networks with indirect interactions. Here we introduce a two-step strategy to resolve the reconstruction problem, where in the first step, we recover both direct and indirect interactions by employing the Lasso to solve a sparse signal reconstruction problem, and in the second step, we use matrix transformation and optimization to distinguish between direct and indirect interactions. The network structure corresponding to direct interactions can be fully uncovered. We exploit the public goods game occurring on complex networks as a paradigm for characterizing indirect interactions and test our reconstruction approach. We find that high reconstruction accuracy can be achieved for both homogeneous and heterogeneous networks, and a number of empirical networks in spite of insufficient data measurement contaminated by noise. Although a general framework for reconstructing complex networks with arbitrary types of indirect interactions is yet lacking, our approach opens new routes to separate direct and indirect interactions in a representative complex system.

  7. Atomic Spectrum in Ramsey Separated Oscillating Fields with Three Interaction Regions

    Institute of Scientific and Technical Information of China (English)

    CHEN Jingbiao; WANG Fengzhi; YANG Donghai; WANG YiQiu

    2001-01-01

    Comparing with the situation of Ramsey separated oscillating fields used in Cesium atomic beam frequency standard, the transition probability spectrum of two-level atoms in the Ramsey separated oscillating fields with three interaction regions has been derived under the condition of near resonance. The new characteristic of atomic spectrum with excessive microwave power was analyzed in detail. Meantime, the predicted new characteristic of atomic spectrum was confirmed by numerical method in this paper.

  8. Atomic Interaction Effects on Electromagnetically Induced Transparency and Slow Light in Ultracold Bose Gas

    Institute of Scientific and Technical Information of China (English)

    胡正峰; 杜春光; 李代军; 李师群

    2002-01-01

    We investigate electromagnetically induced transparency and slow group velocity of light in ultracold Bose gas with a two-photon Raman process. The properties of electromagnetically induced transparency and light speed can be changed by controlling the atomic interaction. Atomic interaction can be used as a knob to control the optical properties of atomic media. This can be realized in experiment by using the Feshbach resonance technique.

  9. Concentration of Unknown Atomic Entangled States via Entanglement Swapping through Raman Interaction

    Institute of Scientific and Technical Information of China (English)

    ZOU Jin-Hua; HU Xiang-Ming

    2008-01-01

    We show that entanglement concentration of unknown atomic entangled states is achieved via the implementation of entanglement swapping based on Raman interaction in cavity QED. A maximally entangled state is obtained from a pair of partially entangled states probabilistically. Due to Raman interaction of two atoms with a cavity mode and an external driving field, the influence of atomic spontaneous emission has been eliminated. Because of the virtual excitation of the cavity mode, the decoherence of cavity decay and thermal field is neglected.

  10. Atom-light interactions in quasi-1D nanostructures: a Green's function perspective

    CERN Document Server

    Asenjo-Garcia, A; Chang, D E; Kimble, H J

    2016-01-01

    Based on a formalism that describes atom-light interactions in terms of the classical electromagnetic Green's function, we study the optical response of atoms and other quantum emitters coupled to one-dimensional photonic structures, such as cavities, waveguides, and photonic crystals. We demonstrate a clear mapping between the transmission spectra and the local Green's function that allows to identify signatures of dispersive and dissipative interactions between atoms, gaining insight into recent experiments.

  11. Scheme for teleporting an unknown atomic state to any node in a quantum communication network

    Institute of Scientific and Technical Information of China (English)

    宋克慧; 张为俊; 郭光灿

    2002-01-01

    We propose a scheme for teleporting an unknown atomic state. In order to realize the teleportation to any node ina quantum communication network, an n-atom Greenberger-Horne-Zeilinger (GHZ) state is needed, which is utilizedas the quantum channel. From this n-atom GHZ state, two-node entanglement of processing and receiving teleportedstates can be obtained through the quantum logic gate manipulation. Finally, for the unequally weighted GHZ state,probabilistic teleportation is shown.

  12. International Conference on the Interaction of atoms, molecules and plasmas with intense ultrashort laser pulses. Book of abstracts

    International Nuclear Information System (INIS)

    International Conference on the Interaction of atoms, molecules and plasmas with intense ultrashort laser pulses was held in Hungary in 2006. This conference which joined the ULTRA COST activity ('Laser-matter interactions with ultra-short pulses, high-frequency pulses and ultra-intense pulses. From attophysics to petawatt physics') and the XTRA ('Ultrashort XUV Pulses for Time-Resolved and Non-Linear Applications') Marie-Curie Research Training Network, intends to offer a possibility to the members of both of these activities to exchange ideas on recent theoretical and experimental results on the interaction of ultrashort laser pulses with matter giving a broad view from theoretical models to practical and technical applications. Ultrashort laser pulses reaching extra high intensities open new windows to obtain information about molecular and atomic processes. These pulses are even able to penetrate into atomic scalelengths not only by generating particles of ultrahigh energy but also inside the spatial and temporal atomic scalelengths. New regimes of laser-matter interaction were opened in the last decade with an increasing number of laboratories and researchers in these fields. (S.I.)

  13. Van der Waals interactions and the limits of isolated atom models at interfaces

    Science.gov (United States)

    Kawai, Shigeki; Foster, Adam S.; Björkman, Torbjörn; Nowakowska, Sylwia; Björk, Jonas; Canova, Filippo Federici; Gade, Lutz H.; Jung, Thomas A.; Meyer, Ernst

    2016-05-01

    Van der Waals forces are among the weakest, yet most decisive interactions governing condensation and aggregation processes and the phase behaviour of atomic and molecular matter. Understanding the resulting structural motifs and patterns has become increasingly important in studies of the nanoscale regime. Here we measure the paradigmatic van der Waals interactions represented by the noble gas atom pairs Ar-Xe, Kr-Xe and Xe-Xe with a Xe-functionalized tip of an atomic force microscope at low temperature. Individual rare gas atoms were fixed at node sites of a surface-confined two-dimensional metal-organic framework. We found that the magnitude of the measured force increased with the atomic radius, yet detailed simulation by density functional theory revealed that the adsorption induced charge redistribution strengthened the van der Waals forces by a factor of up to two, thus demonstrating the limits of a purely atomic description of the interaction in these representative systems.

  14. The architecture of functional interaction networks in the retina.

    Science.gov (United States)

    Ganmor, Elad; Segev, Ronen; Schneidman, Elad

    2011-02-23

    Sensory information is represented in the brain by the joint activity of large groups of neurons. Recent studies have shown that, although the number of possible activity patterns and underlying interactions is exponentially large, pairwise-based models give a surprisingly accurate description of neural population activity patterns. We explored the architecture of maximum entropy models of the functional interaction networks underlying the response of large populations of retinal ganglion cells, in adult tiger salamander retina, responding to natural and artificial stimuli. We found that we can further simplify these pairwise models by neglecting weak interaction terms or by relying on a small set of interaction strengths. Comparing network interactions under different visual stimuli, we show the existence of local network motifs in the interaction map of the retina. Our results demonstrate that the underlying interaction map of the retina is sparse and dominated by local overlapping interaction modules.

  15. Studies on the interaction of hydrogen atoms with diamond surface

    International Nuclear Information System (INIS)

    The vibration modes of hydrogen-atom adsorption on the diamond surface were studied with high resolution-electron energy loss spectroscopy. Two main losses were observed at 360 MeV and 160 MeV. They are assigned to the C-H stretch vibrations and the angle-changing deformation vibrations respectively. Replacing H-atom with D-atom, isotopic shifts were observed in the loss spectra. Heating the diamond surface to 900 deg C, all of the loss features disappear, but an inelastic continuous loss-structure was observed. Due to H-atom desorption, the dangling-bonds became horizontal bonds on the diamond surface, resulting in the graphitization of diamond surface. The appearance of the inelastic continuous loss-structure was the characteristic of graphite π-band. The graphitization of the diamond surface was affirmed further by UPS and AES studies

  16. Average and extreme multi-atom Van der Waals interactions: Strong coupling of multi-atom Van der Waals interactions with covalent bonding

    Directory of Open Access Journals (Sweden)

    Finkelstein Alexei V

    2007-07-01

    Full Text Available Abstract Background The prediction of ligand binding or protein structure requires very accurate force field potentials – even small errors in force field potentials can make a 'wrong' structure (from the billions possible more stable than the single, 'correct' one. However, despite huge efforts to optimize them, currently-used all-atom force fields are still not able, in a vast majority of cases, even to keep a protein molecule in its native conformation in the course of molecular dynamics simulations or to bring an approximate, homology-based model of protein structure closer to its native conformation. Results A strict analysis shows that a specific coupling of multi-atom Van der Waals interactions with covalent bonding can, in extreme cases, increase (or decrease the interaction energy by about 20–40% at certain angles between the direction of interaction and the covalent bond. It is also shown that on average multi-body effects decrease the total Van der Waals energy in proportion to the square root of the electronic component of dielectric permittivity corresponding to dipole-dipole interactions at small distances, where Van der Waals interactions take place. Conclusion The study shows that currently-ignored multi-atom Van der Waals interactions can, in certain instances, lead to significant energy effects, comparable to those caused by the replacement of atoms (for instance, C by N in conventional pairwise Van der Waals interactions.

  17. Adhesion interaction between atomically defined tip and sample

    OpenAIRE

    CROSS, GRAHAM

    1998-01-01

    PUBLISHED We have measured forces between an atomically defined W(111) tip and an Au(111) sample in ultrahigh vacuum at 150 K. The W tips are manipulated and characterized on an atomic scale both before and after sample approach by field ion microscopy. Forces between the tip and the sample are measured by an in situ differential interferometer. We observe strong attractive adhesion forces, which turn repulsive upon the further approach of the tip towards the Au surface. Unexpected for a m...

  18. Using atom mapping rules for an improved detection of relevant routes in weighted metabolic networks.

    Science.gov (United States)

    Blum, Torsten; Kohlbacher, Oliver

    2008-01-01

    Computational analysis of pathways in metabolic networks has numerous applications in systems biology. While graph theory-based approaches have been presented that find biotransformation routes from one metabolite to another in these networks, most of these approaches suffer from finding too many routes, most of which are biologically infeasible or meaningless. We present a novel approach for finding relevant routes based on atom mapping rules (describing which educt atoms are mapped onto which product atoms in a chemical reaction). This leads to a reformulation of the problem as a lightest path search in a degree-weighted metabolic network. The key component of the approach is a new method of computing optimal atom mapping rules.

  19. Hub Promiscuity in Protein-Protein Interaction Networks

    OpenAIRE

    Haruki Nakamura; Kengo Kinoshita; Ashwini Patil

    2010-01-01

    Hubs are proteins with a large number of interactions in a protein-protein interaction network. They are the principal agents in the interaction network and affect its function and stability. Their specific recognition of many different protein partners is of great interest from the structural viewpoint. Over the last few years, the structural properties of hubs have been extensively studied. We review the currently known features that are particular to hubs, possibly affecting their binding ...

  20. Ontology integration to identify protein complex in protein interaction networks

    OpenAIRE

    Yang Zhihao; Lin Hongfei; Xu Bo

    2011-01-01

    Abstract Background Protein complexes can be identified from the protein interaction networks derived from experimental data sets. However, these analyses are challenging because of the presence of unreliable interactions and the complex connectivity of the network. The integration of protein-protein interactions with the data from other sources can be leveraged for improving the effectiveness of protein complexes detection algorithms. Methods We have developed novel semantic similarity metho...

  1. Long-range interactions of excited He atoms with the alkaline earth atoms Mg, Ca, and Sr

    KAUST Repository

    Zhang, J.-Y.

    2013-04-05

    Dispersion coefficients for the long-range interactions of the first four excited states of He, i.e., He(2 1, 3 S) and He(2 1, 3 P), with the low-lying states of the alkaline earth atoms Mg, Ca, and Sr are calculated by summing over the reduced matrix elements of multipole transition operators.

  2. Missing and spurious interactions and the reconstruction of complex networks

    CERN Document Server

    Guimera, R; 10.1073/pnas.0908366106

    2010-01-01

    Network analysis is currently used in a myriad of contexts: from identifying potential drug targets to predicting the spread of epidemics and designing vaccination strategies, and from finding friends to uncovering criminal activity. Despite the promise of the network approach, the reliability of network data is a source of great concern in all fields where complex networks are studied. Here, we present a general mathematical and computational framework to deal with the problem of data reliability in complex networks. In particular, we are able to reliably identify both missing and spurious interactions in noisy network observations. Remarkably, our approach also enables us to obtain, from those noisy observations, network reconstructions that yield estimates of the true network properties that are more accurate than those provided by the observations themselves. Our approach has the potential to guide experiments, to better characterize network data sets, and to drive new discoveries.

  3. Atom probe tomography of lithium-doped network glasses

    Energy Technology Data Exchange (ETDEWEB)

    Greiwe, Gerd-Hendrik, E-mail: g_grei01@uni-muenster.de [Institute of Materials Physics, University of Münster, Wilhelm-Klemm-Str. 10, D-48149 Münster (Germany); Balogh, Zoltan; Schmitz, Guido [Institute of Material Science, University of Stuttgart, Heisenberg Straße 3, D-70569 Stuttgart (Germany)

    2014-06-01

    Li-doped silicate and borate glasses are electronically insulating, but provide considerable ionic conductivity. Under measurement conditions of laser-assisted atom probe tomography, mobile Li ions are redistributed in response to high electric fields. In consequence, the direct interpretation of measured composition profiles is prevented. It is demonstrated that composition profiles are nevertheless well understood by a complex model taking into account the electronic structure of dielectric materials, ionic mobility and field screening. Quantitative data on band bending and field penetration during measurement are derived which are important in understanding laser-assisted atom probe tomography of dielectric materials. - Highlights: • Atom probe tomography is performed on ion conducting glasses. • Redistribution of ions during the measurement is observed. • An electrostatic model is applied to describe the electric field and ion diffusion. • Measurement is conducted of the absolute temperature during laser pulses.

  4. Atomic and plasma-material interaction data for fusion. Vol.1

    International Nuclear Information System (INIS)

    The International Atomic Energy Agency, through its Atomic and Molecular Data Unit, coordinates a wide spectrum of programmes for the compilation, evaluation, and generation of atomic, molecular, and plasma-wall interaction data for fusion research. The present, first, volume of Atomic and Plasma-Material Interaction Data for Fusion, contains extended versions of the reviews presented at the IAEA Advisory Group Meeting on Particle-Surface Interaction Data for Fusion, held 19-21 April 1989 at the IAEA Headquarters in Vienna, The plasma-wall interaction processes covered here are those considered most important for the operational performance of magnetic confinement fusion reactors. In addition to processes due to particle impact under normal operation, plasma-wall interaction effects due to off-normal plasma events (disruptions, electron runaway bombardment) are covered, and a summary of the status of data information on these processes is given from the point of view of magnetic fusion reactor design. Refs, figs and tabs

  5. Predicting and validating protein interactions using network structure.

    Directory of Open Access Journals (Sweden)

    Pao-Yang Chen

    Full Text Available Protein interactions play a vital part in the function of a cell. As experimental techniques for detection and validation of protein interactions are time consuming, there is a need for computational methods for this task. Protein interactions appear to form a network with a relatively high degree of local clustering. In this paper we exploit this clustering by suggesting a score based on triplets of observed protein interactions. The score utilises both protein characteristics and network properties. Our score based on triplets is shown to complement existing techniques for predicting protein interactions, outperforming them on data sets which display a high degree of clustering. The predicted interactions score highly against test measures for accuracy. Compared to a similar score derived from pairwise interactions only, the triplet score displays higher sensitivity and specificity. By looking at specific examples, we show how an experimental set of interactions can be enriched and validated. As part of this work we also examine the effect of different prior databases upon the accuracy of prediction and find that the interactions from the same kingdom give better results than from across kingdoms, suggesting that there may be fundamental differences between the networks. These results all emphasize that network structure is important and helps in the accurate prediction of protein interactions. The protein interaction data set and the program used in our analysis, and a list of predictions and validations, are available at http://www.stats.ox.ac.uk/bioinfo/resources/PredictingInteractions.

  6. Photoassociation of a cold atom-molecule pair: long-range quadrupole-quadrupole interactions

    CERN Document Server

    Lepers, M; Kokoouline, V

    2010-01-01

    The general formalism of the multipolar expansion of electrostatic interactions is applied to the calculation the potential energy between an excited atom and a ground state diatomic molecule at large separations. Both partners exhibit a permanent quadrupole moment, so that their mutual quadrupole-quadrupole long-range interaction is attractive enough to bind trimers. Numerical results are given for an excited Cs(6P) atom and a ground state Cs2 molecule. The prospects for achieving photoassociation of a cold atom/dimer pair is thus discussed and found promising. The formalism can be easily generalized to the long-range interaction between molecules to investigate the formation of cold tetramers.

  7. The RING 2.0 web server for high quality residue interaction networks.

    Science.gov (United States)

    Piovesan, Damiano; Minervini, Giovanni; Tosatto, Silvio C E

    2016-07-01

    Residue interaction networks (RINs) are an alternative way of representing protein structures where nodes are residues and arcs physico-chemical interactions. RINs have been extensively and successfully used for analysing mutation effects, protein folding, domain-domain communication and catalytic activity. Here we present RING 2.0, a new version of the RING software for the identification of covalent and non-covalent bonds in protein structures, including π-π stacking and π-cation interactions. RING 2.0 is extremely fast and generates both intra and inter-chain interactions including solvent and ligand atoms. The generated networks are very accurate and reliable thanks to a complex empirical re-parameterization of distance thresholds performed on the entire Protein Data Bank. By default, RING output is generated with optimal parameters but the web server provides an exhaustive interface to customize the calculation. The network can be visualized directly in the browser or in Cytoscape. Alternatively, the RING-Viz script for Pymol allows visualizing the interactions at atomic level in the structure. The web server and RING-Viz, together with an extensive help and tutorial, are available from URL: http://protein.bio.unipd.it/ring. PMID:27198219

  8. The RING 2.0 web server for high quality residue interaction networks.

    Science.gov (United States)

    Piovesan, Damiano; Minervini, Giovanni; Tosatto, Silvio C E

    2016-07-01

    Residue interaction networks (RINs) are an alternative way of representing protein structures where nodes are residues and arcs physico-chemical interactions. RINs have been extensively and successfully used for analysing mutation effects, protein folding, domain-domain communication and catalytic activity. Here we present RING 2.0, a new version of the RING software for the identification of covalent and non-covalent bonds in protein structures, including π-π stacking and π-cation interactions. RING 2.0 is extremely fast and generates both intra and inter-chain interactions including solvent and ligand atoms. The generated networks are very accurate and reliable thanks to a complex empirical re-parameterization of distance thresholds performed on the entire Protein Data Bank. By default, RING output is generated with optimal parameters but the web server provides an exhaustive interface to customize the calculation. The network can be visualized directly in the browser or in Cytoscape. Alternatively, the RING-Viz script for Pymol allows visualizing the interactions at atomic level in the structure. The web server and RING-Viz, together with an extensive help and tutorial, are available from URL: http://protein.bio.unipd.it/ring.

  9. Propagation of light through small clouds of cold interacting atoms

    OpenAIRE

    Jennewein, S; Sortais, Y. R. P.; Greffet, J. -J.; Browaeys, A.

    2015-01-01

    We demonstrate experimentally that a cloud of cold atoms with a size comparable to the wavelength of light can induce large group delays on a laser pulse when the laser is tightly focused on it and is close to an atomic resonance. Delays as large as -10 ns are observed, corresponding to "superluminal" propagation with negative group velocities as low as -300 m/s. Strikingly, this large delay is associated with a moderate extinction owing to the very small size of the cloud and to the light-in...

  10. Atoms

    Institute of Scientific and Technical Information of China (English)

    刘洪毓

    2007-01-01

    Atoms(原子)are all around us.They are something like the bricks (砖块)of which everything is made. The size of an atom is very,very small.In just one grain of salt are held millions of atoms. Atoms are very important.The way one object acts depends on what

  11. Progress towards realization of quantum networks using atomic ensembles

    Science.gov (United States)

    Matthew, Eisaman

    2005-05-01

    We report on our progress towards generation, storage and communication of single photon states using atomic memory. Specifically, we describe proof-of principle experiments demonstrating generation of single photon pulses of light with controllable propagation direction, timing, and pulse shapes [1]. The approach is based on preparation of an atomic ensemble in a state with a desired number of atomic spin excitations, which is later converted into a photon pulse by exploiting long-lived coherent memory for photon states and electromagnetically induced transparency (EIT). We describe our efforts to optimize the performance of such a novel single photon source. Specifically we propose and demonstrate a novel propagation geometry that optimizes mode matching and signal to noise ratio. We discuss our progress towards transmitting single photon states between two atomic memory nodes connected by photonic channels and outline the prospects for long-distance quantum communication using these techniques. [1] M. D. Eisaman, L. Childress, A. Andr'e, F. Massou, A. S. Zibrov, and M. D. Lukin, Phys. Rev. Lett. 93, 233602 (2004).

  12. Quantum Correlation of Two Entangled Atoms Interacting with the Binomial Optical Field

    Science.gov (United States)

    Liu, Tang-Kun; Tao, Yu; Shan, Chuan-Jia; Liu, Ji-bing

    2016-10-01

    Quantum correlations of two atoms in a system of two entangled atoms interacting with the binomial optical field are investigated. In eight different initial states of the two atoms, the influence of the strength of the dipole-dipole interaction, probabilities of a the Bernoulli trial and particle number of the binomial optical field on the temporal evolution of the geometrical quantum discord between two atoms are discussed. The result shows that two atoms always exist the correlation for different parameters. In addition, when and only when the two atoms are initially in the maximally entangled state, the temporal evolution of geometrical quantum discord is not affected by the parameters, and always keep in the degree of geometrical quantum discord that is a fixed value.

  13. Simulations of the angular dependence of the dipole–dipole interaction among Rydberg atoms

    Science.gov (United States)

    Bigelow, Jacob L.; Paul, Jacob T.; Peleg, Matan; Sanford, Veronica L.; Carroll, Thomas J.; Noel, Michael W.

    2016-08-01

    The dipole–dipole interaction between two Rydberg atoms depends on the relative orientation of the atoms and on the change in the magnetic quantum number. We simulate the effect of this anisotropy on the energy transport in an amorphous many atom system subject to a homogeneous applied electric field. We consider two experimentally feasible geometries and find that the effects should be measurable in current generation imaging experiments. In both geometries atoms of p character are localized to a small region of space which is immersed in a larger region that is filled with atoms of s character. Energy transfer due to the dipole–dipole interaction can lead to a spread of p character into the region initially occupied by s atoms. Over long timescales the energy transport is confined to the volume near the border of the p region which suggests Anderson localization. We calculate a correlation length of 6.3 μm for one particular geometry.

  14. Do networks of social interactions reflect patterns of kinship?

    Institute of Scientific and Technical Information of China (English)

    Joah R. MADDEN; Johanna F. NIEL SEN; Tim H. CLUTTON-BROCK

    2012-01-01

    The underlying kin structure of groups of animals may be glimpsed from patterns of spatial position or temporal association between individuals,and is presumed to facilitate inclusive fitness benefits.Such structure may be evident at a finer,behavioural,scale with individuals preferentially interacting with kin.We tested whether kin structure within groups of meerkats Suricata suricatta matched three forms of social interaction networks:grooming,dominance or foraging competitions.Networks of dominance interactions were positively related to networks of kinship,with close relatives engaging in dominance interactions with each other.This relationship persisted even after excluding the breeding dominant pair and when we restricted the kinship network to only include links between first order kin,which are most likely to be able to discern kin through simple rules of thumb.Conversely,we found no relationship between kinship networks and either grooming networks or networks of foraging competitions.This is surprising because a positive association between kin in a grooming network,or a negative association between kin in a network of foraging competitions offers opportunities for inclusive fitness benefits.Indeed,the positive association between kin in a network of dominance interactions that we did detect does not offer clear inclusive fitness benefits to group members.We conclude that kin structure in behavioural interactions in meerkats may be driven by factors other than indirect fitness benefits,and that networks of cooperative behaviours such as grooming may be driven by direct benefits accruing to individuals perhaps through mutualism or manipulation [Current Zoology 58 (2):319-328,2012].

  15. Do networks of social interactions reflect patterns of kinship?

    Directory of Open Access Journals (Sweden)

    Joah R. MADDEN, Johanna F. NIELSEN, Tim H. CLUTTON-BROCK

    2012-04-01

    Full Text Available The underlying kin structure of groups of animals may be glimpsed from patterns of spatial position or temporal association between individuals, and is presumed to facilitate inclusive fitness benefits. Such structure may be evident at a finer, behavioural, scale with individuals preferentially interacting with kin. We tested whether kin structure within groups of meerkats Suricata suricatta matched three forms of social interaction networks: grooming, dominance or foraging competitions. Networks of dominance interactions were positively related to networks of kinship, with close relatives engaging in dominance interactions with each other. This relationship persisted even after excluding the breeding dominant pair and when we restricted the kinship network to only include links between first order kin, which are most likely to be able to discern kin through simple rules of thumb. Conversely, we found no relationship between kinship networks and either grooming networks or networks of foraging competitions. This is surprising because a positive association between kin in a grooming network, or a negative association between kin in a network of foraging competitions offers opportunities for inclusive fitness benefits. Indeed, the positive association between kin in a network of dominance interactions that we did detect does not offer clear inclusive fitness benefits to group members. We conclude that kin structure in behavioural interactions in meerkats may be driven by factors other than indirect fitness benefits, and that networks of cooperative behaviours such as grooming may be driven by direct benefits accruing to individuals perhaps through mutualism or manipulation [Current Zoology 58 (2: 319-328, 2012].

  16. Artificial neural network approach for atomic coordinate prediction of carbon nanotubes

    Science.gov (United States)

    Acı, Mehmet; Avcı, Mutlu

    2016-07-01

    In this paper, four artificial neural network (ANN) models [i.e., feed-forward neural network (FFNN), function fitting neural network (FITNET), cascade-forward neural network (CFNN) and generalized regression neural network] have been developed for atomic coordinate prediction of carbon nanotubes (CNTs). The research reported in this study has two primary objectives: (1) to develop ANN prediction models that calculate atomic coordinates of CNTs instead of using any simulation software and (2) to use results of the ANN models as an initial value of atomic coordinates for reducing number of iterations in calculation process. The dataset consisting of 10,721 data samples was created by combining the atomic coordinates of elements and chiral vectors using BIOVIA Materials Studio CASTEP (CASTEP) software. All prediction models yield very low mean squared normalized error and mean absolute error rates. Multiple correlation coefficient (R) results of FITNET, FFNN and CFNN models are close to 1. Compared with CASTEP, calculation times decrease from days to minutes. It would seem possible to predict CNTs' atomic coordinates using ANN models can be successfully used instead of mathematical calculations.

  17. Dark Entangled Steady States of Interacting Rydberg Atoms

    DEFF Research Database (Denmark)

    Dasari, Durga; Mølmer, Klaus

    2013-01-01

    their short-lived excited states lead to rapid, dissipative formation of an entangled steady state. We show that for a wide range of physical parameters, this entangled state is formed on a time scale given by the strengths of coherent Raman and Rabi fields applied to the atoms, while it is only weakly...

  18. Quantum Statistical Behaviors of Interaction of an Atomic Bose-Einstein Condensate with Laser

    Institute of Scientific and Technical Information of China (English)

    YU Zhao-Xian; JIAO Zhi-Yong

    2001-01-01

    We have investigated quantum statistical behaviors of photons and atoms in interaction of an atomic Bose Einstein condensate with quantized laser field. When the quantized laser field is initially prepared in a superposition state which exhibits holes in its photon-number distribution, while the atomic field is initially in a Fock state, it is found that there is energy exchange between photons and atoms. For the input and output states, the photons and atoms may exhibit the sub-Poissonian distribution. The input and output laser fields may exhibit quadrature squeezing, but for the atomic field, only the output state exhibits quadrature squeezing. It is shown that there exists the violation of the Cauchy-Schwartz inequality, which means that the correlation between photons and atoms is nonclassical.``

  19. Interactions of foreign interstitial and substitutional atoms in bcc iron from ab initio calculations

    International Nuclear Information System (INIS)

    C and N atoms are the most frequent foreign interstitial atoms (FIAs), and often incorporated into the surface layers of steels to enhance their properties by thermochemical treatments. Al, Si, Ti, V, Cr, Mn, Co, Ni, Cu, Nb and Mo are the most common alloying elements in steels, also can be called foreign substitutional atoms (FSAs). The FIA and FSA interactions play an important role in the diffusion of C and N atoms, and the microstructures and mechanical properties of surface modified layers. Ab initio calculations based on the density functional theory are carried out to investigate FIA interactions with FSA in ferromagnetic bcc iron. The FIA–FSA interactions are analyzed systematically from five aspects, including interaction energies, density of states (DOS), bond populations, electron density difference maps and local magnetic moments

  20. Protein interaction network related to Helicobacter pylori infection response

    Institute of Scientific and Technical Information of China (English)

    Kyu Kwang Kim; Han Bok Kim

    2009-01-01

    AIM: To understand the complex reaction of gastric inflammation induced by Helicobacter pylori (H pylori ) in a systematic manner using a protein interaction network. METHODS: The expression of genes significantly changed on microarray during H pylori infection was scanned from the web literary database and translated into proteins. A network of protein interactions was constructed by searching the primary interactions of selected proteins. The constructed network was mathematically analyzed and its biological function was examined. In addition, the nodes on the network were checked to determine if they had any further functional importance or relation to other proteins by extending them.RESULTS: The scale-free network showing the relationship between inflammation and carcinogenesis was constructed. Mathematical analysis showed hub and bottleneck proteins, and these proteins were mostly related to immune response. The network contained pathways and proteins related to H pylori infection, such as the JAK-STAT pathway triggered by interleukins. Activation of nuclear factor (NF)-kB, TLR4, and other proteins known to function as core proteins of immune response were also found.These immune-related proteins interacted on the network with pathways and proteins related to the cell cycle, cell maintenance and proliferation, and transcription regulators such as BRCA1, FOS, REL, and zinc finger proteins. The extension of nodes showed interactions of the immune proteins with cancerrelated proteins. One extended network, the core network, a summarized form of the extended network, and cell pathway model were constructed. CONCLUSION: Immune-related proteins activated by H pylori infection interact with proto-oncogene proteins. The hub and bottleneck proteins are potential drug targets for gastric inflammation and cancer.

  1. Personal Profiles: Enhancing Social Interaction in Learning Networks

    NARCIS (Netherlands)

    Berlanga, Adriana; Bitter-Rijpkema, Marlies; Brouns, Francis; Sloep, Peter; Fetter, Sibren

    2009-01-01

    Berlanga, A. J., Bitter-Rijpkema, M., Brouns, F., Sloep, P. B., & Fetter, S. (2011). Personal Profiles: Enhancing Social Interaction in Learning Networks. International Journal of Web Based Communities, 7(1), 66-82.

  2. A connective differentiation of textual production in interaction networks

    OpenAIRE

    Fabbri, Renato

    2014-01-01

    This paper explores textual production in interaction networks, with special emphasis on its relation to topological measures. Four email lists were selected, in which measures were taken from the texts participants wrote. Peripheral, intermediary and hub sectors of these networks were observed to have discrepant linguistic elaborations. For completeness of exposition, correlation of textual and topological measures were observed for the entire network and for each connective sector. The form...

  3. Competence–Based Support of Interaction between Business Network Members

    OpenAIRE

    Smirnov, Alexander; Kashevnik, Alexey; Shilov, Nikolay

    2008-01-01

    In a complicated business network finding a supplier can be a very time consuming task. The technology of competence management is aimed to support such kind of tasks. The paper presents an approach to support interaction between business network members based on such technologies as competence management and knowledge management. The conceptual models of the context-driven competence management system and production network member competence profile are described. The usage of th...

  4. Ontology integration to identify protein complex in protein interaction networks

    Directory of Open Access Journals (Sweden)

    Yang Zhihao

    2011-10-01

    Full Text Available Abstract Background Protein complexes can be identified from the protein interaction networks derived from experimental data sets. However, these analyses are challenging because of the presence of unreliable interactions and the complex connectivity of the network. The integration of protein-protein interactions with the data from other sources can be leveraged for improving the effectiveness of protein complexes detection algorithms. Methods We have developed novel semantic similarity method, which use Gene Ontology (GO annotations to measure the reliability of protein-protein interactions. The protein interaction networks can be converted into a weighted graph representation by assigning the reliability values to each interaction as a weight. Following the approach of that of the previously proposed clustering algorithm IPCA which expands clusters starting from seeded vertices, we present a clustering algorithm OIIP based on the new weighted Protein-Protein interaction networks for identifying protein complexes. Results The algorithm OIIP is applied to the protein interaction network of Sacchromyces cerevisiae and identifies many well known complexes. Experimental results show that the algorithm OIIP has higher F-measure and accuracy compared to other competing approaches.

  5. Electron quantum dynamics in atom-ion interaction

    Science.gov (United States)

    Sabzyan, H.; Jenabi, M. J.

    2016-04-01

    Electron transfer (ET) process and its dependence on the system parameters are investigated by solving two-dimensional time-dependent Schrödinger equation numerically using split operator technique. Evolution of the electron wavepacket occurs from the one-electron species hydrogen atom to another bare nucleus of charge Z > 1. This evolution is quantified by partitioning the simulation box and defining regional densities belonging to the two nuclei of the system. It is found that the functional form of the time-variations of these regional densities and the extent of ET process depend strongly on the inter-nuclear distance and relative values of the nuclear charges, which define the potential energy surface governing the electron wavepacket evolution. Also, the initial electronic state of the single-electron atom has critical effect on this evolution and its consequent (partial) electron transfer depending on its spreading extent and orientation with respect to the inter-nuclear axis.

  6. Development of Attention Networks and Their Interactions in Childhood

    Science.gov (United States)

    Pozuelos, Joan P.; Paz-Alonso, Pedro M.; Castillo, Alejandro; Fuentes, Luis J.; Rueda, M. Rosario

    2014-01-01

    In the present study, we investigated developmental trajectories of alerting, orienting, and executive attention networks and their interactions over childhood. Two cross-sectional experiments were conducted with different samples of 6-to 12-year-old children using modified versions of the attention network task (ANT). In Experiment 1 (N = 106),…

  7. Simple Theoretical Models for Resonant Cold Atom Interactions

    OpenAIRE

    Julienne, Paul S.; Gao, Bo

    2006-01-01

    Magnetically tunable scattering resonances have been used with great success for precise control of s-wave scattering lengths in ultracold atomic collisions. We describe relatively simple yet quite powerful analytic treatments of such resonances based on the analytic properties of the van der Waals long range potential. This theory can be used to characterize a number of properties of specific resonances that have been used successfully in various experiments with $^{87}$Rb, $^{85}$Rb, $^{40}...

  8. Photoassociation of a cold atom-molecule pair: long-range quadrupole-quadrupole interactions

    OpenAIRE

    Lepers, M.; Dulieu, O.; Kokoouline, V.

    2010-01-01

    The general formalism of the multipolar expansion of electrostatic interactions is applied to the calculation the potential energy between an excited atom (without fine structure) and a ground state diatomic molecule at large separations. Both partners exhibit a permanent quadrupole moment, so that their mutual quadrupole-quadrupole long-range interaction is attractive enough to bind trimers. Numerical results are given for an excited Cs(6P) atom and a ground state Cs2 molecule. The prospects...

  9. Long-range gravitational-like interaction in a neutral atomic cold gas

    CERN Document Server

    Chalony, Maryvonne; Marcos, B; Olivetti, A; Wilkowski, David

    2012-01-01

    A quasi resonant laser induces a long-range attractive force within a cloud of cold atoms. We take advantage of this force to build in the lab quasi 1D systems of particles with a gravitational-like interaction, at a fluid level of modeling. We give experimental evidences of such an interaction in a Strontium cold gas, studying the density profile of the cloud, its size as a function of the number of atoms and its breathing oscillations.

  10. Geometric De-noising of Protein-Protein Interaction Networks

    OpenAIRE

    Kuchaiev, Oleksii; Rasajski, Marija; Higham, Desmond J.; Przul, Natasa; Przytycka, Teresa Maria

    2009-01-01

    Understanding complex networks of protein-protein interactions (PPIs) is one of the foremost challenges of the post-genomic era. Due to the recent advances in experimental bio-technology, including yeast-2-hybrid (Y2H), tandem affinity purification (TAP) and other high-throughput methods for protein-protein interaction (PPI) detection, huge amounts of PPI network data are becoming available. Of major concern, however, are the levels of noise and incompleteness. For example, for Y2H screens, i...

  11. Development of Novel Random Network Theory-Based Approaches to Identify Network Interactions among Nitrifying Bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Shi, Cindy

    2015-07-17

    The interactions among different microbial populations in a community could play more important roles in determining ecosystem functioning than species numbers and their abundances, but very little is known about such network interactions at a community level. The goal of this project is to develop novel framework approaches and associated software tools to characterize the network interactions in microbial communities based on high throughput, large scale high-throughput metagenomics data and apply these approaches to understand the impacts of environmental changes (e.g., climate change, contamination) on network interactions among different nitrifying populations and associated microbial communities.

  12. Nonlinear interaction of meta-atoms through optical coupling

    Energy Technology Data Exchange (ETDEWEB)

    Slobozhanyuk, A. P.; Kapitanova, P. V.; Filonov, D. S.; Belov, P. A. [National Research University of Information Technologies, Mechanics and Optics (ITMO), St. Petersburg 197101 (Russian Federation); Powell, D. A. [Nonlinear Physics Centre and Centre for Ultrahigh-bandwidth Devices for Optical Systems (CUDOS), Australian National University, Canberra, ACT 0200 (Australia); Shadrivov, I. V.; Kivshar, Yu. S. [National Research University of Information Technologies, Mechanics and Optics (ITMO), St. Petersburg 197101 (Russian Federation); Nonlinear Physics Centre and Centre for Ultrahigh-bandwidth Devices for Optical Systems (CUDOS), Australian National University, Canberra, ACT 0200 (Australia); Lapine, M., E-mail: mlapine@physics.usyd.edu.au [National Research University of Information Technologies, Mechanics and Optics (ITMO), St. Petersburg 197101 (Russian Federation); Centre for Ultrahigh-bandwidth Devices for Optical Systems (CUDOS), School of Physics, University of Sydney, New South Wales 2006 (Australia); McPhedran, R. C. [Centre for Ultrahigh-bandwidth Devices for Optical Systems (CUDOS), School of Physics, University of Sydney, New South Wales 2006 (Australia)

    2014-01-06

    We propose and experimentally demonstrate a multi-frequency nonlinear coupling mechanism between split-ring resonators. We engineer the coupling between two microwave resonators through optical interaction, whilst suppressing the direct electromagnetic coupling. This allows for a power-dependent interaction between the otherwise independent resonators, opening interesting opportunities to address applications in signal processing, filtering, directional coupling, and electromagnetic compatibility.

  13. Cooperative tertiary interaction network guides RNA folding

    OpenAIRE

    Behrouzi, Reza; Roh, Joon Ho; Kilburn, Duncan; Briber, Robert M.; Woodson, Sarah A.

    2012-01-01

    Non-coding RNAs form unique three-dimensional structures, which perform many biochemical and regulatory functions. To understand how RNAs fold uniquely despite a small number of tertiary interaction motifs, we mutated the major tertiary interactions in a group I ribozyme. The resulting perturbations to the folding energy landscape were measured using SAXS, ribozyme activity, hydroxyl radical footprinting and native PAGE. Double and triple mutant cycles show that most tertiary interactions hav...

  14. A theoretical and experimental study of neuromorphic atomic switch networks for reservoir computing.

    Science.gov (United States)

    Sillin, Henry O; Aguilera, Renato; Shieh, Hsien-Hang; Avizienis, Audrius V; Aono, Masakazu; Stieg, Adam Z; Gimzewski, James K

    2013-09-27

    Atomic switch networks (ASNs) have been shown to generate network level dynamics that resemble those observed in biological neural networks. To facilitate understanding and control of these behaviors, we developed a numerical model based on the synapse-like properties of individual atomic switches and the random nature of the network wiring. We validated the model against various experimental results highlighting the possibility to functionalize the network plasticity and the differences between an atomic switch in isolation and its behaviors in a network. The effects of changing connectivity density on the nonlinear dynamics were examined as characterized by higher harmonic generation in response to AC inputs. To demonstrate their utility for computation, we subjected the simulated network to training within the framework of reservoir computing and showed initial evidence of the ASN acting as a reservoir which may be optimized for specific tasks by adjusting the input gain. The work presented represents steps in a unified approach to experimentation and theory of complex systems to make ASNs a uniquely scalable platform for neuromorphic computing.

  15. Atomic and plasma-material interaction data for fusion. V. 6

    International Nuclear Information System (INIS)

    Volume 6 of the supplement ''atomic and plasma-material interaction data for fusion'' to the journal ''Nuclear Fusion'' includes critical assessments and results of original experimental and theoretical studies on inelastic collision processes among the basic and dominant impurity constituents of fusion plasmas. Processes considered in the 15 papers constituting this volume are: electron impact excitation of excited Helium atoms, electron impact excitation and ionization of plasma impurity ions and atoms, electron-impurity-ion recombination and excitation, ionization and electron capture in collisions of plasma protons and impurity ions with the main fusion plasma neutral components helium and atomic and molecular hydrogen. Refs, figs, tabs

  16. van der Waals coefficients for positronium interactions with closed-shell atoms

    CERN Document Server

    Swann, A R; Gribakin, G F

    2015-01-01

    The random-phase approximation with exchange (RPAE) is used with a $B$-spline basis to compute dynamic dipole polarizabilities of noble-gas atoms and several other closed-shell atoms (Be, Mg, Ca, Zn, Sr and Cd). From these, values of the van der Waals $C_6$ constants for positronium interactions with these atoms are determined and compared with existing data. Our best predictions of $C_6$ for Ps--noble-gas pairs are expected to be accurate to within 1%, and to within few per cent for the alkaline earths. Implications of increased $C_6$ values for more polarizable atoms are discussed.

  17. Hubbard model for ultracold bosonic atoms interacting via zero-point-energy-induced three-body interactions

    Science.gov (United States)

    Paul, Saurabh; Johnson, P. R.; Tiesinga, Eite

    2016-04-01

    We show that, for ultracold neutral bosonic atoms held in a three-dimensional periodic potential or optical lattice, a Hubbard model with dominant, attractive three-body interactions can be generated. In fact, we derive that the effect of pairwise interactions can be made small or zero starting from the realization that collisions occur at the zero-point energy of an optical lattice site and the strength of the interactions is energy dependent from effective-range contributions. We determine the strength of the two- and three-body interactions for scattering from van der Waals potentials and near Fano-Feshbach resonances. For van der Waals potentials, which for example describe scattering of alkaline-earth atoms, we find that the pairwise interaction can only be turned off for species with a small negative scattering length, leaving the 88Sr isotope a possible candidate. Interestingly, for collisional magnetic Feshbach resonances this restriction does not apply and there often exist magnetic fields where the two-body interaction is small. We illustrate this result for several known narrow resonances between alkali-metal atoms as well as chromium atoms. Finally, we compare the size of the three-body interaction with hopping rates and describe limits due to three-body recombination.

  18. Spectroscopic properties of a two-level atom interacting with a complex spherical nanoshell

    CERN Document Server

    Moroz, A

    2004-01-01

    Frequency shifts, radiative decay rates, the Ohmic loss contribution to the nonradiative decay rates, fluorescence yields, and photobleaching of a two-level atom radiating anywhere inside or outside a complex spherical nanoshell, i.e. a stratified sphere consisting of alternating silica and gold concentric spherical shells, are studied. The changes in the spectroscopic properties of an atom interacting with complex nanoshells are significantly enhanced, often more than two orders of magnitude, compared to the same atom interacting with a homogeneous dielectric sphere. The changes strongly depend on the nanoshell parameters and the atom position. When an atom approaches a metal shell,the radiative decay rates are strongly enhanced and they increase faster than the Ohmic loss contribution to the nonradiative decay rates. However, the majority of the emitted radiation does not escape to spatial infinity but instead is absorbed. The enhancement of the radiative decay rates in a close proximity of metal boundaries...

  19. Identifying the interactions in a colored dynamical network

    Institute of Scientific and Technical Information of China (English)

    吴召艳; 弓晓利

    2015-01-01

    The interactions of a colored dynamical network play a great role in its dynamical behaviour and are denoted by outer and inner coupling matrices. In this paper, the outer and inner coupling matrices are assumed to be unknown and need to be identified. A corresponding network estimator is designed for identifying the unknown interactions by adopting proper adaptive laws. Based on the Lyapunov function method and Barbalat’s lemma, the obtained result is analytically proved. A colored network coupled with chaotic Lorenz, Chen, and L ¨u systems is considered as a numerical example to illustrate the effectiveness of the proposed method.

  20. Model of mobile agents for sexual interactions networks

    CERN Document Server

    González, M C; Lind, P G

    2005-01-01

    We present a novel model to simulate real social networks of complex interactions, based in a granular system of colliding particles (agents). The network is build by keeping track of the collisions and evolves in time with correlations which emerge due to the mobility of the agents. Therefore, statistical features are a consequence only of local collisions among its individual agents. Agent dynamics is realized by an event-driven algorithm of collisions where energy is gained as opposed to granular systems which have dissipation. The model reproduces empirical data from networks of sexual interactions, not previously obtained with other approaches.

  1. Estimation of atomic interaction parameters by quantum measurements

    DEFF Research Database (Denmark)

    Kiilerich, Alexander Holm; Mølmer, Klaus

    Quantum systems, ranging from atomic systems to field modes and mechanical devices are useful precision probes for a variety of physical properties and phenomena. Measurements by which we extract information about the evolution of single quantum systems yield random results and cause a back action...... on the system. This back action may be favourable as it randomly quenches the system and triggers a transient evolution with temporal signal correlations which may depend more strongly than the steady state on the desired physical properties. To identify the quantitative performance of quantum...

  2. Simple Theoretical Models for Resonant Cold Atom Interactions

    CERN Document Server

    Julienne, P S; Julienne, Paul S.; Gao, Bo

    2006-01-01

    Magnetically tunable scattering resonances have been used with great success for precise control of s-wave scattering lengths in ultracold atomic collisions. We describe relatively simple yet quite powerful analytic treatments of such resonances based on the analytic properties of the van der Waals long range potential. This theory can be used to characterize a number of properties of specific resonances that have been used successfully in various experiments with $^{87}$Rb, $^{85}$Rb, $^{40}$K, and $^{6}$Li. Optical Feshbach resonances are also possible and may be practical with narrow intercombination line photoassociative transitions in species like Sr and Yb.

  3. Test of vacuum polarization and hyperfine interaction in muonic atoms

    CERN Document Server

    Backe, H; Engfer, R; Link, R; Michaelsen, R; Petitjean, C; Robert-Tissot, B; Roschert, G; Schellenberg, L; Schneuwly, H; Schröder, W U; Von Gunten, A H; Vuilleumier, J L; Walter, H K; Zehnder, A

    1972-01-01

    In connection with discrepancies between experimental and theoretical values for the vacuum polarization correction in the case of the 5-4 transitions in heavy and medium muonic atoms, the energies of this transition in /sup nat/Hg and /sup 203/Tl were measured at the CERN-SC muon channel. The broadening of the 2/sup +/-0/sup +/- nuclear gamma transition in muonic /sup 190/Os and /sup 192/Os was used to determine the magnetic h.f. splitting of the 2/sup +/ rotational state. The results are compared with the predictions of different models. (7 refs).

  4. Optimization of an interactive distributive computer network

    Science.gov (United States)

    Frederick, V.

    1985-01-01

    The activities under a cooperative agreement for the development of a computer network are briefly summarized. Research activities covered are: computer operating systems optimization and integration; software development and implementation of the IRIS (Infrared Imaging of Shuttle) Experiment; and software design, development, and implementation of the APS (Aerosol Particle System) Experiment.

  5. Interactively Evolving Compositional Sound Synthesis Networks

    DEFF Research Database (Denmark)

    Jónsson, Björn Þór; Hoover, Amy K.; Risi, Sebastian

    2015-01-01

    the space of potential sounds that can be generated through such compositional sound synthesis networks (CSSNs). To study the effect of evolution on subjective appreciation, participants in a listener study ranked evolved timbres by personal preference, resulting in preferences skewed toward the first...

  6. Mean field interaction in biochemical reaction networks

    KAUST Repository

    Tembine, Hamidou

    2011-09-01

    In this paper we establish a relationship between chemical dynamics and mean field game dynamics. We show that chemical reaction networks can be studied using noisy mean field limits. We provide deterministic, noisy and switching mean field limits and illustrate them with numerical examples. © 2011 IEEE.

  7. Retarded Boson-Fermion interaction in atomic systems

    Indian Academy of Sciences (India)

    Sambhu N Datta

    2007-09-01

    The retarded interaction between an electron and a spin-0 nucleus, that has been derived from electro-dynamical perturbation theory is discussed here. A brief account of the derivation is given. The retarded form is correct through order 2/2. Use of the relative coordinates leads to an effective oneelectron operator that can be used through all orders of perturbation theory. A few unitary transformations give rise to the interaction that is valid in the non-relativistic limit.

  8. Coherence and Fluctuations in the Interaction between Moving Atoms and a Quantum Field

    CERN Document Server

    Hu, B L; Raval, Alpan

    1997-01-01

    Mesoscopic physics deals with three fundamental issues: quantum coherence, fluctuations and correlations. Here we analyze these issues for atom optics, using a simplified model of an assembly of atoms (or detectors, which are particles with some internal degree of freedom) moving in arbitrary trajectories in a quantum field. Employing the influence functional formalism, we study the self-consistent effect of the field on the atoms, and their mutual interactions via coupling to the field. We derive the coupled Langevin equations for the atom assemblage and analyze the relation of dissipative dynamics of the atoms with the correlation and fluctuations of the quantum field. This provides a useful theoretical framework for analysing the coherent properties of atom-field systems.

  9. Resonance-enhanced collective effect in a triangle arrangement of Rydberg atoms with anisotropic interactions

    CERN Document Server

    Qian, Jing

    2016-01-01

    We investigate the collective excitation effect in a scheme where three identical Rydberg atoms are arranged in an equilateral triangular lattice. By using a static electric field polarizing the atomic dipoles, the dipole-dipole interactions between two Rydberg atoms are essentially anisotropic and can even disappear in the several special resonance cases. For that fact, we observe collectively enhanced excitation probability of single Rydberg atom in resonant areas in the case of strong blockade, and that of double or triple Rydberg atoms in the case of partial blockade. To give more evidences for this collective excitation enhancement, we study the two-body quantum correlation between three Rydberg atoms, as well as the dependence of the blockade radius on the length of triangle sides, which present a good agreement with the excitation properties.

  10. Cortico-cardio-respiratory network interactions during anesthesia.

    Directory of Open Access Journals (Sweden)

    Yuri Shiogai

    Full Text Available General anesthetics are used during medical and surgical procedures to reversibly induce a state of total unconsciousness in patients. Here, we investigate, from a dynamic network perspective, how the cortical and cardiovascular systems behave during anesthesia by applying nonparametric spectral techniques to cortical electroencephalography, electrocardiogram and respiratory signals recorded from anesthetized rats under two drugs, ketamine-xylazine (KX and pentobarbital (PB. We find that the patterns of low-frequency cortico-cardio-respiratory network interactions may undergo significant changes in network activity strengths and in number of network links at different depths of anesthesia dependent upon anesthetics used.

  11. End of Interactive Emailing from the Technical Network

    CERN Multimedia

    2006-01-01

    According to the CNIC Security Policy for Control Systems (EDMS #584092), interactive emailing on PCs (and other devices) connected to the Technical Network is prohibited. Please note that from November 6th, neither reading emails nor sending emails interactively using e.g. Outlook or Pine mail clients on PCs connected to the Technical Network will be possible anymore. However, automatically generated emails will not be blocked and can still be sent off using CERNMX.CERN.CH as mail server. These restrictions DO NOT apply to PCs connected to any other network, like the General Purpose (or office) network. If you have questions, please do not hesitate to contact Uwe Epting, Pierre Charrue or Stefan Lueders (Technical-Network.Administrator@cern.ch). Your CNIC Working Group

  12. EVALUATING AUSTRALIAN FOOTBALL LEAGUE PLAYER CONTRIBUTIONS USING INTERACTIVE NETWORK SIMULATION

    Directory of Open Access Journals (Sweden)

    Jonathan Sargent

    2013-03-01

    Full Text Available This paper focuses on the contribution of Australian Football League (AFL players to their team's on-field network by simulating player interactions within a chosen team list and estimating the net effect on final score margin. A Visual Basic computer program was written, firstly, to isolate the effective interactions between players from a particular team in all 2011 season matches and, secondly, to generate a symmetric interaction matrix for each match. Negative binomial distributions were fitted to each player pairing in the Geelong Football Club for the 2011 season, enabling an interactive match simulation model given the 22 chosen players. Dynamic player ratings were calculated from the simulated network using eigenvector centrality, a method that recognises and rewards interactions with more prominent players in the team network. The centrality ratings were recorded after every network simulation and then applied in final score margin predictions so that each player's match contribution-and, hence, an optimal team-could be estimated. The paper ultimately demonstrates that the presence of highly rated players, such as Geelong's Jimmy Bartel, provides the most utility within a simulated team network. It is anticipated that these findings will facilitate optimal AFL team selection and player substitutions, which are key areas of interest to coaches. Network simulations are also attractive for use within betting markets, specifically to provide information on the likelihood of a chosen AFL team list "covering the line".

  13. Social Network Extraction and Analysis Based on Multimodal Dyadic Interaction

    Directory of Open Access Journals (Sweden)

    Bogdan Raducanu

    2012-02-01

    Full Text Available Social interactions are a very important component in people’s lives. Social network analysis has become a common technique used to model and quantify the properties of social interactions. In this paper, we propose an integrated framework to explore the characteristics of a social network extracted from multimodal dyadic interactions. For our study, we used a set of videos belonging to New York Times’ Blogging Heads opinion blog. The Social Network is represented as an oriented graph, whose directed links are determined by the Influence Model. The links’ weights are a measure of the “influence” a person has over the other. The states of the Influence Model encode automatically extracted audio/visual features from our videos using state-of-the art algorithms. Our results are reported in terms of accuracy of audio/visual data fusion for speaker segmentation and centrality measures used to characterize the extracted social network.

  14. Modeling the dynamical interaction between epidemics on overlay networks

    CERN Document Server

    Marceau, Vincent; Hébert-Dufresne, Laurent; Allard, Antoine; Dubé, Louis J

    2011-01-01

    Epidemics seldom occur as isolated phenomena. Typically, two or more viral agents spread within the same host population and may interact dynamically with each other. We present a general model where two viral agents interact via an immunity mechanism as they propagate simultaneously on two networks connecting the same set of nodes. Exploiting a correspondence between the propagation dynamics and a dynamical process performing progressive network generation, we develop an analytic approach that accurately captures the dynamical interaction between epidemics on overlay networks. The formalism allows for overlay networks with arbitrary joint degree distribution and overlap. To illustrate the versatility of our approach, we consider a hypothetical delayed intervention scenario in which an immunizing agent is disseminated in a host population to hinder the propagation of an undesirable agent (e.g. the spread of preventive information in the context of an emerging infectious disease).

  15. Evidence of probabilistic behaviour in protein interaction networks

    Directory of Open Access Journals (Sweden)

    Reifman Jaques

    2008-01-01

    Full Text Available Abstract Background Data from high-throughput experiments of protein-protein interactions are commonly used to probe the nature of biological organization and extract functional relationships between sets of proteins. What has not been appreciated is that the underlying mechanisms involved in assembling these networks may exhibit considerable probabilistic behaviour. Results We find that the probability of an interaction between two proteins is generally proportional to the numerical product of their individual interacting partners, or degrees. The degree-weighted behaviour is manifested throughout the protein-protein interaction networks studied here, except for the high-degree, or hub, interaction areas. However, we find that the probabilities of interaction between the hubs are still high. Further evidence is provided by path length analyses, which show that these hubs are separated by very few links. Conclusion The results suggest that protein-protein interaction networks incorporate probabilistic elements that lead to scale-rich hierarchical architectures. These observations seem to be at odds with a biologically-guided organization. One interpretation of the findings is that we are witnessing the ability of proteins to indiscriminately bind rather than the protein-protein interactions that are actually utilized by the cell in biological processes. Therefore, the topological study of a degree-weighted network requires a more refined methodology to extract biological information about pathways, modules, or other inferred relationships among proteins.

  16. Connecting the dots in Huntington's disease with protein interaction networks

    OpenAIRE

    Giorgini, Flaviano; Muchowski, Paul J.

    2005-01-01

    Analysis of protein-protein interaction networks is becoming important for inferring the function of uncharacterized proteins. A recent study using this approach has identified new proteins and interactions that might be involved in the pathogenesis of the neurodegenerative disorder Huntington's disease, including a GTPase-activating protein that co-localizes with protein aggregates in Huntington's disease patients.

  17. Bilingual Lexical Interactions in an Unsupervised Neural Network Model

    Science.gov (United States)

    Zhao, Xiaowei; Li, Ping

    2010-01-01

    In this paper we present an unsupervised neural network model of bilingual lexical development and interaction. We focus on how the representational structures of the bilingual lexicons can emerge, develop, and interact with each other as a function of the learning history. The results show that: (1) distinct representations for the two lexicons…

  18. A Framework for Networked Interactive Surfaces

    OpenAIRE

    CUYPERS, Tom; Frederix, Karel; RAYMAEKERS, Chris; Bekaert, Philippe

    2009-01-01

    The development of interactive surfaces has led to a number of applications as it allows for natural interaction and collaboration. The use of co-located collaboration on this kind of surfaces provides new possibilities. It is our belief, however, that an even higher degree of collaboration can be achieved by overcoming the boundaries of a single device or setup. Therefore, we extended our previously built multi-touch framework to realize collaborative multi-device setups. In order to assess ...

  19. Major component analysis of dynamic networks of physiologic organ interactions

    Science.gov (United States)

    Liu, Kang K. L.; Bartsch, Ronny P.; Ma, Qianli D. Y.; Ivanov, Plamen Ch

    2015-09-01

    The human organism is a complex network of interconnected organ systems, where the behavior of one system affects the dynamics of other systems. Identifying and quantifying dynamical networks of diverse physiologic systems under varied conditions is a challenge due to the complexity in the output dynamics of the individual systems and the transient and nonlinear characteristics of their coupling. We introduce a novel computational method based on the concept of time delay stability and major component analysis to investigate how organ systems interact as a network to coordinate their functions. We analyze a large database of continuously recorded multi-channel physiologic signals from healthy young subjects during night-time sleep. We identify a network of dynamic interactions between key physiologic systems in the human organism. Further, we find that each physiologic state is characterized by a distinct network structure with different relative contribution from individual organ systems to the global network dynamics. Specifically, we observe a gradual decrease in the strength of coupling of heart and respiration to the rest of the network with transition from wake to deep sleep, and in contrast, an increased relative contribution to network dynamics from chin and leg muscle tone and eye movement, demonstrating a robust association between network topology and physiologic function.

  20. Interaction Network, State Space and Control in Social Dynamics

    CERN Document Server

    Aydogdu, Aylin; McQuade, Sean; Piccoli, Benedetto; Duteil, Nastassia Pouradier; Rossi, Francesco; Trélat, Emmanuel

    2016-01-01

    In the present chapter we study the emergence of global patterns in large groups in first and second-order multi-agent systems, focusing on two ingredients that influence the dynamics: the interaction network and the state space. The state space determines the types of equilibrium that can be reached by the system. Meanwhile, convergence to specific equilibria depends on the connectivity of the interaction network and on the interaction potential. When the system does not satisfy the necessary conditions for convergence to the desired equilibrium, control can be exerted, both on finite-dimensional systems and on their mean-field limit.

  1. Geometric de-noising of protein-protein interaction networks.

    Directory of Open Access Journals (Sweden)

    Oleksii Kuchaiev

    2009-08-01

    Full Text Available Understanding complex networks of protein-protein interactions (PPIs is one of the foremost challenges of the post-genomic era. Due to the recent advances in experimental bio-technology, including yeast-2-hybrid (Y2H, tandem affinity purification (TAP and other high-throughput methods for protein-protein interaction (PPI detection, huge amounts of PPI network data are becoming available. Of major concern, however, are the levels of noise and incompleteness. For example, for Y2H screens, it is thought that the false positive rate could be as high as 64%, and the false negative rate may range from 43% to 71%. TAP experiments are believed to have comparable levels of noise.We present a novel technique to assess the confidence levels of interactions in PPI networks obtained from experimental studies. We use it for predicting new interactions and thus for guiding future biological experiments. This technique is the first to utilize currently the best fitting network model for PPI networks, geometric graphs. Our approach achieves specificity of 85% and sensitivity of 90%. We use it to assign confidence scores to physical protein-protein interactions in the human PPI network downloaded from BioGRID. Using our approach, we predict 251 interactions in the human PPI network, a statistically significant fraction of which correspond to protein pairs sharing common GO terms. Moreover, we validate a statistically significant portion of our predicted interactions in the HPRD database and the newer release of BioGRID. The data and Matlab code implementing the methods are freely available from the web site: http://www.kuchaev.com/Denoising.

  2. Environment, Network Interactions and Innovation Performance

    OpenAIRE

    Zhao, Yan; Zhou, Wen; Hüsig, Stefan; VANHAVERBEKE, Wim

    2010-01-01

    Purpose – The purpose of this paper is to categorize industrial clusters, and then compare three industrial clusters of three countries from the perspectives of hard environment, soft environment, factors from supply and demand sides, and the network mechanism. Design/methodology/approach – Data were collected through interview with cluster coordinators. Qualitative case studies were conducted. Findings – The center of excellence behaves well in nearly all aspects, while the spatial...

  3. Modeling human dynamics of face-to-face interaction networks

    CERN Document Server

    Starnini, Michele; Pastor-Satorras, Romualdo

    2013-01-01

    Face-to-face interaction networks describe social interactions in human gatherings, and are the substrate for processes such as epidemic spreading and gossip propagation. The bursty nature of human behavior characterizes many aspects of empirical data, such as the distribution of conversation lengths, of conversations per person, or of inter-conversation times. Despite several recent attempts, a general theoretical understanding of the global picture emerging from data is still lacking. Here we present a simple model that reproduces quantitatively most of the relevant features of empirical face-to-face interaction networks. The model describes agents which perform a random walk in a two dimensional space and are characterized by an attractiveness whose effect is to slow down the motion of people around them. The proposed framework sheds light on the dynamics of human interactions and can improve the modeling of dynamical processes taking place on the ensuing dynamical social networks.

  4. How do oncoprotein mutations rewire protein-protein interaction networks?

    Science.gov (United States)

    Bowler, Emily H; Wang, Zhenghe; Ewing, Rob M

    2015-01-01

    The acquisition of mutations that activate oncogenes or inactivate tumor suppressors is a primary feature of most cancers. Mutations that directly alter protein sequence and structure drive the development of tumors through aberrant expression and modification of proteins, in many cases directly impacting components of signal transduction pathways and cellular architecture. Cancer-associated mutations may have direct or indirect effects on proteins and their interactions and while the effects of mutations on signaling pathways have been widely studied, how mutations alter underlying protein-protein interaction networks is much less well understood. Systematic mapping of oncoprotein protein interactions using proteomics techniques as well as computational network analyses is revealing how oncoprotein mutations perturb protein-protein interaction networks and drive the cancer phenotype. PMID:26325016

  5. A Study of Feature Interactions in Intelligent Networks

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    @@ Plain Old Telephone Services (POTS) are used to establish the voice connection between two telephone users; and supplementary services such as call waiting, call forwarding, and call completion to busy subscribers, provide additional functions to POTS. In order to facilitate the communication between users, telecommunication networks should provide new services to end users in a quick way. However, the introduction of new telecommunication services into the existing network may interfere with the existing services, thus causing feature interactions. In many cases, feature interactions bring the unwanted or undesired system behavior to end users, decreasing the service quality. Although new technology like Intelligent Networks (IN) enables the quick introduction of new telecommunication services, but owing to the feature interaction, and the vast effort has to be put into checking the compatibility between telecommunication services. Feature interactions has become the bottle-neck problem to the development of new telecommunication services.

  6. Quantum entanglement in the system of two two-level atoms interacting with a single-mode vacuum field

    Institute of Scientific and Technical Information of China (English)

    Zeng Ke; Fang Mao-Fa

    2005-01-01

    The entanglement properties of the system of two two-level atoms interacting with a single-mode vacuum field are explored. The quantum entanglement between two two-level atoms and a single-mode vacuum field is investigated by using the quantum reduced entropy; the quantum entanglement between two two-level atoms, and that between a single two-level atom and a single-mode vacuum field are studied in terms of the quantum relative entropy. The influences of the atomic dipole-dipole interaction on the quantum entanglement of the system are also discussed. Our results show that three entangled states of two atoms-field, atom-atom, and atom-field can be prepared via two two-level atoms interacting with a single-mode vacuum field.

  7. How people interact in evolving online affiliation networks

    CERN Document Server

    Gallos, Lazaros K; Liljeros, Fredrik; Havlin, Shlomo; Makse, Hernan A

    2011-01-01

    The study of human interactions is of central importance for understanding the behavior of individuals, groups and societies. Here, we observe the formation and evolution of networks by monitoring the addition of all new links and we analyze quantitatively the tendencies used to create ties in these evolving online affiliation networks. We first show that an accurate estimation of these probabilistic tendencies can only be achieved by following the time evolution of the network. For example, actions that are attributed to the usual friend of a friend mechanism through a static snapshot of the network are overestimated by a factor of two. A detailed analysis of the dynamic network evolution shows that half of those triangles were generated through other mechanisms, in spite of the characteristic static pattern. We start by characterizing every single link when the tie was established in the network. This allows us to describe the probabilistic tendencies of tie formation and extract sociological conclusions as...

  8. [Atomic force field FFsol for calculation of molecular interactions of in water environment].

    Science.gov (United States)

    Pereiaslavets, L B; Finkel'shtein, A V

    2010-01-01

    Detailed calculations of protein interactions with explicitly considered water takes enormous computer time. The calculation becomes faster if water is considered implicitly (as a continuous media rather than as molecules); however, these calculations are much less precise, unless one uses an additional (and also volumes) computation of the solvent-accessible areas of protein atoms. The aim of our study was to obtain parameters for non-bonded atom-atom interactions for the case when water surrounding is considered implicitly and the solvent-accessible areas are not computed. Since the "in-vacuum" interactions of atoms are obtained from experimental structures of crystals and enthalpies of their sublimation, the "in-water" interactions of atoms must be corrected using solvation free energies of molecules, which can be obtained from the Henry constants. Taken 58 structures of molecular crystals and thermodynamic data on their sublimation and solubility, we obtained parameters for "in-water" attraction and repulsion of atoms typical of protein structures (H, C, N, O, S) in various covalently-bonded states, as well as parameters for electrostatic interactions. All necessary for calculations parameters of covalent interactions have been taken from the ENCAD force field, and partial charges of all atoms of separate molecules of a crystal have been obtained from quantum-mechanical calculations. The sought parameters of the "in-water" van der Waals and electrostatic interactions were optimized so as to achieve the best description of equilibrium crystal structures and their sublimation and solvation at the room temperature. With the optimized parameters, the average error in calculation of the effective cohesion energy of molecules in crystals was less than 10% both in the "in-vacuum" and "in-water" cases. PMID:20586195

  9. Spin-1/2 Collective Excitations in BEC of Interacting Spin-1 Atoms

    OpenAIRE

    Zhou, Fei

    2001-01-01

    We construct spin-1/2 collective excitations in BEC of interacting spin-1 atoms. These excitations exist in states with a maximal global degeneracy. The stability and energy of these objects are determined by interactions with spin fluctuations and are studied based on a duality relation between hyper-monopoles and magnetic monopoles in physical space.

  10. An atomic force microscopy study of the interactions between indolicidin and supported planar bilayers

    DEFF Research Database (Denmark)

    Askou, Hans Jakob; Jakobsen, Rasmus Neergaard; Fojan, Peter

    2008-01-01

    Indolicidin, a tryptophane-rich antimicrobial peptide , was used to investigate the interactions with a zwitterionic phosphatidylcholine as a model membrane system. In situ atomic force microscopy in liquid medium and phosphatidylcholine supported planar bilayers enabled the study of the interact...

  11. Effect of Phase Shifted Frequency Modulation on Two Level Atom-Field Interaction

    Institute of Scientific and Technical Information of China (English)

    K.V. Priyesh; Ramesh Babu Thayyullathil

    2012-01-01

    We have studied the effect of phase shifted frequency modulation on two level atom with field interaction using Jaynes-Cummings model. Here the frequency of the interacting field is sinusoidally varying with time with a constant phase. Due to the presence of phase in the frequency modulation, the variation of population inversion with time is different from the standard case. There are no exact collapses and revivals in the variation of population inversion but it oscillates sinusoidally with time. In coherent field atom interaction the population inversion behaves as in the case of Fock state atom interaction, when frequency modulation with a non zero phase is applied. The study done with squeezed field has shown the same behavior of the population inversion.

  12. Long-range interactions between the alkali-metal atoms and alkaline earth ions

    CERN Document Server

    Kaur, Jasmeet; Arora, Bindiya; Sahoo, B K

    2014-01-01

    Accurate knowledge of interaction potentials among the alkali atoms and alkaline earth ions is very useful in the studies of cold atom physics. Here we carry out theoretical studies of the long-range interactions among the Li, Na, K, and Rb alkali atoms with the Ca$^+$, Ba$^+$, Sr$^+$, and Ra$^+$ alkaline earth ions systematically which are largely motivated by their importance in a number of applications. These interactions are expressed as a power series in the inverse of the internuclear separation $R$. Both the dispersion and induction components of these interactions are determined accurately from the algebraic coefficients corresponding to each power combination in the series. Ultimately, these coefficients are expressed in terms of the electric multipole polarizabilities of the above mentioned systems which are calculated using the matrix elements obtained from a relativistic coupled-cluster method and core contributions to these quantities from the random phase approximation. We also compare our estim...

  13. Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction

    Science.gov (United States)

    Yeger-Lotem, Esti; Sattath, Shmuel; Kashtan, Nadav; Itzkovitz, Shalev; Milo, Ron; Pinter, Ron Y.; Alon, Uri; Margalit, Hanah

    2004-04-01

    Genes and proteins generate molecular circuitry that enables the cell to process information and respond to stimuli. A major challenge is to identify characteristic patterns in this network of interactions that may shed light on basic cellular mechanisms. Previous studies have analyzed aspects of this network, concentrating on either transcription-regulation or protein-protein interactions. Here we search for composite network motifs: characteristic network patterns consisting of both transcription-regulation and protein-protein interactions that recur significantly more often than in random networks. To this end we developed algorithms for detecting motifs in networks with two or more types of interactions and applied them to an integrated data set of protein-protein interactions and transcription regulation in Saccharomyces cerevisiae. We found a two-protein mixed-feedback loop motif, five types of three-protein motifs exhibiting coregulation and complex formation, and many motifs involving four proteins. Virtually all four-protein motifs consisted of combinations of smaller motifs. This study presents a basic framework for detecting the building blocks of networks with multiple types of interactions.

  14. van der Waals interaction between an atom and a spherical plasma shell

    International Nuclear Information System (INIS)

    The van der Waals interaction energy of an atom with an infinitely thin sphere with finite conductivity is investigated in the framework of the hydrodynamic approach. Thin sphere models the fullerene. We put the sphere into a spherical cavity inside the infinite dielectric media then calculate the energy of vacuum fluctuations in the context of the ζ-function approach. The interaction energy for a single atom is obtained from this expression in the limit of the rare media. The Casimir-Polder expression for an atom and plate is recovered in the limit of the infinite radius of the sphere. Assuming a finite radius of the sphere, the interaction energy of an atom falls down to a third power of distance between the atom and sphere for short distances and to a seventh power for large distances from the sphere. Numerically the interaction energy is 3.8 eV for the hydrogen atom placed on the surface of the sphere with parameters of fullerene C60. We also show that the polarizability of fullerene is merely a cube of its radius.

  15. Protein interaction networks--more than mere modules.

    Directory of Open Access Journals (Sweden)

    Stefan Pinkert

    2010-01-01

    Full Text Available It is widely believed that the modular organization of cellular function is reflected in a modular structure of molecular networks. A common view is that a "module" in a network is a cohesively linked group of nodes, densely connected internally and sparsely interacting with the rest of the network. Many algorithms try to identify functional modules in protein-interaction networks (PIN by searching for such cohesive groups of proteins. Here, we present an alternative approach independent of any prior definition of what actually constitutes a "module". In a self-consistent manner, proteins are grouped into "functional roles" if they interact in similar ways with other proteins according to their functional roles. Such grouping may well result in cohesive modules again, but only if the network structure actually supports this. We applied our method to the PIN from the Human Protein Reference Database (HPRD and found that a representation of the network in terms of cohesive modules, at least on a global scale, does not optimally represent the network's structure because it focuses on finding independent groups of proteins. In contrast, a decomposition into functional roles is able to depict the structure much better as it also takes into account the interdependencies between roles and even allows groupings based on the absence of interactions between proteins in the same functional role. This, for example, is the case for transmembrane proteins, which could never be recognized as a cohesive group of nodes in a PIN. When mapping experimental methods onto the groups, we identified profound differences in the coverage suggesting that our method is able to capture experimental bias in the data, too. For example yeast-two-hybrid data were highly overrepresented in one particular group. Thus, there is more structure in protein-interaction networks than cohesive modules alone and we believe this finding can significantly improve automated function

  16. MDM2-MDM4 molecular interaction investigated by atomic force spectroscopy and surface plasmon resonance.

    Science.gov (United States)

    Moscetti, Ilaria; Teveroni, Emanuela; Moretti, Fabiola; Bizzarri, Anna Rita; Cannistraro, Salvatore

    2016-01-01

    Murine double minute 2 (MDM2) and 4 (MDM4) are known as the main negative regulators of p53, a tumor suppressor. They are able to form heterodimers that are much more effective in the downregulation of p53. Therefore, the MDM2-MDM4 complex could be a target for promising therapeutic restoration of p53 function. To this aim, a deeper understanding of the molecular mechanisms underlining the heterodimerization is needed. The kinetic and thermodynamic characterization of the MDM2-MDM4 complex was performed with two complementary approaches: atomic force spectroscopy and surface plasmon resonance. Both techniques revealed an equilibrium dissociation constant (KD ) in the micromolar range for the MDM2-MDM4 heterodimer, similar to related complexes involved in the p53 network. Furthermore, the MDM2-MDM4 complex is characterized by a relatively high free energy, through a single energy barrier, and by a lifetime in the order of tens of seconds. New insights into the MDM2-MDM4 interaction could be highly important for developing innovative anticancer drugs focused on p53 reactivation. PMID:27621617

  17. Improved limits on interactions of low-mass spin-0 dark matter from atomic clock spectroscopy

    Science.gov (United States)

    Stadnik, Y. V.; Flambaum, V. V.

    2016-08-01

    Low-mass (sub-eV) spin-0 dark matter particles, which form a coherently oscillating classical field ϕ =ϕ0cos(mϕt ) , can induce oscillating variations in the fundamental constants through their interactions with the standard model sector. We calculate the effects of such possible interactions, which may include the linear interaction of ϕ with the Higgs boson, on atomic and molecular transitions. Using recent atomic clock spectroscopy measurements, we derive limits on the linear interaction of ϕ with the Higgs boson, as well as its quadratic interactions with the photon and light quarks. For the linear interaction of ϕ with the Higgs boson, our derived limits improve on existing constraints by up to 2-3 orders of magnitude.

  18. Emergent criticality in complex turing B-type atomic switch networks.

    Science.gov (United States)

    Stieg, Adam Z; Avizienis, Audrius V; Sillin, Henry O; Martin-Olmos, Cristina; Aono, Masakazu; Gimzewski, James K

    2012-01-10

    Recent advances in the neuromorphic operation of atomic switches as individual synapse-like devices demonstrate the ability to process information with both short-term and long-term memorization in a single two terminal junction. Here it is shown that atomic switches can be self-assembled within a highly interconnected network of silver nanowires similar in structure to Turing’s “B-Type unorganized machine”, originally proposed as a randomly connected network of NAND logic gates. In these experimental embodiments,complex networks of coupled atomic switches exhibit emergent criticality similar in nature to previously reported electrical activity of biological brains and neuron assemblies. Rapid fluctuations in electrical conductance display metastability and power law scaling of temporal correlation lengths that are attributed to dynamic reorganization of the interconnected electro-ionic network resulting from induced non-equilibrium thermodynamic instabilities. These collective properties indicate a potential utility for realtime,multi-input processing of distributed sensory data through reservoir computation. We propose these highly coupled, nonlinear electronic networks as an implementable hardware-based platform toward the creation of physically intelligent machines. PMID:22329003

  19. Experimental studies of ions and atoms interaction with insulating surface

    International Nuclear Information System (INIS)

    Grazing collisions (+, Ne+, Ne0, Na+ on LiF (001) single crystal, an ionic insulator, are investigated by a time of flight technique. The incident beam is chopped and the scattered particles are collected on a position sensitive detector providing differential cross section while the time of flight gives the energy loss. Deflection plates allow the charge state analysis. Secondary electrons are detected in coincidence allowing direct measurements of electron emission yield, angular and energetic distribution through time of flight measurements. The target electronic structure characterized by a large band gap, governs the collisional processes: charge exchange, electronic excitations and electron emission. In particular, these studies show that the population of local target excitations surface excitons is the major contribution to the kinetic energy transfer (stopping power). Auger neutralization of Ne+ and He+ ions reveals the population of quasi-molecular excitons, an exciton bound on two holes. Referenced in the literature as trion. A direct energy balance determines the binding energy associated with these excited states of the surface. Besides these electronic energy loss processes, two nuclear energy loss mechanisms are characterized. These processes imply momentum transfer to individual target atoms during close binary collisions or, if the projectile is charged, to collective mode of optical phonons induced by the projectile coulomb field. The effect of the temperature on the scattering profile, the contribution of topological surface defects to the energy loss profile and to skipping motion on the surface are analyzed in view of classical trajectory simulations. (author)

  20. Long-range interactions between excited helium and alkali-metal atoms

    KAUST Repository

    Zhang, J.-Y.

    2012-12-03

    The dispersion coefficients for the long-range interaction of the first four excited states of He, i.e., He(2 1,3S) and He(2 1,3P), with the low-lying states of the alkali-metal atoms Li, Na, K, and Rb are calculated by summing over the reduced matrix elements of the multipole transition operators. For the interaction between He and Li the uncertainty of the calculations is 0.1–0.5%. For interactions with other alkali-metal atoms the uncertainty is 1–3% in the coefficient C5, 1–5% in the coefficient C6, and 1–10% in the coefficients C8 and C10. The dispersion coefficients Cn for the interaction of He(2 1,3S) and He(2 1,3P) with the ground-state alkali-metal atoms and for the interaction of He(2 1,3S) with the alkali-metal atoms in their first 2P states are presented in this Brief Report. The coefficients for other pairs of atomic states are listed in the Supplemental Material.

  1. Strategy selection in evolutionary game dynamics on group interaction networks.

    Science.gov (United States)

    Tan, Shaolin; Feng, Shasha; Wang, Pei; Chen, Yao

    2014-11-01

    Evolutionary game theory provides an appropriate tool for investigating the competition and diffusion of behavioral traits in biological or social populations. A core challenge in evolutionary game theory is the strategy selection problem: Given two strategies, which one is favored by the population? Recent studies suggest that the answer depends not only on the payoff functions of strategies but also on the interaction structure of the population. Group interactions are one of the fundamental interactive modes within populations. This work aims to investigate the strategy selection problem in evolutionary game dynamics on group interaction networks. In detail, the strategy selection conditions are obtained for some typical networks with group interactions. Furthermore, the obtained conditions are applied to investigate selection between cooperation and defection in populations. The conditions for evolution of cooperation are derived for both the public goods game and volunteer's dilemma game. Numerical experiments validate the above analytical results.

  2. Nonlinear Dynamics of Cantilever Tip-Sample Surface Interactions in Atomic Force Microscopy

    OpenAIRE

    Cantrell, John H.; Cantrell, Sean A.

    2010-01-01

    The various dynamical implementations of the atomic force microscope have become important nanoscale characterization tools for the development of novel materials and devices. One of the most significant factors affecting all dynamical AFM modalities is the cantilever tip-sample surface interaction force. We have developed a detailed mathematical model of this interaction that includes a quantitative consideration of the nonlinearity of the interaction force as a function of the cantilever ti...

  3. Human cancer protein-protein interaction network: a structural perspective.

    Directory of Open Access Journals (Sweden)

    Gozde Kar

    2009-12-01

    Full Text Available Protein-protein interaction networks provide a global picture of cellular function and biological processes. Some proteins act as hub proteins, highly connected to others, whereas some others have few interactions. The dysfunction of some interactions causes many diseases, including cancer. Proteins interact through their interfaces. Therefore, studying the interface properties of cancer-related proteins will help explain their role in the interaction networks. Similar or overlapping binding sites should be used repeatedly in single interface hub proteins, making them promiscuous. Alternatively, multi-interface hub proteins make use of several distinct binding sites to bind to different partners. We propose a methodology to integrate protein interfaces into cancer interaction networks (ciSPIN, cancer structural protein interface network. The interactions in the human protein interaction network are replaced by interfaces, coming from either known or predicted complexes. We provide a detailed analysis of cancer related human protein-protein interfaces and the topological properties of the cancer network. The results reveal that cancer-related proteins have smaller, more planar, more charged and less hydrophobic binding sites than non-cancer proteins, which may indicate low affinity and high specificity of the cancer-related interactions. We also classified the genes in ciSPIN according to phenotypes. Within phenotypes, for breast cancer, colorectal cancer and leukemia, interface properties were found to be discriminating from non-cancer interfaces with an accuracy of 71%, 67%, 61%, respectively. In addition, cancer-related proteins tend to interact with their partners through distinct interfaces, corresponding mostly to multi-interface hubs, which comprise 56% of cancer-related proteins, and constituting the nodes with higher essentiality in the network (76%. We illustrate the interface related affinity properties of two cancer-related hub

  4. Ecology 2.0: Coexistence and Domination of Interacting Networks

    CERN Document Server

    Kleineberg, Kaj-Kolja

    2014-01-01

    The overwhelming success of the web 2.0, with online social networks as key actors, has induced a paradigm shift in the nature of human interactions. The user-driven character of these services for the first time has allowed researchers to quantify large-scale social patterns. However, the mechanisms that determine the fate of networks at a system level are still poorly understood. For instance, the simultaneous existence of numerous digital services naturally raises the question under which conditions these services can coexist. In analogy to population dynamics, the digital world is forming a complex ecosystem of interacting networks whose fitnesses depend on their ability to attract and maintain users' attention, which constitutes a limited resource. In this paper, we introduce an ecological theory of the digital world which exhibits a stable coexistence of several networks as well as the domination of a single one, in contrast to the principle of competitive exclusion. Interestingly, our model also predic...

  5. Layered vanadyl (IV) nitroprusside: Magnetic interaction through a network of hydrogen bonds

    Science.gov (United States)

    Gil, D. M.; Osiry, H.; Pomiro, F.; Varetti, E. L.; Carbonio, R. E.; Alejandro, R. R.; Ben Altabef, A.; Reguera, E.

    2016-07-01

    The hydrogen bond and π-π stacking are two non-covalent interactions able to support cooperative magnetic ordering between paramagnetic centers. This contribution reports the crystal structure and related magnetic properties for VO[Fe(CN)5NO]·2H2O, which has a layered structure. This solid crystallizes with an orthorhombic unit cell, in the Pna21 space group, with cell parameters a=14.1804(2), b=10.4935(1), c=7.1722(8) Å and four molecules per unit cell (Z=4). Its crystal structure was solved and refined from powder X-ray diffraction data. Neighboring layers remain linked through a network of hydrogen bonds involving a water molecule coordinated to the axial position for the V atom and the unbridged axial NO and CN ligands. An uncoordinated water molecule is found forming a triple bridge between these last two ligands and the coordinated water molecule. The magnetic measurements, recorded down to 2 K, shows a ferromagnetic interaction between V atoms located at neighboring layers, with a Curie-Weiss constant of 3.14 K. Such ferromagnetic behavior was interpreted as resulting from a superexchange interaction through the network of strong OH····OH2O, OH····NCN, and OH····ONO hydrogen bonds that connects neighboring layers. The interaction within the layer must be of antiferromagnetic nature and it was detected close to 2 K.

  6. Interactions between C and Cu atoms in single-layer graphene: direct observation and modelling.

    Science.gov (United States)

    Kano, Emi; Hashimoto, Ayako; Kaneko, Tomoaki; Tajima, Nobuo; Ohno, Takahisa; Takeguchi, Masaki

    2016-01-01

    Metal doping into the graphene lattice has been studied recently to develop novel nanoelectronic devices and to gain an understanding of the catalytic activities of metals in nanocarbon structures. Here we report the direct observation of interactions between Cu atoms and single-layer graphene by transmission electron microscopy. We document stable configurations of Cu atoms in the graphene sheet and unique transformations of graphene promoted by Cu atoms. First-principles calculations based on density functional theory reveal a reduction of energy barrier that caused rotation of C-C bonds near Cu atoms. We discuss two driving forces, electron irradiation and in situ heating, and conclude that the observed transformations were mainly promoted by electron irradiation. Our results suggest that individual Cu atoms can promote reconstruction of single-layer graphene. PMID:26645468

  7. Dispersion coefficients for the interaction of inert gas atoms with alkali and alkaline earth ions and alkali atoms with their singly ionized ions

    CERN Document Server

    Singh, Sukhjit; Sahoo, B K; Arora, Bindiya

    2016-01-01

    We report the dispersion coefficients for the interacting inert gas atoms with the alkali ions, alkaline earth ions and alkali atoms with their singly charged ions. We use our relativistic coupled-cluster method to determine dynamic dipole and quadrupole polarizabilities of the alkali atoms and singly ionized alkaline earth atoms, whereas a relativistic random phase approximation approach has been adopted to evaluate these quantities for the closed-shell configured inert gas atoms and the singly and doubly ionized alkali and alkaline earth atoms, respectively. Accuracies of these results are adjudged from the comparison of their static polarizability values with their respective experimental results. These polarizabilities are further compared with the other theoretical results. Reason for the improvement in the accuracies of our estimated dispersion coefficients than the data listed in [At. Data and Nucl. Data Tables 101, 58 (2015)] are discussed. Results for some of the atom-ion interacting systems were not...

  8. Interacting epidemics and coinfection on contact networks

    CERN Document Server

    Newman, M E J

    2013-01-01

    The spread of certain diseases can be promoted, in some cases substantially, by prior infection with another disease. One example is that of HIV, whose immunosuppressant effects significantly increase the chances of infection with other pathogens. Such coinfection processes, when combined with nontrivial structure in the contact networks over which diseases spread, can lead to complex patterns of epidemiological behavior. Here we consider a mathematical model of two diseases spreading through a single population, where infection with one disease is dependent on prior infection with the other. We solve exactly for the sizes of the outbreaks of both diseases in the limit of large population size, along with the complete phase diagram of the system. Among other things, we use our model to demonstrate how diseases can be controlled not only by reducing the rate of their spread, but also by reducing the spread of other infections upon which they depend.

  9. Interacting epidemics and coinfection on contact networks.

    Directory of Open Access Journals (Sweden)

    M E J Newman

    Full Text Available The spread of certain diseases can be promoted, in some cases substantially, by prior infection with another disease. One example is that of HIV, whose immunosuppressant effects significantly increase the chances of infection with other pathogens. Such coinfection processes, when combined with nontrivial structure in the contact networks over which diseases spread, can lead to complex patterns of epidemiological behavior. Here we consider a mathematical model of two diseases spreading through a single population, where infection with one disease is dependent on prior infection with the other. We solve exactly for the sizes of the outbreaks of both diseases in the limit of large population size, along with the complete phase diagram of the system. Among other things, we use our model to demonstrate how diseases can be controlled not only by reducing the rate of their spread, but also by reducing the spread of other infections upon which they depend.

  10. Classical-field description of the quantum effects in the light-atom interaction

    CERN Document Server

    Rashkovskiy, Sergey A

    2016-01-01

    In this paper I show that light-atom interaction can be described using purely classical field theory without any quantization. In particular, atom excitation by light that accounts for damping due to spontaneous emission is fully described in the framework of classical field theory. I show that three well-known laws of the photoelectric effect can also be derived and that all of its basic properties can be described within classical field theory.

  11. Synergetic control of social networking services actors’ interactions

    OpenAIRE

    Hryshchyk, R.; Molodetska, K.; Грищук, Р. В.; Молодецька, К.В.; Молодецкая, К. В.

    2016-01-01

    A method for process control of interaction of actors in social networking services. Using the proposed concept will ensure the emergence of self-organization processes in virtual communities and the transition to a predetermined state of information security. There are some models introduced. The evolutionary process of social networking is a transition from one state to another through chaos that features high system sensitivity to external disturbances. Thus, a system may be in a certai...

  12. Kinetic theory of particle interactions mediated by dynamical networks

    OpenAIRE

    Barré, Julien; Degond, Pierre; Zatorska, Ewelina

    2016-01-01

    We provide a detailed multiscale analysis of a system of particles interacting through a dynamical network of links. Starting from a microscopic model, via the mean field limit, we formally derive coupled kinetic equations for the particle and link densities, following the approach of [Degond et al., M3AS, 2016]. Assuming that the process of remodelling the network is very fast, we simplify the description to a macroscopic model taking the form of single aggregation-diffusion equation for the...

  13. Characterizing interactions in online social networks during exceptional events

    CERN Document Server

    Omodei, Elisa; Arenas, Alex

    2015-01-01

    Nowadays, millions of people interact on a daily basis on online social media like Facebook and Twitter, where they share and discuss information about a wide variety of topics. In this paper, we focus on a specific online social network, Twitter, and we analyze multiple datasets each one consisting of individuals' online activity before, during and after an exceptional event in terms of volume of the communications registered. We consider important events that occurred in different arenas that range from policy to culture or science. For each dataset, the users' online activities are modeled by a multilayer network in which each layer conveys a different kind of interaction, specifically: retweeting, mentioning and replying. This representation allows us to unveil that these distinct types of interaction produce networks with different statistical properties, in particular concerning the degree distribution and the clustering structure. These results suggests that models of online activity cannot discard the...

  14. Interactions between C and Cu atoms in single-layer graphene: direct observation and modelling

    Science.gov (United States)

    Kano, Emi; Hashimoto, Ayako; Kaneko, Tomoaki; Tajima, Nobuo; Ohno, Takahisa; Takeguchi, Masaki

    2015-12-01

    Metal doping into the graphene lattice has been studied recently to develop novel nanoelectronic devices and to gain an understanding of the catalytic activities of metals in nanocarbon structures. Here we report the direct observation of interactions between Cu atoms and single-layer graphene by transmission electron microscopy. We document stable configurations of Cu atoms in the graphene sheet and unique transformations of graphene promoted by Cu atoms. First-principles calculations based on density functional theory reveal a reduction of energy barrier that caused rotation of C-C bonds near Cu atoms. We discuss two driving forces, electron irradiation and in situ heating, and conclude that the observed transformations were mainly promoted by electron irradiation. Our results suggest that individual Cu atoms can promote reconstruction of single-layer graphene.Metal doping into the graphene lattice has been studied recently to develop novel nanoelectronic devices and to gain an understanding of the catalytic activities of metals in nanocarbon structures. Here we report the direct observation of interactions between Cu atoms and single-layer graphene by transmission electron microscopy. We document stable configurations of Cu atoms in the graphene sheet and unique transformations of graphene promoted by Cu atoms. First-principles calculations based on density functional theory reveal a reduction of energy barrier that caused rotation of C-C bonds near Cu atoms. We discuss two driving forces, electron irradiation and in situ heating, and conclude that the observed transformations were mainly promoted by electron irradiation. Our results suggest that individual Cu atoms can promote reconstruction of single-layer graphene. Electronic supplementary information (ESI) available: Three TEM movies, additional TEM data corresponding to movies, calculated models, and lifetime results. See DOI: 10.1039/c5nr05913e

  15. Tuning Casimir-Polder interactions in atom-metamaterial hybrid devices

    CERN Document Server

    Chan, Eng Aik; Adamo, Giorgio; Laliotis, Athanasios; Ducloy, Martial; Wilkowski, David

    2016-01-01

    We report on the coupling of a surface plasmonic mode with a thermal vapor of cesium atoms. The plasmonic resonance is created using a nano-structured metallic surface. By changing the geometrical properties of the metamaterial, we tune the plasmonic resonance wavelength with respect to the D2 line of cesium. When the two resonances are close, we observe a strong modification of the Casimir-Polder interaction accompanied by a change of the atomic lifetime. A proper tuning leads to an almost suppression of the frequency shift of the cesium transition. This result paves the way for precision atomic spectroscopy in the vicinity of a material surface.

  16. Periodic trends governing the interactions between impurity atoms [H-Ar] and (alpha)-U

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, Christopher David [Los Alamos National Laboratory

    2008-01-01

    The binding energies, geometries, charges and electronic structures of a series of impurity atoms [H-Ar] interacting with the {alpha}-U lattice in various configurations were assessed by means of density functional theory calculations. Periodic trends governing the binding energy were highlighted and related to the electronic properties of the impurity atoms, with some consideration given to the band-structure of {alpha}-U. The strongest bound impurity atoms include [C, N, O] and [Si, P, S]. The general trends in the binding energy can be reproduced by a simple parameterisation in terms of the electronegativity (charge-transfer) and covalent radius (elasticity theory) of the impurity atom. The strongest bound atoms deviate from this model, due to their ability to bind with an optimum mixture of covalency and ionicity. This last point is evidenced by the partial overlap of the impurity atom p-band with the hybrid d-/f-band of {alpha}-U. It is expected that the trends and general behaviour reported in this work can be extended to the interactions of impurity atoms with other metallic systems.

  17. The evolution of generalized reciprocity on social interaction networks.

    Science.gov (United States)

    van Doorn, Gerrit Sander; Taborsky, Michael

    2012-03-01

    Generalized reciprocity (help anyone, if helped by someone) is a minimal strategy capable of supporting cooperation between unrelated individuals. Its simplicity makes it an attractive model to explain the evolution of reciprocal altruism in animals that lack the information or cognitive skills needed for other types of reciprocity. Yet, generalized reciprocity is anonymous and thus defenseless against exploitation by defectors. Recognizing that animals hardly ever interact randomly, we investigate whether social network structure can mitigate this vulnerability. Our results show that heterogeneous interaction patterns strongly support the evolution of generalized reciprocity. The future probability of being rewarded for an altruistic act is inversely proportional to the average connectivity of the social network when cooperators are rare. Accordingly, sparse networks are conducive to the invasion of reciprocal altruism. Moreover, the evolutionary stability of cooperation is enhanced by a modular network structure. Communities of reciprocal altruists are protected against exploitation, because modularity increases the mean access time, that is, the average number of steps that it takes for a random walk on the network to reach a defector. Sparseness and community structure are characteristic properties of vertebrate social interaction patterns, as illustrated by network data from natural populations ranging from fish to primates.

  18. Strong Interactions of Single Atoms and Photons near a Dielectric Boundary

    CERN Document Server

    Alton, D J; Aoki, Takao; Lee, H; Ostby, E; Vahala, K J; Kimble, H J

    2010-01-01

    Modern research in optical physics has achieved quantum control of strong interactions between a single atom and one photon within the setting of cavity quantum electrodynamics (cQED). However, to move beyond current proof-of-principle experiments involving one or two conventional optical cavities to more complex scalable systems that employ N >> 1 microscopic resonators requires the localization of individual atoms on distance scales < 100 nm from a resonator's surface. In this regime an atom can be strongly coupled to a single intracavity photon while at the same time experiencing significant radiative interactions with the dielectric boundaries of the resonator. Here, we report an initial step into this new regime of cQED by way of real-time detection and high-bandwidth feedback to select and monitor single Cesium atoms localized ~100 nm from the surface of a micro-toroidal optical resonator. We employ strong radiative interactions of atom and cavity field to probe atomic motion through the evanescent f...

  19. Interaction of nanofiber-guided light with a warm atomic vapor

    Science.gov (United States)

    Jones, Daniel E.

    Systems allowing controllable photon-atom interactions are becoming increasingly important for quantum communication applications. One promising platform involves the interaction of the tightly-confined evanescent mode of an optical nanofiber with surrounding atoms. This dissertation will overview our work on the interaction of nanofiber-guided light with a warm rubidium vapor. In comparison to related work with cold atom clouds or trapped atoms, the "warm atom-nanofiber" system is fairly robust but operates in a regime where motional effects of the atoms are significant. We will first discuss a detailed study of saturated absorption in this system, with an emphasis on the role of motional effects in hyperfine pumping rates and various line broadening mechanisms. The power needed to saturate the system is essentially a measure of the system's capability to enable nonlinear optical interactions of the kind that are needed for quantum communication applications, and we observe remarkably ultralow saturation powers of 10's of nW (corresponding to only ˜ 10 photons passing through the nanofiber at a given time). We then utilize this strong nonlinearity to demonstrate 3-level ladder-type electromagnetically induced transparency (EIT) and all-optical modulation with ultralow control-field powers on the order of only a few muW. Finally, we discuss a novel nanofiber-segment nonlinear ring resonator comprised of a large loop of conventional single-mode fiber with a short nanofiber segment surrounded by a warm rubidium vapor. In this device, the cavity enhanced evanescent field of the nanofiber enables even stronger photon-atom interactions.

  20. Motion of Rydberg atoms with strong permanent-electric-dipole interactions

    Science.gov (United States)

    Gonçalves, Luís Felipe; Thaicharoen, Nithiwadee; Raithel, Georg

    2016-08-01

    Using classical trajectories simulations, we investigate the dynamics of a cold sample of Rydberg atoms with high permanent electric dipole moments. The dipolar state can be created using an adiabatic passage through an avoided crossing between an S-like state and a linear Stark state. The simulations yield the pair-correlation functions (PCF) of the atom samples, which allow us to extract the motion of Rydberg-atom pairs in the many-body system. The results reveal the strength and the anisotropic character of the underlying interaction. The simulation is employed to test the suitability of experimental methods designed to derive interaction parameters from PCF. Insight is obtained about the stability of the method against variation of experimentally relevant parameters. Transient correlations due to interaction-induced heating are observed.

  1. Stable BLOCH oscillations of cold atoms with time-dependent interaction.

    Science.gov (United States)

    Gaul, C; Lima, R P A; Díaz, E; Müller, C A; Domínguez-Adame, F

    2009-06-26

    We investigate Bloch oscillations of interacting cold atoms in a mean-field framework. In general, atom-atom interaction causes dephasing and destroys Bloch oscillations. Here we show that Bloch oscillations are persistent if the interaction is modulated harmonically with suitable frequency and phase. For other modulations, Bloch oscillations are rapidly damped. We explain this behavior in terms of collective coordinates whose Hamiltonian dynamics permits one to predict a whole family of stable solutions. In order to describe also the unstable cases, we carry out a stability analysis for Bogoliubov excitations. Using Floquet theory, we are able to predict the unstable modes as well as their growth rate, found to be in excellent agreement with numerical simulations.

  2. Dispersion coefficients for the interaction of Cs atom with different material media

    Science.gov (United States)

    Kaur, Kiranpreet; Kaur, Jasmeet; Sahoo, B. K.; Arora, Bindiya

    2016-10-01

    Motivated by a large number of applications, the dispersion (C3) coefficients for the interaction of a Cs atom with different material media such as Au (metal), Si (semiconductor) and various dielectric surfaces like vitreous SiO2, SiNx, sapphire and YAG are determined using accurate values of the dynamic polarizabilities of the Cs atom obtained employing the relativistic coupled-cluster approach and the dynamic dielectric constants of the walls. Moreover, we also give the retardation function in the graphical representation as functions of separation distances to describe the interaction potentials between the Cs atom with the above considered material media. For the easy access to the interaction potentials at a given distance of separation, we give a simple working functional fitting form for the retardation functions in terms of four fitting parameters that are quoted for the respective medium.

  3. Two simple schemes for implementing Toffoli gate via atom-cavity field interaction in cavity quantum electrodynamics

    Institute of Scientific and Technical Information of China (English)

    Shao Xiao-Qiang; Chen Li; Zhang Shou

    2009-01-01

    This paper proposes two schemes for implementing three-qubit Toffoli gate with an atom (as target qubit) sent through a two-mode cavity (as control qubits). The first scheme is based on the large-detuning atom-cavity field interaction and the second scheme is based on the resonant atom-field interaction. Both the situations with and without cavity decay and atomic spontaneous emission are considered. The advantages and the experimental feasibility of these two schemes are discussed.

  4. Two-body interactions and decay of three-level Rydberg-dressed atoms

    CERN Document Server

    Helmrich, S; Pehoviak, N; Whitlock, S

    2015-01-01

    We theoretically analyze the interactions and decay rates for atoms dressed by multiple laser fields to strongly interacting Rydberg states using a quantum master equation approach. In this framework a comparison of two-level and three-level Rydberg-dressing schemes is presented. We identify a resonant enhancement of the three-level dressed interaction strength which originates from cooperative multiphoton couplings as well as small distance dependent decay rates. In this regime the soft-core shape of the potential is independent of the sign of the bare Rydberg-Rydberg interaction, while its sign can be repulsive or attractive depending on the intermediate state detuning. As a consequence, near-resonant Rydberg dressing in three-level atomic systems may enable the realization of laser driven quantum fluids with long-range and anisotropic interactions and with controllable dissipation.

  5. Two-body interactions and decay of three-level Rydberg-dressed atoms

    Science.gov (United States)

    Helmrich, S.; Arias, A.; Pehoviak, N.; Whitlock, S.

    2016-02-01

    We theoretically analyze the interactions and decay rates for atoms dressed by multiple laser fields to strongly interacting Rydberg states using a quantum master equation approach. In this framework a comparison of two-level and three-level Rydberg-dressing schemes is presented. We identify a resonant enhancement of the three-level dressed interaction strength which originates from cooperative multiphoton couplings as well as small distance dependent decay rates. In this regime the soft-core shape of the potential is independent of the sign of the bare Rydberg-Rydberg interaction, while its sign can be repulsive or attractive depending on the intermediate state detuning. As a consequence, near-resonant Rydberg dressing in three-level atomic systems may enable the realization of laser driven quantum fluids with long-range and anisotropic interactions and with controllable dissipation.

  6. Hazard interactions and interaction networks (cascades) within multi-hazard methodologies

    Science.gov (United States)

    Gill, Joel C.; Malamud, Bruce D.

    2016-08-01

    This paper combines research and commentary to reinforce the importance of integrating hazard interactions and interaction networks (cascades) into multi-hazard methodologies. We present a synthesis of the differences between multi-layer single-hazard approaches and multi-hazard approaches that integrate such interactions. This synthesis suggests that ignoring interactions between important environmental and anthropogenic processes could distort management priorities, increase vulnerability to other spatially relevant hazards or underestimate disaster risk. In this paper we proceed to present an enhanced multi-hazard framework through the following steps: (i) description and definition of three groups (natural hazards, anthropogenic processes and technological hazards/disasters) as relevant components of a multi-hazard environment, (ii) outlining of three types of interaction relationship (triggering, increased probability, and catalysis/impedance), and (iii) assessment of the importance of networks of interactions (cascades) through case study examples (based on the literature, field observations and semi-structured interviews). We further propose two visualisation frameworks to represent these networks of interactions: hazard interaction matrices and hazard/process flow diagrams. Our approach reinforces the importance of integrating interactions between different aspects of the Earth system, together with human activity, into enhanced multi-hazard methodologies. Multi-hazard approaches support the holistic assessment of hazard potential and consequently disaster risk. We conclude by describing three ways by which understanding networks of interactions contributes to the theoretical and practical understanding of hazards, disaster risk reduction and Earth system management. Understanding interactions and interaction networks helps us to better (i) model the observed reality of disaster events, (ii) constrain potential changes in physical and social vulnerability

  7. Probing Magnetism in 2D Molecular Networks after in Situ Metalation by Transition Metal Atoms.

    Science.gov (United States)

    Schouteden, K; Ivanova, Ts; Li, Z; Iancu, V; Janssens, E; Van Haesendonck, C

    2015-03-19

    Metalated molecules are the ideal building blocks for the bottom-up fabrication of, e.g., two-dimensional arrays of magnetic particles for spintronics applications. Compared to chemical synthesis, metalation after network formation by an atom beam can yield a higher degree of control and flexibility and allows for mixing of different types of magnetic atoms. We report on successful metalation of tetrapyridyl-porphyrins (TPyP) by Co and Cr atoms, as demonstrated by scanning tunneling microscopy experiments. For the metalation, large periodic networks formed by the TPyP molecules on a Ag(111) substrate are exposed in situ to an atom beam. Voltage-induced dehydrogenation experiments support the conclusion that the porphyrin macrocycle of the TPyP molecule incorporates one transition metal atom. The newly synthesized Co-TPyP and Cr-TPyP complexes exhibit striking differences in their electronic behavior, leading to a magnetic character for Cr-TPyP only as evidenced by Kondo resonance measurements.

  8. Reduced matrix elements of spin–spin interactions for the atomic f-electron configurations

    Energy Technology Data Exchange (ETDEWEB)

    Yeung, Y.Y., E-mail: yeungy@acm.org

    2014-03-15

    A re-examination of some major references on the intra-atomic magnetic interactions over the last six decades reveals that there exist some gaps or puzzles concerning the previous studies of the spin–spin interactions for the atomic f-shell electrons. Hence, tables are provided for the relevant reduced matrix elements of the four double-tensor operators z{sub r} (r=1,2,3, and 4) of rank 2 in both the orbital and spin spaces. The range of the tables covers all states of the configurations from f{sup 4} to f{sup 7}.

  9. Time-dependent restricted active space Configuration Interaction for the photoionization of many-electron atoms

    CERN Document Server

    Hochstuhl, David

    2012-01-01

    We introduce the time-dependent restricted active space Configuration Interaction method to solve the time-dependent Schr\\"odinger equation for many-electron atoms, and particularly apply it to the treatment of photoionization processes in atoms. The method is presented in a very general formulation and incorporates a wide range of commonly used approximation schemes, like the single-active electron approximation, time-dependent Configuration Interaction with single-excitations, or the time-dependent R-matrix method. We proof the applicability of the method by calculating the photoionization cross sections of Helium and Beryllium.

  10. Model for Interaction Between Photon and Cold Atom in QED Cavity

    Institute of Scientific and Technical Information of China (English)

    ZHANG Li; WANG Cheng; LI Yan-Min; RUAN Sheng-Ping; XUAN Li

    2004-01-01

    A model has been established for the interaction between a single-mode optical field and a 2-energy-level cold atom with exact analytic solutions given. The processes of momentum and energy exchanges between the optical field and the cold atom due to the interaction between them are discussed in detail, and a formula has been given for the variation of momentum and energy exchange volumes with time t in dress state while both the effects of photon recoil and Doppler effect are taken into consideration.

  11. The thermal Casimir-Polder interaction of an atom with spherical plasma shell

    OpenAIRE

    Khusnutdinov, Nail R.

    2012-01-01

    The van der Waals and Casimir-Polder interaction energy of an atom with an infinitely thin sphere with finite conductivity is investigated in the framework of the hydrodynamic approach at finite temperature. This configuration models the real interaction of an atom with fullerene. The Lifshitz approach is used to find the free energy. We find the explicit expression for the free energy and perform the analysis of it for i) high and low temperatures, ii) large radii of sphere and ii) short sep...

  12. Ecological Networks: Structure, Interaction Strength, and Stability

    Science.gov (United States)

    Bhattacharyya, Samit; Sinha, Somdatta

    The fundamental building blocks of any ecosystem, the food webs, which are assemblages of species through various interconnections, provide a central concept in ecology. The study of a food web allows abstractions of the complexity and interconnectedness of natural communities that transcend the specific details of the underlying systems. For example, Fig. 1 shows a typical food web, where the species are connected through their feeding relationships. The top predator, Heliaster (starfish) feeds on many gastropods like Hexaplex, Morula, Cantharus, etc., some of whom predate on each other [129]. Interactions between species in a food web can be of many types, such as predation, competition, mutualism, commensalism, and ammensalism (see Section 1.1, Fig. 2).

  13. GINI: from ISH images to gene interaction networks.

    Directory of Open Access Journals (Sweden)

    Kriti Puniyani

    Full Text Available Accurate inference of molecular and functional interactions among genes, especially in multicellular organisms such as Drosophila, often requires statistical analysis of correlations not only between the magnitudes of gene expressions, but also between their temporal-spatial patterns. The ISH (in-situ-hybridization-based gene expression micro-imaging technology offers an effective approach to perform large-scale spatial-temporal profiling of whole-body mRNA abundance. However, analytical tools for discovering gene interactions from such data remain an open challenge due to various reasons, including difficulties in extracting canonical representations of gene activities from images, and in inference of statistically meaningful networks from such representations. In this paper, we present GINI, a machine learning system for inferring gene interaction networks from Drosophila embryonic ISH images. GINI builds on a computer-vision-inspired vector-space representation of the spatial pattern of gene expression in ISH images, enabled by our recently developed [Formula: see text] system; and a new multi-instance-kernel algorithm that learns a sparse Markov network model, in which, every gene (i.e., node in the network is represented by a vector-valued spatial pattern rather than a scalar-valued gene intensity as in conventional approaches such as a Gaussian graphical model. By capturing the notion of spatial similarity of gene expression, and at the same time properly taking into account the presence of multiple images per gene via multi-instance kernels, GINI is well-positioned to infer statistically sound, and biologically meaningful gene interaction networks from image data. Using both synthetic data and a small manually curated data set, we demonstrate the effectiveness of our approach in network building. Furthermore, we report results on a large publicly available collection of Drosophila embryonic ISH images from the Berkeley Drosophila Genome

  14. Hazard Interactions and Interaction Networks (Cascades) within Multi-Hazard Methodologies

    Science.gov (United States)

    Gill, Joel; Malamud, Bruce D.

    2016-04-01

    Here we combine research and commentary to reinforce the importance of integrating hazard interactions and interaction networks (cascades) into multi-hazard methodologies. We present a synthesis of the differences between 'multi-layer single hazard' approaches and 'multi-hazard' approaches that integrate such interactions. This synthesis suggests that ignoring interactions could distort management priorities, increase vulnerability to other spatially relevant hazards or underestimate disaster risk. We proceed to present an enhanced multi-hazard framework, through the following steps: (i) describe and define three groups (natural hazards, anthropogenic processes and technological hazards/disasters) as relevant components of a multi-hazard environment; (ii) outline three types of interaction relationship (triggering, increased probability, and catalysis/impedance); and (iii) assess the importance of networks of interactions (cascades) through case-study examples (based on literature, field observations and semi-structured interviews). We further propose visualisation frameworks to represent these networks of interactions. Our approach reinforces the importance of integrating interactions between natural hazards, anthropogenic processes and technological hazards/disasters into enhanced multi-hazard methodologies. Multi-hazard approaches support the holistic assessment of hazard potential, and consequently disaster risk. We conclude by describing three ways by which understanding networks of interactions contributes to the theoretical and practical understanding of hazards, disaster risk reduction and Earth system management. Understanding interactions and interaction networks helps us to better (i) model the observed reality of disaster events, (ii) constrain potential changes in physical and social vulnerability between successive hazards, and (iii) prioritise resource allocation for mitigation and disaster risk reduction.

  15. Ecological interaction and phylogeny, studying functionality on composed networks

    Science.gov (United States)

    Cruz, Claudia P. T.; Fonseca, Carlos Roberto; Corso, Gilberto

    2012-02-01

    We study a class of composed networks that are formed by two tree networks, TP and TA, whose end points touch each other through a bipartite network BPA. We explore this network using a functional approach. We are interested in how much the topology, or the structure, of TX (X=A or P) determines the links of BPA. This composed structure is a useful model in evolutionary biology, where TP and TA are the phylogenetic trees of plants and animals that interact in an ecological community. We make use of ecological networks of dispersion of fruits, which are formed by frugivorous animals and plants with fruits; the animals, usually birds, eat fruits and disperse their seeds. We analyse how the phylogeny of TX determines or is correlated with BPA using a Monte Carlo approach. We use the phylogenetic distance among elements that interact with a given species to construct an index κ that quantifies the influence of TX over BPA. The algorithm is based on the assumption that interaction matrices that follows a phylogeny of TX have a total phylogenetic distance smaller than the average distance of an ensemble of Monte Carlo realisations. We find that the effect of phylogeny of animal species is more pronounced in the ecological matrix than plant phylogeny.

  16. Strain field of interstitial hydrogen atom in body-centered cubic iron and its effect on hydrogen-dislocation interaction

    OpenAIRE

    Wang, Shuai; Takahashi, Keisuke; Hashimoto, Naoyuki; Isobe, Shigehito; Ohnuki, Somei

    2013-01-01

    Effect of hydrogen in body-centered cubic iron is explored by using the density function theory. Hydrogen atoms increase the concentration of free electrons in the simulation cell and have bonding interaction with Fe atom. Caused by anisotropic strain components of hydrogen atoms in the tetrahedral sites, elastic interaction for hydrogen with screw dislocation has been found. The dependence of hydrogen-screw dislocation interaction on hydrogen concentration is confirmed by repeated stress rel...

  17. An integrated text mining framework for metabolic interaction network reconstruction.

    Science.gov (United States)

    Patumcharoenpol, Preecha; Doungpan, Narumol; Meechai, Asawin; Shen, Bairong; Chan, Jonathan H; Vongsangnak, Wanwipa

    2016-01-01

    Text mining (TM) in the field of biology is fast becoming a routine analysis for the extraction and curation of biological entities (e.g., genes, proteins, simple chemicals) as well as their relationships. Due to the wide applicability of TM in situations involving complex relationships, it is valuable to apply TM to the extraction of metabolic interactions (i.e., enzyme and metabolite interactions) through metabolic events. Here we present an integrated TM framework containing two modules for the extraction of metabolic events (Metabolic Event Extraction module-MEE) and for the construction of a metabolic interaction network (Metabolic Interaction Network Reconstruction module-MINR). The proposed integrated TM framework performed well based on standard measures of recall, precision and F-score. Evaluation of the MEE module using the constructed Metabolic Entities (ME) corpus yielded F-scores of 59.15% and 48.59% for the detection of metabolic events for production and consumption, respectively. As for the testing of the entity tagger for Gene and Protein (GP) and metabolite with the test corpus, the obtained F-score was greater than 80% for the Superpathway of leucine, valine, and isoleucine biosynthesis. Mapping of enzyme and metabolite interactions through network reconstruction showed a fair performance for the MINR module on the test corpus with F-score >70%. Finally, an application of our integrated TM framework on a big-scale data (i.e., EcoCyc extraction data) for reconstructing a metabolic interaction network showed reasonable precisions at 69.93%, 70.63% and 46.71% for enzyme, metabolite and enzyme-metabolite interaction, respectively. This study presents the first open-source integrated TM framework for reconstructing a metabolic interaction network. This framework can be a powerful tool that helps biologists to extract metabolic events for further reconstruction of a metabolic interaction network. The ME corpus, test corpus, source code, and virtual

  18. Simulating market dynamics: interactions between consumer psychology and social networks.

    Science.gov (United States)

    Janssen, Marco A; Jager, Wander

    2003-01-01

    Markets can show different types of dynamics, from quiet markets dominated by one or a few products, to markets with continual penetration of new and reintroduced products. In a previous article we explored the dynamics of markets from a psychological perspective using a multi-agent simulation model. The main results indicated that the behavioral rules dominating the artificial consumer's decision making determine the resulting market dynamics, such as fashions, lock-in, and unstable renewal. Results also show the importance of psychological variables like social networks, preferences, and the need for identity to explain the dynamics of markets. In this article we extend this work in two directions. First, we will focus on a more systematic investigation of the effects of different network structures. The previous article was based on Watts and Strogatz's approach, which describes the small-world and clustering characteristics in networks. More recent research demonstrated that many large networks display a scale-free power-law distribution for node connectivity. In terms of market dynamics this may imply that a small proportion of consumers may have an exceptional influence on the consumptive behavior of others (hubs, or early adapters). We show that market dynamics is a self-organized property depending on the interaction between the agents' decision-making process (heuristics), the product characteristics (degree of satisfaction of unit of consumption, visibility), and the structure of interactions between agents (size of network and hubs in a social network). PMID:14761255

  19. Nonlinear Zeno dynamics due to atomic interactions in Bose–Einstein condensate

    International Nuclear Information System (INIS)

    We show that nonlinear interactions induce both the Zeno and anti-Zeno effects in the generalized Bose–Josephson model (with the on-site interactions and the second-order tunneling) describing Bose–Einstein condensate in double-well trap subject to particle removal from one of the wells. We find that the on-site interactions induce only the Zeno effect, which appears at long evolution times, whereas the second-order tunneling leads to a strong decay of the atomic population at short evolution times, reminiscent of the anti-Zeno effect, and destroys the nonlinear Zeno effect due to the on-site interactions at long times

  20. Nonlinear Zeno dynamics due to atomic interactions in Bose–Einstein condensate

    Energy Technology Data Exchange (ETDEWEB)

    Navarro, V.G.; Shchesnovich, V.S., E-mail: valery@ufabc.edu.br

    2014-12-01

    We show that nonlinear interactions induce both the Zeno and anti-Zeno effects in the generalized Bose–Josephson model (with the on-site interactions and the second-order tunneling) describing Bose–Einstein condensate in double-well trap subject to particle removal from one of the wells. We find that the on-site interactions induce only the Zeno effect, which appears at long evolution times, whereas the second-order tunneling leads to a strong decay of the atomic population at short evolution times, reminiscent of the anti-Zeno effect, and destroys the nonlinear Zeno effect due to the on-site interactions at long times.

  1. Characterizing interactions in online social networks during exceptional events

    Science.gov (United States)

    Omodei, Elisa; De Domenico, Manlio; Arenas, Alex

    2015-08-01

    Nowadays, millions of people interact on a daily basis on online social media like Facebook and Twitter, where they share and discuss information about a wide variety of topics. In this paper, we focus on a specific online social network, Twitter, and we analyze multiple datasets each one consisting of individuals' online activity before, during and after an exceptional event in terms of volume of the communications registered. We consider important events that occurred in different arenas that range from policy to culture or science. For each dataset, the users' online activities are modeled by a multilayer network in which each layer conveys a different kind of interaction, specifically: retweeting, mentioning and replying. This representation allows us to unveil that these distinct types of interaction produce networks with different statistical properties, in particular concerning the degree distribution and the clustering structure. These results suggests that models of online activity cannot discard the information carried by this multilayer representation of the system, and should account for the different processes generated by the different kinds of interactions. Secondly, our analysis unveils the presence of statistical regularities among the different events, suggesting that the non-trivial topological patterns that we observe may represent universal features of the social dynamics on online social networks during exceptional events.

  2. Signed Networks, Triadic Interactions and the Evolution of Cooperation

    Directory of Open Access Journals (Sweden)

    Károly Takács

    2013-09-01

    Full Text Available We outline a model to study the evolution of cooperation in a population of agents playing the prisoner's dilemma in signed networks. We highlight that if only dyadic interactions are taken into account, cooperation never evolves. However, when triadic considerations are introduced, a window of opportunity for emergence of cooperation as a stable behaviour emerges.

  3. Prediction of oncogenic interactions and cancer-related signaling networks based on network topology.

    Directory of Open Access Journals (Sweden)

    Marcio Luis Acencio

    Full Text Available Cancer has been increasingly recognized as a systems biology disease since many investigators have demonstrated that this malignant phenotype emerges from abnormal protein-protein, regulatory and metabolic interactions induced by simultaneous structural and regulatory changes in multiple genes and pathways. Therefore, the identification of oncogenic interactions and cancer-related signaling networks is crucial for better understanding cancer. As experimental techniques for determining such interactions and signaling networks are labor-intensive and time-consuming, the development of a computational approach capable to accomplish this task would be of great value. For this purpose, we present here a novel computational approach based on network topology and machine learning capable to predict oncogenic interactions and extract relevant cancer-related signaling subnetworks from an integrated network of human genes interactions (INHGI. This approach, called graph2sig, is twofold: first, it assigns oncogenic scores to all interactions in the INHGI and then these oncogenic scores are used as edge weights to extract oncogenic signaling subnetworks from INHGI. Regarding the prediction of oncogenic interactions, we showed that graph2sig is able to recover 89% of known oncogenic interactions with a precision of 77%. Moreover, the interactions that received high oncogenic scores are enriched in genes for which mutations have been causally implicated in cancer. We also demonstrated that graph2sig is potentially useful in extracting oncogenic signaling subnetworks: more than 80% of constructed subnetworks contain more than 50% of original interactions in their corresponding oncogenic linear pathways present in the KEGG PATHWAY database. In addition, the potential oncogenic signaling subnetworks discovered by graph2sig are supported by experimental evidence. Taken together, these results suggest that graph2sig can be a useful tool for investigators involved

  4. Field-matter interaction in atomic and plasma physics, from fluctuations to the strongly nonlinear regime

    International Nuclear Information System (INIS)

    This manuscript provides a theoretical description, sometimes illustrated by experimental results, of several examples of field-matter interaction in various domains of physics, showing how the same basic concepts and theoretical methods may be used in very different physics situations. The issues addressed here are nonlinear field-matter interaction in plasma physics within the framework of classical mechanics (with a particular emphasis on wave-particle interaction), the linear analysis of beam-plasma instabilities in the relativistic regime, and the quantum description of laser-atom interaction, including quantum electrodynamics. Novel methods are systematically introduced in order to solve some very old problems, like the nonlinear counterpart of the Landau damping rate in plasma physics, for example. Moreover, our results directly apply to inertial confinement fusion, laser propagation in an atomic vapor, ion acceleration in a magnetized plasma and the physics of the Reversed Field Pinch for magnetic fusion. (author)

  5. Domain-Domain Interactions Underlying Herpesvirus-Human Protein-Protein Interaction Networks

    OpenAIRE

    Zohar Itzhaki

    2011-01-01

    Protein-domains play an important role in mediating protein-protein interactions. Furthermore, the same domain-pairs mediate different interactions in different contexts and in various organisms, and therefore domain-pairs are considered as the building blocks of interactome networks. Here we extend these principles to the host-virus interface and find the domain-pairs that potentially mediate human-herpesvirus interactions. Notably, we find that the same domain-pairs used by other organisms ...

  6. Interaction between two SU(1 , 1) quantum systems and a two-level atom

    Science.gov (United States)

    Abdalla, M. Sebawe; Khalil, E. M.; Obada, A. S.-F.

    2016-07-01

    We consider a two-level atom interacting with two coupled quantum systems that can be represented in terms of su(1 , 1) Lie algebra. The wave function that is obtained using the evolution operator for the atom is initially in a superposition state and the coupled su(1 , 1) systems in a pair coherent Barut-Girardello coherent state. We then discuss atomic inversion, where more periods of revivals are observed and compared with a single su(1 , 1) quantum system. For entanglement and squeezing phenomena, the atomic angles coherence and phase as well as the detuning are effective parameters. The second-order correlation function displays Bunching and anti-Bunching behavior.

  7. Atomic and plasma-material interaction data for fusion. V. 2

    International Nuclear Information System (INIS)

    This issues of the Atomic and Plasma-Material Interaction Data for Fusion contains 9 papers on atomic and molecular processes in the edge region of magnetically confined fusion plasmas, including spectroscopic data for fusion edge plasmas; electron collision processes with plasma edge neutrals; electron-ion collisions in the plasma edge; cross-section data for collisions of electrons with hydrocarbon molecules; dissociative and energy transfer reactions involving vibrationally excited hydrogen or deuterium molecules; an assessment of ion-atom collision data for magnetic fusion plasma edge modeling; an extended scaling of cross sections for the ionization of atomic and molecular hydrogen as well as helium by multiply-charged ions; ion-molecule collision processes relevant to fusion edge plasmas; and radiative losses and electron cooling rates for carbon and oxygen plasma impurities. Refs, figs and tabs

  8. Interaction and dynamics of add-atoms with 2-dimensional structures

    CERN Multimedia

    The interaction and dynamics of add-atoms with graphene, graphene-derivate structures and, later, MoSi$_2$, two-dimensional – single and few – atomic layers will be studied with the Perturbed Angular Correlation – PAC – technique. Graphene is also envisaged as new platform for growing semiconductor nanostructure devices, such as quantum dots and as a particularly powerful catalyst. Understanding nucleation of nanostructures and clusters on graphene and related phases in wet conditions as they are used in chemical methods in research and industry require complementary studies. These systems will therefore be studied systematically using radioactive probe atoms attaching via a transfer media (e.g., water in catalysis process) or being deposited with soft-landing techniques under vacuum and UHV conditions, as put in place at the ASPIC setup at ISOLDE. The hyperfine fields obtained under different environments are expected to reveal basic information on the rich atomic and physical mechanisms associated w...

  9. Entangled states in the two-mode coherent fields interacting With a two-level atom

    Institute of Scientific and Technical Information of China (English)

    刘小娟; 方卯发

    2003-01-01

    We investigate the entanglement properties of the two-mode coherent fields inter,ting with a two-level atom via the two-photon transition.We discuss the quantum entanglement between the two-mode coherent fields and the two-level atom by using the quantum reduced entropy and that between the two-mode coherent fields by using the quantum relative entropy.We also examine the influences of the initial states of the atom and the two-mode coherent fields on the quantum entanglement of the system.Our results show that three types of entangled states can be prepared via the two-mode coherent fields interacting with a two-level atom and choosing appropriately the initial-state parameters of the system.

  10. Broadband photon-photon interactions mediated by cold atoms in a photonic crystal fiber

    Science.gov (United States)

    Litinskaya, Marina; Tignone, Edoardo; Pupillo, Guido

    2016-05-01

    We demonstrate theoretically that photon-photon attraction can be engineered in the continuum of scattering states for pairs of photons propagating in a hollow-core photonic crystal fiber filled with cold atoms. The atoms are regularly spaced in an optical lattice configuration and the photons are resonantly tuned to an internal atomic transition. We show that the hard-core repulsion resulting from saturation of the atomic transitions induces bunching in the photonic component of the collective atom-photon modes (polaritons). Bunching is obtained in a frequency range as large as tens of GHz, and can be controlled by the inter-atomic separation. We provide a fully analytical explanation for this phenomenon by proving that correlations result from a mismatch of the quantization volumes for atomic excitations and photons in the continuum. Even stronger correlations can be observed for in-gap two-polariton bound states. Our theoretical results use parameters relevant for current experiments and suggest a simple and feasible way to induce interactions between photons.

  11. van der Waals interaction of finite metallic systems: A study of cluster-atom scattering

    International Nuclear Information System (INIS)

    Absolute integral cross sections for elastic collisions of neutral sodium clusters Nan (n=2--20) with sodium atoms have been measured and the van der Waals interaction constants determined. The center-of-mass cross sections are very large (up to thousands of square angstroms), reflecting high cluster polarizabilities. It is found that the dispersion theory based on measured response parameters of alkali-metal clusters tends to overestimate the interaction strength

  12. Mechanism of interaction between gold atoms and donor impurity in silicon

    International Nuclear Information System (INIS)

    Analysis of experimental results on radiation and thermal effects on Si and literary data permitted to make supposition on mechanism of interaction of donor impurity and gold atoms in interstitial position allowing presence of exchange vacancy. Taking into account this interaction the following experimental results are explained: 1)appearance under high-temperature warm-up and electron irradiation (T=300-500 deg C) of a center with Ec-0.30 eV forbidden gap level, connected with a complex of donor impurity atom and eigen vacancy (E-center) under some hardening conditions of investigated complex material; 3)availability of correlated distribution of phosphorus and gold atoms in substituting position

  13. The thermal Casimir–Polder interaction of an atom with a spherical plasma shell

    International Nuclear Information System (INIS)

    The van der Waals and Casimir–Polder interaction energy of an atom with an infinitely thin sphere with finite conductivity is investigated in the framework of the hydrodynamic approach at finite temperature. This configuration models the real interaction of an atom with fullerene. The Lifshitz approach is used to find the free energy. We find the explicit expression for the free energy and perform its analysis for (i) high and low temperatures, (ii) large radii of the sphere and (iii) short separation between an atom and sphere. At low temperatures the thermal part of the free energy approaches zero as the fourth power of the temperature, while for high temperatures it is proportional to the first degree of the temperature. The entropy of this system is positive for small radii of the sphere and it becomes negative at low temperatures and for large radii of the sphere. (paper)

  14. Far-field resonance fluorescence from a dipole-interacting laser-driven cold atomic gas

    CERN Document Server

    Jones, Ryan; Olmos, Beatriz

    2016-01-01

    We analyze the temporal response of the fluorescence light that is emitted from a dense gas of cold atoms driven by a laser. When the average interatomic distance is smaller than the wavelength of the photons scattered by the atoms, the system exhibits strong dipolar interactions and collective dissipation. We solve the exact dynamics of small systems with different geometries and show how these collective features are manifest in the scattered light properties such as the photon emission rate, the power spectrum and the second-order correlation function. By calculating these quantities beyond the weak driving limit, we make progress in understanding the signatures of collective behavior in these many-body systems. Furthermore, we clarify the role of disorder on the resonance fluorescence, of direct relevance for recent experimental efforts that aim at the exploration of many-body effects in dipole-dipole interacting gases of atoms.

  15. Response of the mosquito protein interaction network to dengue infection

    Directory of Open Access Journals (Sweden)

    Pike Andrew D

    2010-06-01

    Full Text Available Abstract Background Two fifths of the world's population is at risk from dengue. The absence of effective drugs and vaccines leaves vector control as the primary intervention tool. Understanding dengue virus (DENV host interactions is essential for the development of novel control strategies. The availability of genome sequences for both human and mosquito host greatly facilitates genome-wide studies of DENV-host interactions. Results We developed the first draft of the mosquito protein interaction network using a computational approach. The weighted network includes 4,214 Aedes aegypti proteins with 10,209 interactions, among which 3,500 proteins are connected into an interconnected scale-free network. We demonstrated the application of this network for the further annotation of mosquito proteins and dissection of pathway crosstalk. Using three datasets based on physical interaction assays, genome-wide RNA interference (RNAi screens and microarray assays, we identified 714 putative DENV-associated mosquito proteins. An integrated analysis of these proteins in the network highlighted four regions consisting of highly interconnected proteins with closely related functions in each of replication/transcription/translation (RTT, immunity, transport and metabolism. Putative DENV-associated proteins were further selected for validation by RNAi-mediated gene silencing, and dengue viral titer in mosquito midguts was significantly reduced for five out of ten (50.0% randomly selected genes. Conclusions Our results indicate the presence of common host requirements for DENV in mosquitoes and humans. We discuss the significance of our findings for pharmacological intervention and genetic modification of mosquitoes for blocking dengue transmission.

  16. How People Interact in Evolving Online Affiliation Networks

    Science.gov (United States)

    Gallos, Lazaros K.; Rybski, Diego; Liljeros, Fredrik; Havlin, Shlomo; Makse, Hernán A.

    2012-07-01

    The study of human interactions is of central importance for understanding the behavior of individuals, groups, and societies. Here, we observe the formation and evolution of networks by monitoring the addition of all new links, and we analyze quantitatively the tendencies used to create ties in these evolving online affiliation networks. We show that an accurate estimation of these probabilistic tendencies can be achieved only by following the time evolution of the network. Inferences about the reason for the existence of links using statistical analysis of network snapshots must therefore be made with great caution. Here, we start by characterizing every single link when the tie was established in the network. This information allows us to describe the probabilistic tendencies of tie formation and extract meaningful sociological conclusions. We also find significant differences in behavioral traits in the social tendencies among individuals according to their degree of activity, gender, age, popularity, and other attributes. For instance, in the particular data sets analyzed here, we find that women reciprocate connections 3 times as much as men and that this difference increases with age. Men tend to connect with the most popular people more often than women do, across all ages. On the other hand, triangular tie tendencies are similar, independent of gender, and show an increase with age. These results require further validation in other social settings. Our findings can be useful to build models of realistic social network structures and to discover the underlying laws that govern establishment of ties in evolving social networks.

  17. Cancer risk at low doses of ionizing radiation: artificial neural networks inference from atomic bomb survivors

    OpenAIRE

    Sasaki, Masao S.; Tachibana, Akira; Takeda, Shunichi

    2013-01-01

    Cancer risk at low doses of ionizing radiation remains poorly defined because of ambiguity in the quantitative link to doses below 0.2 Sv in atomic bomb survivors in Hiroshima and Nagasaki arising from limitations in the statistical power and information available on overall radiation dose. To deal with these difficulties, a novel nonparametric statistics based on the ‘integrate-and-fire’ algorithm of artificial neural networks was developed and tested in cancer databases established by the R...

  18. Cancer risk at low doses of ionizing radiation: artificial neural networks inference from atomic bomb survivors.

    OpenAIRE

    Sasaki, Masao S.; Tachibana, Akira; Takeda, Shunichi

    2014-01-01

    Cancer risk at low doses of ionizing radiation remains poorly defined because of ambiguity in the quantitative link to doses below 0.2 Sv in atomic bomb survivors in Hiroshima and Nagasaki arising from limitations in the statistical power and information available on overall radiation dose. To deal with these difficulties, a novel nonparametric statistics based on the 'integrate-and-fire' algorithm of artificial neural networks was developed and tested in cancer databases established by the R...

  19. The Intrinsic Geometric Structure of Protein-Protein Interaction Networks for Protein Interaction Prediction.

    Science.gov (United States)

    Fang, Yi; Sun, Mengtian; Dai, Guoxian; Ramain, Karthik

    2016-01-01

    Recent developments in high-throughput technologies for measuring protein-protein interaction (PPI) have profoundly advanced our ability to systematically infer protein function and regulation. However, inherently high false positive and false negative rates in measurement have posed great challenges in computational approaches for the prediction of PPI. A good PPI predictor should be 1) resistant to high rate of missing and spurious PPIs, and 2) robust against incompleteness of observed PPI networks. To predict PPI in a network, we developed an intrinsic geometry structure (IGS) for network, which exploits the intrinsic and hidden relationship among proteins in network through a heat diffusion process. In this process, all explicit PPIs participate simultaneously to glue local infinitesimal and noisy experimental interaction data to generate a global macroscopic descriptions about relationships among proteins. The revealed implicit relationship can be interpreted as the probability of two proteins interacting with each other. The revealed relationship is intrinsic and robust against individual, local and explicit protein interactions in the original network. We apply our approach to publicly available PPI network data for the evaluation of the performance of PPI prediction. Experimental results indicate that, under different levels of the missing and spurious PPIs, IGS is able to robustly exploit the intrinsic and hidden relationship for PPI prediction with a higher sensitivity and specificity compared to that of recently proposed methods. PMID:26886733

  20. Learning Predictive Interactions Using Information Gain and Bayesian Network Scoring.

    Directory of Open Access Journals (Sweden)

    Xia Jiang

    Full Text Available The problems of correlation and classification are long-standing in the fields of statistics and machine learning, and techniques have been developed to address these problems. We are now in the era of high-dimensional data, which is data that can concern billions of variables. These data present new challenges. In particular, it is difficult to discover predictive variables, when each variable has little marginal effect. An example concerns Genome-wide Association Studies (GWAS datasets, which involve millions of single nucleotide polymorphism (SNPs, where some of the SNPs interact epistatically to affect disease status. Towards determining these interacting SNPs, researchers developed techniques that addressed this specific problem. However, the problem is more general, and so these techniques are applicable to other problems concerning interactions. A difficulty with many of these techniques is that they do not distinguish whether a learned interaction is actually an interaction or whether it involves several variables with strong marginal effects.We address this problem using information gain and Bayesian network scoring. First, we identify candidate interactions by determining whether together variables provide more information than they do separately. Then we use Bayesian network scoring to see if a candidate interaction really is a likely model. Our strategy is called MBS-IGain. Using 100 simulated datasets and a real GWAS Alzheimer's dataset, we investigated the performance of MBS-IGain.When analyzing the simulated datasets, MBS-IGain substantially out-performed nine previous methods at locating interacting predictors, and at identifying interactions exactly. When analyzing the real Alzheimer's dataset, we obtained new results and results that substantiated previous findings. We conclude that MBS-IGain is highly effective at finding interactions in high-dimensional datasets. This result is significant because we have increasingly

  1. Long-range interacting many-body systems with alkaline-earth-metal atoms.

    Science.gov (United States)

    Olmos, B; Yu, D; Singh, Y; Schreck, F; Bongs, K; Lesanovsky, I

    2013-04-01

    Alkaline-earth-metal atoms can exhibit long-range dipolar interactions, which are generated via the coherent exchange of photons on the (3)P(0) - (3)D(1) transition of the triplet manifold. In the case of bosonic strontium, which we discuss here, this transition has a wavelength of 2.6 μm and a dipole moment of 4.03 D, and there exists a magic wavelength permitting the creation of optical lattices that are identical for the states (3)P(0) and (3)D(1). This interaction enables the realization and study of mixtures of hard-core lattice bosons featuring long-range hopping, with tunable disorder and anisotropy. We derive the many-body master equation, investigate the dynamics of excitation transport, and analyze spectroscopic signatures stemming from coherent long-range interactions and collective dissipation. Our results show that lattice gases of alkaline-earth-metal atoms permit the creation of long-lived collective atomic states and constitute a simple and versatile platform for the exploration of many-body systems with long-range interactions. As such, they represent an alternative to current related efforts employing Rydberg gases, atoms with large magnetic moment, or polar molecules.

  2. Quantum computing with atomic qubits and Rydberg interactions: Progress and challenges

    CERN Document Server

    Saffman, Mark

    2016-01-01

    We present a review of quantum computation with neutral atom qubits. After an overview of architectural options we examine Rydberg mediated gate protocols and fidelity for two- and multi-qubit interactions. We conclude with a summary of the current status and give an outlook for future progress.

  3. Systematic discovery of new recognition peptides mediating protein interaction networks

    DEFF Research Database (Denmark)

    Neduva, Victor; Linding, Rune; Su-Angrand, Isabelle;

    2005-01-01

    Many aspects of cell signalling, trafficking, and targeting are governed by interactions between globular protein domains and short peptide segments. These domains often bind multiple peptides that share a common sequence pattern, or "linear motif" (e.g., SH3 binding to PxxP). Many domains...... molecular details of how interaction networks are constructed, and can explain how one protein is able to bind to very different partners. Here we show that binding motifs can be detected using data from genome-scale interaction studies, and thus avoid the normally slow discovery process. Our approach based...... that binds Translin with a KD of 43 microM. We estimate that there are dozens or even hundreds of linear motifs yet to be discovered that will give molecular insight into protein networks and greatly illuminate cellular processes.Many aspects of cell signalling, trafficking, and targeting are governed...

  4. Digital Ecology: Coexistence and Domination among Interacting Networks

    Science.gov (United States)

    Kleineberg, Kaj-Kolja; Boguñá, Marián

    2015-05-01

    The overwhelming success of Web 2.0, within which online social networks are key actors, has induced a paradigm shift in the nature of human interactions. The user-driven character of Web 2.0 services has allowed researchers to quantify large-scale social patterns for the first time. However, the mechanisms that determine the fate of networks at the system level are still poorly understood. For instance, the simultaneous existence of multiple digital services naturally raises questions concerning which conditions these services can coexist under. Analogously to the case of population dynamics, the digital world forms a complex ecosystem of interacting networks. The fitness of each network depends on its capacity to attract and maintain users’ attention, which constitutes a limited resource. In this paper, we introduce an ecological theory of the digital world which exhibits stable coexistence of several networks as well as the dominance of an individual one, in contrast to the competitive exclusion principle. Interestingly, our theory also predicts that the most probable outcome is the coexistence of a moderate number of services, in agreement with empirical observations.

  5. Graphical Features of Functional Genes in Human Protein Interaction Network.

    Science.gov (United States)

    Wang, Pei; Chen, Yao; Lu, Jinhu; Wang, Qingyun; Yu, Xinghuo

    2016-06-01

    With the completion of the human genome project, it is feasible to investigate large-scale human protein interaction network (HPIN) with complex networks theory. Proteins are encoded by genes. Essential, viable, disease, conserved, housekeeping (HK) and tissue-enriched (TE) genes are functional genes, which are organized and functioned via interaction networks. Based on up-to-date data from various databases or literature, two large-scale HPINs and six subnetworks are constructed. We illustrate that the HPINs and most of the subnetworks are sparse, small-world, scale-free, disassortative and with hierarchical modularity. Among the six subnetworks, essential, disease and HK subnetworks are more densely connected than the others. Statistical analysis on the topological structures of the HPIN reveals that the lethal, the conserved, the HK and the TE genes are with hallmark graphical features. Receiver operating characteristic (ROC) curves indicate that the essential genes can be distinguished from the viable ones with accuracy as high as almost 70%. Closeness, semi-local and eigenvector centralities can distinguish the HK genes from the TE ones with accuracy around 82%. Furthermore, the Venn diagram, cluster dendgrams and classifications of disease genes reveal that some classes of disease genes are with hallmark graphical features, especially for cancer genes, HK disease genes and TE disease genes. The findings facilitate the identification of some functional genes via topological structures. The investigations shed some light on the characteristics of the compete interactome, which have potential implications in networked medicine and biological network control. PMID:26841412

  6. Passing messages between biological networks to refine predicted interactions.

    Directory of Open Access Journals (Sweden)

    Kimberly Glass

    Full Text Available Regulatory network reconstruction is a fundamental problem in computational biology. There are significant limitations to such reconstruction using individual datasets, and increasingly people attempt to construct networks using multiple, independent datasets obtained from complementary sources, but methods for this integration are lacking. We developed PANDA (Passing Attributes between Networks for Data Assimilation, a message-passing model using multiple sources of information to predict regulatory relationships, and used it to integrate protein-protein interaction, gene expression, and sequence motif data to reconstruct genome-wide, condition-specific regulatory networks in yeast as a model. The resulting networks were not only more accurate than those produced using individual data sets and other existing methods, but they also captured information regarding specific biological mechanisms and pathways that were missed using other methodologies. PANDA is scalable to higher eukaryotes, applicable to specific tissue or cell type data and conceptually generalizable to include a variety of regulatory, interaction, expression, and other genome-scale data. An implementation of the PANDA algorithm is available at www.sourceforge.net/projects/panda-net.

  7. High-efficiency atomic entanglement concentration for quantum communication network assisted by cavity QED

    Science.gov (United States)

    Wang, Guan-Yu; Li, Tao; Deng, Fu-Guo

    2015-04-01

    Quantum entanglement is the key resource in quantum information processing, especially in quantum communication network. However, affected by the environment noise, the maximally entangled states usually collapse into nonmaximally entangled ones or even mixed states. Here we present two high-efficiency schemes to complete the entanglement concentration of nonlocal two-atom systems. Our first scheme is used to concentrate the nonlocal atomic systems in the partially entangled states with known parameters, and it has the optimal success probability. The second scheme is used to concentrate the entanglement of the nonlocal two-atom systems in the partially entangled states with unknown parameters. Compared with the other schemes for the entanglement concentration of atomic systems, our two protocols are more efficient and practical. They require only an ancillary single photon to judge whether they succeed or not, and they work in a heralded way with detection inefficiency and absence of sophisticated single-photon detectors in practical applications. Moreover, they are insensitive to both the cavity decay and atomic spontaneous emission.

  8. Coherent Atom-Phonon Interaction through Mode Field Coupling in Hybrid Optomechanical Systems

    CERN Document Server

    Cotrufo, Michele; Verhagen, Ewold

    2016-01-01

    We propose a novel type of optomechanical coupling which enables a tripartite interaction between a quantum emitter, an optical mode and a macroscopic mechanical oscillator. The interaction uses a mechanism we term mode field coupling: mechanical displacement modifies the spatial distribution of the optical mode field, which in turn modulates the atom-photon coupling rate. In properly designed multimode optomechanical systems, we can achieve situations in which mode field coupling is the only possible interaction pathway for the system. This enables, for example, swapping of a single excitation between emitter and phonon, creation of nonclassical states of motion and mechanical ground-state cooling in the bad-cavity regime. Importantly, the emitter-phonon coupling rate can be enhanced through an optical drive field, allowing active control of strong atom-phonon coupling for realistic experimental parameters.

  9. Entanglement in a system of two two-level atoms interacting with a single-mode field

    Institute of Scientific and Technical Information of China (English)

    Jin Li-Juan; Fang Mao-Fa

    2006-01-01

    We investigate the entanglement in a system of two coupling atoms interacting with a single-mode field by means of quantum information entropy theory. The quantum entanglement between the two atoms and the coherent field is discussed by using the quantum reduced entropy, and the entanglement between the two coupling atoms is also investigated by using the quantum relative entropy. In addition, the influences of the atomic dipole-dipole interaction intensity and the average photon number of the coherent field on the degree of the entanglement is examined. The results show that the evolution of the degree of entanglement between the two atoms and the field is just opposite to that of the degree of entanglement between the two atoms. And the properties of the quantum entanglement in the system rely on the atomic dipole-dipole interaction and the average photon number of the coherent field.

  10. Self-organization of social hierarchy on interaction networks

    International Nuclear Information System (INIS)

    In order to examine the effects of interaction network structures on the self-organization of social hierarchy, we introduce the agent-based model: each individual as on a node of a network has its own power and its internal state changes by fighting with its neighbors and relaxation. We adopt three different networks: regular lattice, small-world network and scale-free network. For the regular lattice, we find the emergence of classes distinguished by the internal state. The transition points where each class emerges are determined analytically, and we show that each class is characterized by the local ranking relative to their neighbors. We also find that the antiferromagnetic-like configuration emerges just above the critical point. For the heterogeneous networks, individuals become winners (or losers) in descending order of the number of their links. By using mean-field analysis, we reveal that the transition point is determined by the maximum degree and the degree distribution in its neighbors

  11. UROX 2.0: an interactive tool for fitting atomic models into electron-microscopy reconstructions

    International Nuclear Information System (INIS)

    UROX is software designed for the interactive fitting of atomic models into electron-microscopy reconstructions. The main features of the software are presented, along with a few examples. Electron microscopy of a macromolecular structure can lead to three-dimensional reconstructions with resolutions that are typically in the 30–10 Å range and sometimes even beyond 10 Å. Fitting atomic models of the individual components of the macromolecular structure (e.g. those obtained by X-ray crystallography or nuclear magnetic resonance) into an electron-microscopy map allows the interpretation of the latter at near-atomic resolution, providing insight into the interactions between the components. Graphical software is presented that was designed for the interactive fitting and refinement of atomic models into electron-microscopy reconstructions. Several characteristics enable it to be applied over a wide range of cases and resolutions. Firstly, calculations are performed in reciprocal space, which results in fast algorithms. This allows the entire reconstruction (or at least a sizeable portion of it) to be used by taking into account the symmetry of the reconstruction both in the calculations and in the graphical display. Secondly, atomic models can be placed graphically in the map while the correlation between the model-based electron density and the electron-microscopy reconstruction is computed and displayed in real time. The positions and orientations of the models are refined by a least-squares minimization. Thirdly, normal-mode calculations can be used to simulate conformational changes between the atomic model of an individual component and its corresponding density within a macromolecular complex determined by electron microscopy. These features are illustrated using three practical cases with different symmetries and resolutions. The software, together with examples and user instructions, is available free of charge at http://mem.ibs.fr/UROX/

  12. Graphene-like optical light field and its interaction with two-level atoms

    Science.gov (United States)

    Lembessis, V. E.; Courtial, Johannes; Radwell, N.; Selyem, A.; Franke-Arnold, S.; Aldossary, O. M.; Babiker, M.

    2015-12-01

    The theoretical basis leading to the creation of a light field with a hexagonal honeycomb structure resembling graphene is considered along with its experimental realization and its interaction with atoms. It is argued that associated with such a light field is an optical dipole potential which leads to the diffraction of the atoms, but the details depend on whether the transverse spread of the atomic wave packet is larger than the transverse dimensions of the optical lattice (resonant Kapitza-Dirac effect) or smaller (optical Stern-Gerlach effect). Another effect in this context involves the creation of gauge fields due to the Berry phase acquired by the atom moving in the light field. The experimental realization of the light field with a honeycomb hexagonal structure is described using holographic methods and we proceed to explore the atom diffraction in the Kapitza-Dirac regime as well as the optical Stern-Gerlach regime, leading to momentum distributions with characteristic but different hexagonal structures. The artificial gauge fields too are shown to have the same hexagonal spatial structure and their magnitude can be significantly large. The effects are discussed with reference to typical parameters for the atoms and the fields.

  13. Engineering the Dynamics of Effective Spin-Chain Models for Strongly Interacting Atomic Gases

    DEFF Research Database (Denmark)

    Volosniev, A. G.; Petrosyan, D.; Valiente, M.;

    2015-01-01

    We consider a one-dimensional gas of cold atoms with strong contact interactions and construct an effective spin-chain Hamiltonian for a two-component system. The resulting Heisenberg spin model can be engineered by manipulating the shape of the external confining potential of the atomic gas. We ...... of the dynamics of few- and many-body quantum systems; as an illustrative example relevant to quantum computation and communication, we consider state transfer in the simplest non-trivial system of four particles representing exchange-coupled qubits....

  14. Restricted Thermalization for Two Interacting Atoms in a Multimode Harmonic Waveguide

    CERN Document Server

    Yurovsky, V A

    2010-01-01

    In this article, we study the thermalizability of a system consisting of two atoms in a circular, transversely harmonic waveguide in the multimode regime. While showing some signatures of the quantum-chaotic behavior, the system fails to reach a thermal equilibrium in a relaxation from an initial state, even when the interaction between the atoms is infinitely strong. We relate this phenomenon to the previously addressed unattainability of a complete quantum chaos in the Seba billiard [P. Seba, Phys. Rev. Lett., 64, 1855 (1990)], and we conjecture the absence of a complete thermalization to be a generic property of integrable quantum systems perturbed by a non-integrable but well localized perturbation.

  15. Combining configuration interaction with perturbation theory for atoms with large number of valence electrons

    CERN Document Server

    Dzuba, V A; Harabati, C; Flambaum, V V

    2016-01-01

    A version of the configuration interaction (CI) method is developed which treats highly excited many-electron basis states perturbatively, so that their inclusion does not affect the size of the CI matrix. This removes, at least in principle, the main limitation of the CI method in dealing with many-electron atoms or ions. We perform calculations of the spectra of iodine and its ions, tungsten, and ytterbium as examples of atoms with open $s$, $p$, $d$ and $f$-shells. Good agreement of the calculated data with experiment illustrates the power of the method. Its advantages and limitations are discussed.

  16. Multiscale quantum-defect theory for two interacting atoms in a symmetric harmonic trap

    OpenAIRE

    Chen, Yujun; Gao, Bo

    2007-01-01

    We present a multiscale quantum-defect theory (QDT) for two identical atoms in a symmetric harmonic trap that combines the quantum-defect theory for the van der Waals interaction [B. Gao, Phys. Rev. A \\textbf{64}, 010701(R) (2001)] at short distances with a quantum-defect theory for the harmonic trapping potential at large distances. The theory provides a systematic understanding of two atoms in a trap, from deeply bound molecular states and states of different partial waves, to highly excite...

  17. Interaction of slow and highly charged ions with surfaces: formation of hollow atoms

    Energy Technology Data Exchange (ETDEWEB)

    Stolterfoht, N.; Grether, M.; Spieler, A.; Niemann, D. [Hahn-Meitner Institut, Berlin (Germany). Bereich Festkoerperphysik; Arnau, A.

    1997-03-01

    The method of Auger spectroscopy was used to study the interaction of highly charged ions with Al and C surfaces. The formation of hollow Ne atoms in the first surface layers was evaluated by means of a Density Functional theory including non-linear screening effects. The time-dependent filling of the hollow atom was determined from a cascade model yielding information about the structure of the K-Auger spectra. Variation of total intensities of the L- and K-Auger peaks were interpreted by the cascade model in terms of attenuation effects on the electrons in the solid. (author)

  18. Atom-Resonant Heralded Single Photons by Interaction-Free Measurement

    OpenAIRE

    Wolfgramm, Florian; Astiz, Yannick A. de Icaza; Beduini, Federica A.; Cere, Alessandro; Mitchell, Morgan W.

    2011-01-01

    We demonstrate the generation of rubidium-resonant heralded single photons for quantum memories. Photon pairs are created by cavity-enhanced down-conversion and narrowed in bandwidth to 7 MHz with a novel atom-based filter operating by "interaction-free measurement" principles. At least 94% of the heralded photons are atom-resonant as demonstrated by a direct absorption measurement with rubidium vapor. A heralded auto-correlation measurement shows $g_c^{(2)}(0)=0.040 \\pm 0.012$, i.e., suppres...

  19. Precision X-ray spectroscopy of kaonic atoms as a probe of low-energy kaon-nucleus interaction

    CERN Document Server

    Shi, H; Beer, G; Bellotti, G; Berucci, C; Bragadireanu, A M; Bosnar, D; Cargnelli, M; Curceanu, C; Butt, A D; d'Uffizi, A; Fiorini, C; Ghio, F; Guaraldo, C; Hayano, R S; Iliescu, M; Ishiwatari, T; Iwasaki, M; Sandri, P Levi; Marton, J; Okada, S; Pietreanu, D; Piscicchia, K; Vidal, A Romero; Sbardella, E; Scordo, A; Sirghi, D L; Sirghi, F; Tatsuno, H; Doce, O Vazquez; Widmann, E; Zmeskal, J

    2016-01-01

    In the exotic atoms where one atomic $1s$ electron is replaced by a $K^{-}$, the strong interaction between the $K^{-}$ and the nucleus introduces an energy shift and broadening of the low-lying kaonic atomic levels which are determined by only the electromagnetic interaction. By performing X-ray spectroscopy for Z=1,2 kaonic atoms, the SIDDHARTA experiment determined with high precision the shift and width for the $1s$ state of $K^{-}p$ and the $2p$ state of kaonic helium-3 and kaonic helium-4. These results provided unique information of the kaon-nucleus interaction in the low energy limit.

  20. Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database

    Directory of Open Access Journals (Sweden)

    Bickerton George R

    2011-07-01

    Full Text Available Abstract Background Structural studies are increasingly providing huge amounts of information on multi-protein assemblies. Although a complete understanding of cellular processes will be dependent on an explicit characterization of the intermolecular interactions that underlie these assemblies and mediate molecular recognition, these are not well described by standard representations. Results Here we present PICCOLO, a comprehensive relational database capturing the details of structurally characterized protein-protein interactions. Interactions are described at the level of interacting pairs of atoms, residues and polypeptide chains, with the physico-chemical nature of the interactions being characterized. Distance and angle terms are used to distinguish 12 different interaction types, including van der Waals contacts, hydrogen bonds and hydrophobic contacts. The explicit aim of PICCOLO is to underpin large-scale analyses of the properties of protein-protein interfaces. This is exemplified by an analysis of residue propensity and interface contact preferences derived from a much larger data set than previously reported. However, PICCOLO also supports detailed inspection of particular systems of interest. Conclusions The current PICCOLO database comprises more than 260 million interacting atom pairs from 38,202 protein complexes. A web interface for the database is available at http://www-cryst.bioc.cam.ac.uk/piccolo.

  1. Feed forward neural networks modeling for K-P interactions

    International Nuclear Information System (INIS)

    Artificial intelligence techniques involving neural networks became vital modeling tools where model dynamics are difficult to track with conventional techniques. The paper make use of the feed forward neural networks (FFNN) to model the charged multiplicity distribution of K-P interactions at high energies. The FFNN was trained using experimental data for the multiplicity distributions at different lab momenta. Results of the FFNN model were compared to that generated using the parton two fireball model and the experimental data. The proposed FFNN model results showed good fitting to the experimental data. The neural network model performance was also tested at non-trained space and was found to be in good agreement with the experimental data

  2. Auditing medical records accesses via healthcare interaction networks.

    Science.gov (United States)

    Chen, You; Nyemba, Steve; Malin, Bradley

    2012-01-01

    Healthcare organizations are deploying increasingly complex clinical information systems to support patient care. Traditional information security practices (e.g., role-based access control) are embedded in enterprise-level systems, but are insufficient to ensure patient privacy. This is due, in part, to the dynamic nature of healthcare, which makes it difficult to predict which care providers need access to what and when. In this paper, we show that modeling operations at a higher level of granularity (e.g., the departmental level) are stable in the context of a relational network, which may enable more effective auditing strategies. We study three months of access logs from a large academic medical center to illustrate that departmental interaction networks exhibit certain invariants, such as the number, strength, and reciprocity of relationships. We further show that the relations extracted from the network can be leveraged to assess the extent to which a patient's care satisfies expected organizational behavior. PMID:23304277

  3. Multifunctional proteins revealed by overlapping clustering in protein interaction network

    OpenAIRE

    Becker, Emmanuelle; Robisson, Benoît; Chapple, Charles E.; Guénoche, Alain; Brun, Christine

    2011-01-01

    Motivation: Multifunctional proteins perform several functions. They are expected to interact specifically with distinct sets of partners, simultaneously or not, depending on the function performed. Current graph clustering methods usually allow a protein to belong to only one cluster, therefore impeding a realistic assignment of multifunctional proteins to clusters. Results: Here, we present Overlapping Cluster Generator (OCG), a novel clustering method which decomposes a network into overla...

  4. Effects of peer network interactions on adolescent cannabis use

    OpenAIRE

    Moriarty, John; Higgins, Kathryn

    2015-01-01

    PurposeThis study capitalises on three waves of longitudinal data from a cohort of 4351 secondary school pupils to examine the effects on individuals’ cannabis use uptake of both peer cannabis use and position within a peer network.Design/methodology/approachBoth cross-sectional and individual fixed effects models are used to estimate the effect on cannabis use of nominated friends’ cannabis use, of reciprocity and transitivity of nominations across the friendship cluster, and of interactions...

  5. Consensus of Multiagent Networks with Intermittent Interaction and Directed Topology

    Directory of Open Access Journals (Sweden)

    Li Xiao

    2014-01-01

    Full Text Available Intermittent interaction control is introduced to solve the consensus problem for second-order multiagent networks due to the limited sensing abilities and environmental changes periodically. And, we get some sufficient conditions for the agents to reach consensus with linear protocol from the theoretical findings by using the Lyapunov control approach. Finally, the validity of the theoretical results is validated through the numerical example.

  6. Games as Actors - Interaction, Play, Design, and Actor Network Theory

    OpenAIRE

    Jessen, Jari Due; Jessen, Carsten

    2014-01-01

    When interacting with computer games, users are forced to follow the rules of the game in return for the excitement, joy, fun, or other pursued experiences. In this paper, we investigate how games a chieve these experiences in the perspective of Actor Network Theory (ANT). Based on a qualitative data from a study of board games , computer games, and exergames, we conclude that games are actors that produce experiences by exercising power over the user’ s abilities, for example their cognitive...

  7. NATO Advanced Study Institute on Laser Interactions with Atoms, Solids,and Plasmas

    CERN Document Server

    1994-01-01

    The aim of this NATO Advanced Study Institute was to bring together scientists and students working in the field of laser matter interactions in order to review and stimulate developmentoffundamental science with ultra-short pulse lasers. New techniques of pulse compression and colliding-pulse mode-locking have made possible the construction of lasers with pulse lengths in the femtosecond range. Such lasers are now in operation at several research laboratories in Europe and the United States. These laser facilities present a new and exciting research direction with both pure and applied science components. In this ASI the emphasis is on fundamental processes occurring in the interaction of short laser pulses with atoms, molecules, solids, and plasmas. In the case of laser-atom (molecule) interactions, high power lasers provide the first access to extreme high-intensity conditions above 10'8 Watts/em', a new frontier for nonlinear interaction of photons with atoms and molecules. New phenomena observed include ...

  8. Modularity detection in protein-protein interaction networks

    Directory of Open Access Journals (Sweden)

    Narayanan Tejaswini

    2011-12-01

    Full Text Available Abstract Background Many recent studies have investigated modularity in biological networks, and its role in functional and structural characterization of constituent biomolecules. A technique that has shown considerable promise in the domain of modularity detection is the Newman and Girvan (NG algorithm, which relies on the number of shortest-paths across pairs of vertices in the network traversing a given edge, referred to as the betweenness of that edge. The edge with the highest betweenness is iteratively eliminated from the network, with the betweenness of the remaining edges recalculated in every iteration. This generates a complete dendrogram, from which modules are extracted by applying a quality metric called modularity denoted by Q. This exhaustive computation can be prohibitively expensive for large networks such as Protein-Protein Interaction Networks. In this paper, we present a novel optimization to the modularity detection algorithm, in terms of an efficient termination criterion based on a target edge betweenness value, using which the process of iterative edge removal may be terminated. Results We validate the robustness of our approach by applying our algorithm on real-world protein-protein interaction networks of Yeast, C.Elegans and Drosophila, and demonstrate that our algorithm consistently has significant computational gains in terms of reduced runtime, when compared to the NG algorithm. Furthermore, our algorithm produces modules comparable to those from the NG algorithm, qualitatively and quantitatively. We illustrate this using comparison metrics such as module distribution, module membership cardinality, modularity Q, and Jaccard Similarity Coefficient. Conclusions We have presented an optimized approach for efficient modularity detection in networks. The intuition driving our approach is the extraction of holistic measures of centrality from graphs, which are representative of inherent modular structure of the

  9. Evaluation and Comparison of the Configuration Interaction Calculations for Complex Atoms

    Directory of Open Access Journals (Sweden)

    Charlotte Froese Fischer

    2014-03-01

    Full Text Available Configuration interaction (CI methods are the method of choice for the determination of wave functions for complex atomic systems from which a variety of atomic properties may be computed. When applied to highly ionized atoms, where few, if any, energy levels from observed wavelengths are available, the question arises as to how a calculation may be evaluated. Many different codes are available for such calculations. Agreement between the results from different codes in itself is not a check on accuracy, but may be due to a similarity in the computational procedures. This paper reviews basic theory, which, when applied in a systematic manner, can be the basis for the evaluation of accuracy. Results will be illustrated in the study of 4s24p5 (odd and 4s24p44d (even levels in W39+ and the transitions between them.

  10. Effective atomic numbers and mass attenuation coefficients of some thermoluminescent dosimetric compounds for total photon interaction

    International Nuclear Information System (INIS)

    Effective atomic numbers for total gamma-ray interaction with some selected thermoluminescent dosimetric compounds such as barium acetate, barium sulfate, calcium carbonate, calcium sulfate, calcium sulfate dihydrate, cadmium sulfate (anhydrous), cadmium sulfate, strontium sulfate, and lithium fluoride have been calculated in the 1-keV to 20-MeV energy region. Experimental mass attenuation coefficients and effective atomic numbers for these compounds at selected photon energies of 26.3, 33.2, 59.54, and 661.6 keV have been obtained from good geometry transmission measurements and compared with theoretical values. The effect of absorption edge on effective atomic numbers and its variation with energy, and nonvalidity of the Bragg's mixture rule at incident photon energies closer to the absorption edges of constituent elements of compounds are discussed

  11. Hypervalent Nonbonded Interactions of a Divalent Sulfur Atom. Implications in Protein Architecture and the Functions

    Directory of Open Access Journals (Sweden)

    Noriyoshi Isozumi

    2012-06-01

    Full Text Available In organic molecules a divalent sulfur atom sometimes adopts weak coordination to a proximate heteroatom (X. Such hypervalent nonbonded S···X interactions can control the molecular structure and chemical reactivity of organic molecules, as well as their assembly and packing in the solid state. In the last decade, similar hypervalent interactions have been demonstrated by statistical database analysis to be present in protein structures. In this review, weak interactions between a divalent sulfur atom and an oxygen or nitrogen atom in proteins are highlighted with several examples. S···O interactions in proteins showed obviously different structural features from those in organic molecules (i.e., πO → σS* versus nO → σS* directionality. The difference was ascribed to the HOMO of the amide group, which expands in the vertical direction (πO rather than in the plane (nO. S···X interactions in four model proteins, phospholipase A2 (PLA2, ribonuclease A (RNase A, insulin, and lysozyme, have also been analyzed. The results suggested that S···X interactions would be important factors that control not only the three-dimensional structure of proteins but also their functions to some extent. Thus, S···X interactions will be useful tools for protein engineering and the ligand design.

  12. KNOWNET: Exploring Interactive Knowledge Networking across Insurance Supply Chains

    Directory of Open Access Journals (Sweden)

    Susan Grant

    2014-01-01

    Full Text Available Social media has become an extremely powerful phenomenon with millions of users who post status updates, blog, links and pictures on social networking sites such as Facebook, LinkedIn, and Twitter. However, social networking has so far spread mainly among consumers. Businesses are only now beginning to acknowledge the benefits of using social media to enhance employee and supplier collaboration to support new ideas and innovation through knowledge sharing across functions and organizational boundaries. Many businesses are still trying to understand the various implications of integrating internal communication systems with social media tools and private collaboration and networking platforms. Indeed, a current issue in organizations today is to explore the value of social media mechanisms across a range of functions within their organizations and across their supply chains.The KNOWNET project (an EC funded Marie Curie IAPP seeks to assess the value of social networking for knowledge exchange across Insurance supply chains. A key objective of the project being to develop and build a web based interactive environment - a Supplier Social Network or SSN, to support and facilitate exchange of good ideas, insights, knowledge, innovations etc across a diverse group of suppliers within a multi level supply chain within the Insurance sector.

  13. Interactive control over a programmable computer network using a multi-touch surface

    NARCIS (Netherlands)

    R.J. Strijkers; L. Muller; M.L. Cristea; R. Belleman; C. de Laat; P. Sloot; R. Meijer

    2009-01-01

    This article introduces the Interactive Network concept and describes the design and implementation of the first prototype. In an Interactive Network humans become an integral part of the control system to manage programmable networks and grid networks. The implementation consists of a multi-touch t

  14. Effective atomic numbers and electron densities of bioactive glasses for photon interaction

    Science.gov (United States)

    Shantappa, Anil; Hanagodimath, S. M.

    2015-08-01

    This work was carried out to study the nature of mass attenuation coefficient of bioactive glasses for gamma rays. Bioactive glasses are a group of synthetic silica-based bioactive materials with unique bone bonding properties. In the present study, we have calculated the effective atomic number, electron density for photon interaction of some selected bioactive glasses viz., SiO2-Na2O, SiO2-Na2O-CaO and SiO2-Na2O-P2O5 in the energy range 1 keV to 100 MeV. We have also computed the single valued effective atomic number by using XMuDat program. It is observed that variation in effective atomic number (ZPI, eff) depends also upon the weight fractions of selected bioactive glasses and range of atomic numbers of the elements. The results shown here on effective atomic number, electron density will be more useful in the medical dosimetry for the calculation of absorbed dose and dose rate.

  15. AtPIN: Arabidopsis thaliana Protein Interaction Network

    Directory of Open Access Journals (Sweden)

    Silva-Filho Marcio C

    2009-12-01

    Full Text Available Abstract Background Protein-protein interactions (PPIs constitute one of the most crucial conditions to sustain life in living organisms. To study PPI in Arabidopsis thaliana we have developed AtPIN, a database and web interface for searching and building interaction networks based on publicly available protein-protein interaction datasets. Description All interactions were divided into experimentally demonstrated or predicted. The PPIs in the AtPIN database present a cellular compartment classification (C3 which divides the PPI into 4 classes according to its interaction evidence and subcellular localization. It has been shown in the literature that a pair of genuine interacting proteins are generally expected to have a common cellular role and proteins that have common interaction partners have a high chance of sharing a common function. In AtPIN, due to its integrative profile, the reliability index for a reported PPI can be postulated in terms of the proportion of interaction partners that two proteins have in common. For this, we implement the Functional Similarity Weight (FSW calculation for all first level interactions present in AtPIN database. In order to identify target proteins of cytosolic glutamyl-tRNA synthetase (Cyt-gluRS (AT5G26710 we combined two approaches, AtPIN search and yeast two-hybrid screening. Interestingly, the proteins glutamine synthetase (AT5G35630, a disease resistance protein (AT3G50950 and a zinc finger protein (AT5G24930, which has been predicted as target proteins for Cyt-gluRS by AtPIN, were also detected in the experimental screening. Conclusions AtPIN is a friendly and easy-to-use tool that aggregates information on Arabidopsis thaliana PPIs, ontology, and sub-cellular localization, and might be a useful and reliable strategy to map protein-protein interactions in Arabidopsis. AtPIN can be accessed at http://bioinfo.esalq.usp.br/atpin.

  16. Spin-orbit interactions and quantum spin dynamics in cold ion-atom collisions

    CERN Document Server

    Tscherbul, Timur V; Buchachenko, Alexei A

    2015-01-01

    We present accurate ab initio and quantum scattering calculations on a prototypical hybrid ion-atom system Yb$^+$-Rb, recently suggested as a promising candidate for the experimental study of open quantum systems, quantum information processing, and quantum simulation. We identify the second-oder spin-orbit (SO) interaction as the dominant source of hyperfine relaxation and decoherence in cold Yb$^+$-Rb collisions. Our results are in good agreement with recent experimental observations [L. Ratschbacher et al., Phys. Rev. Lett. 110, 160402 (2013)] of hyperfine relaxation rates of trapped Yb$^+$ immersed in an ultracold Rb gas. The calculated rates are 4 times smaller than predicted by the Langevin capture theory and display a weak $T^{-0.3}$ temperature dependence, indicating significant deviations from statistical behavior. Our analysis underscores the deleterious nature of the SO interaction and implies that light ion-atom combinations such as Yb$^+$-Li should be used to minimize hyperfine relaxation and dec...

  17. Partial as Well as Total Photon Interaction Effective Atomic Numbers for Some Concretes

    Directory of Open Access Journals (Sweden)

    Tejbir Singh

    2013-08-01

    Full Text Available Photon interaction effective atomic number (Zeff for partial as well as total photon interaction processes has been computed using logarithmic interpolation method for seven different concretes viz. (i Ordinary, (ii Hematite - Serpentine, (iii Ilmenite - Limonite, (iv Basalt - magnetite, (v Ilmenite, (vi Steel - scrap and (vii Steel - magnetite concrete in the wide energy range from 10.0 keV to 100 GeV. It has been concluded that this method has an advantage over the atomic to electronic cross-section ratio method especially for mixtures in the intermediate energy level. However, due to lack of experimental data in the higher energy region, it is difficult to discuss, its validity in these energy regions.

  18. Solving the self-interaction problem in Kohn-Sham density functional theory: Application to atoms

    Science.gov (United States)

    Däne, M.; Gonis, A.; Nicholson, D. M.; Stocks, G. M.

    2015-04-01

    In previous work, we proposed a computational methodology that addresses the elimination of the self-interaction error from the Kohn-Sham formulation of the density functional theory. We demonstrated how the exchange potential can be obtained, and presented results of calculations for atomic systems up to Kr carried out within a Cartesian coordinate system. In this paper, we provide complete details of this self-interaction free method formulated in spherical coordinates based on the explicit equidensity basis ansatz. We prove analytically that derivatives obtained using this method satisfy the Virial theorem for spherical orbitals, where the problem can be reduced to one dimension. We present the results of calculations of ground-state energies of atomic systems throughout the periodic table carried out within the exchange-only mode.

  19. Fermi orbital derivatives in self-interaction corrected density functional theory: Applications to closed shell atoms.

    Science.gov (United States)

    Pederson, Mark R

    2015-02-14

    A recent modification of the Perdew-Zunger self-interaction-correction to the density-functional formalism has provided a framework for explicitly restoring unitary invariance to the expression for the total energy. The formalism depends upon construction of Löwdin orthonormalized Fermi-orbitals which parametrically depend on variational quasi-classical electronic positions. Derivatives of these quasi-classical electronic positions, required for efficient minimization of the self-interaction corrected energy, are derived and tested, here, on atoms. Total energies and ionization energies in closed-shell singlet atoms, where correlation is less important, using the Perdew-Wang 1992 Local Density Approximation (PW92) functional, are in good agreement with experiment and non-relativistic quantum-Monte-Carlo results albeit slightly too low. PMID:25681892

  20. Fermi Orbital Derivatives in Self-Interaction Corrected Density Functional Theory: Applications to Closed Shell Atoms

    CERN Document Server

    Pederson, Mark R

    2014-01-01

    A recent modification of the Perdew-Zunger self-interaction-correction (SIC) to the density-functional formalism (Pederson, Ruzsinszky, Perdew) has provided a framework for explicitly restoring unitary invariance to the expression for the total energy. The formalism depends upon construction of Lowdin orthonormalized Fermi-orbitals (Luken et al) which parametrically depend on variational quasi-classical electronic positions. Derivatives of these quasi-classical electronic positions, required for efficient minimization of the self-interaction corrected energy, are derived and tested here on atoms. Total energies and ionization energies in closed-shell atoms, where correlation is less important, using the PW92 LDA functional are in very good to excellent agreement with experiment and non-relativistic Quantum-Monte-Carlo (QMC) results.

  1. Quantitative measurement of tip-sample interactions in amplitude modulation atomic force microscopy

    Science.gov (United States)

    Hölscher, H.

    2006-09-01

    The author introduces an algorithm for the reconstruction of the tip-sample interactions in amplitude modulation atomic force microscopy ("tapping mode"). The method is based on the recording of amplitude and phase versus distance curves and allows the reconstruction of tip-sample force and energy dissipation as a function of the actual tip-sample distance. The proposed algorithm is verified by a numerical simulation and applied to a silicon sample in ambient conditions.

  2. Entanglement swapping without joint measurement via a Λ-type atom interacting with bimodal cavity field

    Institute of Scientific and Technical Information of China (English)

    Lin Xiu; Li Hong-Cai; Yang Rong-Can; Huang Zhi-Ping

    2007-01-01

    This paper proposes a scheme for realizing entanglement swapping in cavity QED. The scheme is based on the resonant interaction of a two-mode cavity field with a A-type three-level atom. In contrast with the previously proposed schemes, the present scheme is ascendant, since the fidelity is 1.0 and the joint measurement isn't needed. And the scheme is experimentally feasible based on the current cavity QED technique.

  3. The correlation between fragility, density and atomic interaction in glass-forming liquids

    OpenAIRE

    Wang, Lijin; Guan, Pengfei; Wang, W. H.

    2016-01-01

    The fragility, that controls the temperature-dependent viscous properties of liquids as the glass transition is approached, in various glass-forming liquids with different atomic interactions and densities is investigated by molecular dynamic simulations. We show the landscape of fragility in purely repulsive systems can be separated into three regions with qualitatively disparate dynamic behaviors, suggesting that the density plays an unexpected role for understanding the repulsive steepness...

  4. FAST TRACK COMMUNICATION: Two interacting atoms in a cavity: exact solutions, entanglement and decoherence

    Science.gov (United States)

    Torres, J. M.; Sadurní, E.; Seligman, T. H.

    2010-05-01

    We address the problem of two interacting atoms of different species inside a cavity and find the explicit solutions of the corresponding eigenvalues and eigenfunctions using a new variant. This model encompasses various commonly used models. By way of example we obtain closed expressions for concurrence and purity as a function of time for the case where the cavity is prepared in a number state. We discuss the behaviour of these quantities and their relative behaviour in the concurrence-purity plane.

  5. Interaction of Triply-Dressing Electromagnetically Induced Transparency in Five-level Folding Atomic System

    Institute of Scientific and Technical Information of China (English)

    LI Chang-Biao; NIE Zhi-Qiang; ZHANG Wei-Feng; ZHANG Yan-Peng; SONG Jian-Ping; LI Yuan-Yuan; LU Ke-Qing

    2008-01-01

    @@ We consider a five-level atomic folding system, which involve two kinds of dressing mechanisms (the nested-cascade and the sequential-cascade) in interaction of three-dressing fields, the numerical results show that three-dressing fields are interchangeable under certain conditions, which can be considered as two four-level sub-system configurations (a nested-cascade N configuration and a sequential-cascade inverted-Y configuration).

  6. Intense laser interacting with a two level atom: WKB expressions for dipole transitions and population inversion

    OpenAIRE

    Lejarreta, J. D.; Cervero, J. M.

    2001-01-01

    In a previous paper, we have already considered the system composed by a two level atom interacting with a coherent external electromagnetic field. No application whatsoever has been made of the rotating wave approximation. Being specially interested in the problem of higher harmonic generations for the case of very intense laser fields, we have developed in this letter a much more efficient way to obtain these solutions as well as to carry out some calculations in a range in which the parame...

  7. Oligomeric protein structure networks: insights into protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Brinda KV

    2005-12-01

    Full Text Available Abstract Background Protein-protein association is essential for a variety of cellular processes and hence a large number of investigations are being carried out to understand the principles of protein-protein interactions. In this study, oligomeric protein structures are viewed from a network perspective to obtain new insights into protein association. Structure graphs of proteins have been constructed from a non-redundant set of protein oligomer crystal structures by considering amino acid residues as nodes and the edges are based on the strength of the non-covalent interactions between the residues. The analysis of such networks has been carried out in terms of amino acid clusters and hubs (highly connected residues with special emphasis to protein interfaces. Results A variety of interactions such as hydrogen bond, salt bridges, aromatic and hydrophobic interactions, which occur at the interfaces are identified in a consolidated manner as amino acid clusters at the interface, from this study. Moreover, the characterization of the highly connected hub-forming residues at the interfaces and their comparison with the hubs from the non-interface regions and the non-hubs in the interface regions show that there is a predominance of charged interactions at the interfaces. Further, strong and weak interfaces are identified on the basis of the interaction strength between amino acid residues and the sizes of the interface clusters, which also show that many protein interfaces are stronger than their monomeric protein cores. The interface strengths evaluated based on the interface clusters and hubs also correlate well with experimentally determined dissociation constants for known complexes. Finally, the interface hubs identified using the present method correlate very well with experimentally determined hotspots in the interfaces of protein complexes obtained from the Alanine Scanning Energetics database (ASEdb. A few predictions of interface hot

  8. Effects of the Lorentz invariance violation in Coulomb interaction in nuclei and atoms

    CERN Document Server

    Flambaum, V V

    2016-01-01

    Anisotropy in the speed of light (studied in the Michelson-Morley experiment ) generates anisotropy in the Coulomb interaction. This anisotropy manifests itself in the nuclear and atomic experiments. The experimental results for 21Ne are used to improve the limits on the tensor components characterising the asymmetry of the speed of light and the Coulomb interaction (violation of the Lorentz symmetry in the photon sector) by 7 orders of magnitude in comparison with previous experiments: the speed of light is isotropic to a part in 10E-28.

  9. Intrinsic decoherence in the interaction of two fields with a two-level atom

    Energy Technology Data Exchange (ETDEWEB)

    Juarez-Amaro, R. [Universidad Tecnologica de la Mixteca, Mexico (Mexico); INAOE, Puebla (Mexico); Escudero-Jimenez, J.L. [INAOE, Puebla (Mexico); Moya-Cessa, H.

    2009-06-15

    We study the interaction of a two-level atom and two fields, one of them classical. We obtain an effective Hamiltonian for this system by using a method recently introduced that produces a small rotation to the Hamiltonian that allows to neglect some terms in the rotated Hamiltonian. Then we solve a variation of the Schroedinger equation that models decoherence as the system evolves through intrinsic mechanisms beyond conventional quantum mechanics rather than dissipative interaction with an environment. (Abstract Copyright [2009], Wiley Periodicals, Inc.)

  10. Intrinsic Decoherence of a Two-Atom System with Dipole-Dipole Interaction

    Institute of Scientific and Technical Information of China (English)

    QI Lin-Na; ZHU Ai-Dong; ZHANG Shou

    2008-01-01

    @@ We investigate the effect of dipole-dipole interaction on the intrinsic decoherence of a system which consists of two two-level atoms and an optical cavity. The entanglement of the system is calculated by making use of concurrence. Our results show that the appropriate choice for the coupling constant Ω of dipole-dipole interaction can restrain the intrinsic decoherence of the system. We also find a special phenomenon. No matter what the value of γ is, the concurrence of system slowly increases and cannot exceed 0.71 when Ω= 1.

  11. Spin Diffusion in Trapped Clouds of Cold Atoms with Resonant Interactions

    DEFF Research Database (Denmark)

    Bruun, Georg Morten; Pethick, C. J.

    2011-01-01

    We show that puzzling recent experimental results on spin diffusion in a strongly interacting atomic gas may be understood in terms of the predicted spin diffusion coefficient for a generic strongly interacting system. Three important features play a central role: (a) Fick’s law for diffusion mus...... be modified to allow for the trapping potential; (b) the diffusion coefficient is inhomogeneous, due to the density variations in the cloud; and (c) the diffusion approximation fails in the outer parts of the cloud, where the mean free path is long....

  12. Quantum computing with atomic qubits and Rydberg interactions: progress and challenges

    Science.gov (United States)

    Saffman, M.

    2016-10-01

    We present a review of quantum computation with neutral atom qubits. After an overview of architectural options and approaches to preparing large qubit arrays we examine Rydberg mediated gate protocols and fidelity for two- and multi-qubit interactions. Quantum simulation and Rydberg dressing are alternatives to circuit based quantum computing for exploring many body quantum dynamics. We review the properties of the dressing interaction and provide a quantitative figure of merit for the complexity of the coherent dynamics that can be accessed with dressing. We conclude with a summary of the current status and an outlook for future progress.

  13. Long-range interacting many-body systems with alkaline-earth-metal atoms

    CERN Document Server

    Olmos, B; Singh, Y; Schreck, F; Bongs, K; Lesanovsky, I

    2012-01-01

    Alkaline-earth-metal atoms exhibit long-range dipolar interactions, which are generated via the coherent exchange of photons on the 3P_0-3D_1-transition of the triplet manifold. In case of bosonic strontium, which we discuss here, this transition has a wavelength of 2.7 \\mu m and a dipole moment of 2.46 Debye, and there exists a magic wavelength permitting the creation of optical lattices that are identical for the states 3P_0 and 3D_1. This interaction enables the realization and study of mixtures of hard-core lattice bosons featuring long-range hopping, with tuneable disorder and anisotropy. We derive the many-body Master equation, investigate the dynamics of excitation transport and analyze spectroscopic signatures stemming from coherent long-range interactions and collective dissipation. Our results show that lattice gases of alkaline-earth-metal atoms permit the creation of long-lived collective atomic states and constitute a simple and versatile platform for the exploration of many-body systems with lon...

  14. Measuring Asymmetric Interactions in Resting State Brain Networks.

    Science.gov (United States)

    Joshi, Anand A; Salloum, Ronald; Bhushan, Chitresh; Leahy, Richard M

    2015-01-01

    Directed graph representations of brain networks are increasingly being used to indicate the direction and level of influence among brain regions. Most of the existing techniques for directed graph representations are based on time series analysis and the concept of causality, and use time lag information in the brain signals. These time lag-based techniques can be inadequate for functional magnetic resonance imaging (fMRI) signal analysis due to the limited time resolution of fMRI as well as the low frequency hemodynamic response. The aim of this paper is to present a novel measure of necessity that uses asymmetry in the joint distribution of brain activations to infer the direction and level of interaction among brain regions. We present a mathematical formula for computing necessity and extend this measure to partial necessity, which can potentially distinguish between direct and indirect interactions. These measures do not depend on time lag for directed modeling of brain interactions and therefore are more suitable for fMRI signal analysis. The necessity measures were used to analyze resting state fMRI data to determine the presence of hierarchy and asymmetry of brain interactions during resting state. We performed ROI-wise analysis using the proposed necessity measures to study the default mode network. The empirical joint distribution of the fMRI signals was determined using kernel density estimation, and was used for computation of the necessity and partial necessity measures. The significance of these measures was determined using a one-sided Wilcoxon rank-sum test. Our results are consistent with the hypothesis that the posterior cingulate cortex plays a central role in the default mode network. PMID:26221690

  15. Interactions between fluorescence of atomically layered graphene oxide and metallic nanoparticles

    Science.gov (United States)

    Wang, Yu; Li, Shao-Sian; Yeh, Yun-Chieh; Yu, Chen-Chieh; Chen, Hsuen-Li; Li, Feng-Chieh; Chang, Yu-Ming; Chen, Chun-Wei

    2013-01-01

    Graphene oxide (GO) demonstrates interesting photoluminescence (PL) because of its unique heterogeneous atomic structure, which consists of variable sp2- and sp3-bonded carbons. In this study, we report the interaction between the luminescence of GO ranging from a single atomic layer to few-layered thin films and localized surface plasmon resonance (LSPR) from silver nanoparticles (Ag NPs). The photoluminescence of GO in the vicinity of the Ag NPs is enhanced significantly due to the near-field plasmonic effect by coupling electron-hole pairs of GO with oscillating electrons in Ag NPs, leading to an increased PL intensity and a decreased PL decay lifetime. The maxima 30-fold enhancement in PL intensity is obtained with an optimized film thickness of GO, and the luminescence image from a single atomic layer GO sheet is successfully observed with the assistance of the LSPR effect. The results provide an ideal platform for exploring the interactions between the fluorescence of two-dimensional layered materials and the LSPR effect.Graphene oxide (GO) demonstrates interesting photoluminescence (PL) because of its unique heterogeneous atomic structure, which consists of variable sp2- and sp3-bonded carbons. In this study, we report the interaction between the luminescence of GO ranging from a single atomic layer to few-layered thin films and localized surface plasmon resonance (LSPR) from silver nanoparticles (Ag NPs). The photoluminescence of GO in the vicinity of the Ag NPs is enhanced significantly due to the near-field plasmonic effect by coupling electron-hole pairs of GO with oscillating electrons in Ag NPs, leading to an increased PL intensity and a decreased PL decay lifetime. The maxima 30-fold enhancement in PL intensity is obtained with an optimized film thickness of GO, and the luminescence image from a single atomic layer GO sheet is successfully observed with the assistance of the LSPR effect. The results provide an ideal platform for exploring the

  16. The entanglement of two dipole-dipole coupled atoms interacting with a thermal field via a two-photon process

    Institute of Scientific and Technical Information of China (English)

    Liao Xiang-Ping; Fang Mao-Fa; Cai Jian-Wu; Zheng Xiao-Juan

    2008-01-01

    This paper studies entanglement between two dipole-dipole coupled atoms interacting with a thermal field via a two-photon process. It shows that the entanglement is dependent on the mean photon number of the thermal field and the dipole-dipole interaction. The results also show that the atom-atom entanglement through the two-photon process is larger than that through the one-photon process and a remarkable amount of entanglement between the atoms still remains at certain times even for a very highly noisy thermal field.

  17. Fractional Dynamics of Network Growth Constrained by Aging Node Interactions.

    Directory of Open Access Journals (Sweden)

    Hadiseh Safdari

    Full Text Available In many social complex systems, in which agents are linked by non-linear interactions, the history of events strongly influences the whole network dynamics. However, a class of "commonly accepted beliefs" seems rarely studied. In this paper, we examine how the growth process of a (social network is influenced by past circumstances. In order to tackle this cause, we simply modify the well known preferential attachment mechanism by imposing a time dependent kernel function in the network evolution equation. This approach leads to a fractional order Barabási-Albert (BA differential equation, generalizing the BA model. Our results show that, with passing time, an aging process is observed for the network dynamics. The aging process leads to a decay for the node degree values, thereby creating an opposing process to the preferential attachment mechanism. On one hand, based on the preferential attachment mechanism, nodes with a high degree are more likely to absorb links; but, on the other hand, a node's age has a reduced chance for new connections. This competitive scenario allows an increased chance for younger members to become a hub. Simulations of such a network growth with aging constraint confirm the results found from solving the fractional BA equation. We also report, as an exemplary application, an investigation of the collaboration network between Hollywood movie actors. It is undubiously shown that a decay in the dynamics of their collaboration rate is found, even including a sex difference. Such findings suggest a widely universal application of the so generalized BA model.

  18. Attractive interactions among intermediate filaments determine network mechanics in vitro.

    Directory of Open Access Journals (Sweden)

    Paul Pawelzyk

    Full Text Available Mechanical and structural properties of K8/K18 and vimentin intermediate filament (IF networks have been investigated using bulk mechanical rheometry and optical microrheology including diffusing wave spectroscopy and multiple particle tracking. A high elastic modulus G0 at low protein concentration c, a weak concentration dependency of G0 (G0 ∼ c(0.5 ± 0.1 and pronounced strain stiffening are found for these systems even without external crossbridgers. Strong attractive interactions among filaments are required to maintain these characteristic mechanical features, which have also been reported for various other IF networks. Filament assembly, the persistence length of the filaments and the network mesh size remain essentially unaffected when a nonionic surfactant is added, but strain stiffening is completely suppressed, G0 drops by orders of magnitude and exhibits a scaling G0 ∼ c(1.9 ± 0.2 in agreement with microrheological measurements and as expected for entangled networks of semi-flexible polymers. Tailless K8Δ/K18ΔT and various other tailless filament networks do not exhibit strain stiffening, but still show high G0 values. Therefore, two binding sites are proposed to exist in IF networks. A weaker one mediated by hydrophobic amino acid clusters in the central rod prevents stretched filaments between adjacent cross-links from thermal equilibration and thus provides the high G0 values. Another strong one facilitating strain stiffening is located in the tail domain with its high fraction of hydrophobic amino acid sequences. Strain stiffening is less pronounced for vimentin than for K8/K18 due to electrostatic repulsion forces partly compensating the strong attraction at filament contact points.

  19. Interaction between single gold atom and the graphene edge: A study via aberration-corrected transmission electron microscopy

    KAUST Repository

    Wang, Hongtao

    2012-01-01

    Interaction between single noble metal atoms and graphene edges has been investigated via aberration-corrected and monochromated transmission electron microscopy. A collective motion of the Au atom and the nearby carbon atoms is observed in transition between energy-favorable configurations. Most trapping and detrapping processes are assisted by the dangling carbon atoms, which are more susceptible to knock-on displacements by electron irradiation. Thermal energy is lower than the activation barriers in transition among different energy-favorable configurations, which suggests electron-beam irradiation can be an efficient way of engineering the graphene edge with metal atoms. © 2012 The Royal Society of Chemistry.

  20. Higher-Order Synaptic Interactions Coordinate Dynamics in Recurrent Networks.

    Science.gov (United States)

    Chambers, Brendan; MacLean, Jason N

    2016-08-01

    Linking synaptic connectivity to dynamics is key to understanding information processing in neocortex. Circuit dynamics emerge from complex interactions of interconnected neurons, necessitating that links between connectivity and dynamics be evaluated at the network level. Here we map propagating activity in large neuronal ensembles from mouse neocortex and compare it to a recurrent network model, where connectivity can be precisely measured and manipulated. We find that a dynamical feature dominates statistical descriptions of propagating activity for both neocortex and the model: convergent clusters comprised of fan-in triangle motifs, where two input neurons are themselves connected. Fan-in triangles coordinate the timing of presynaptic inputs during ongoing activity to effectively generate postsynaptic spiking. As a result, paradoxically, fan-in triangles dominate the statistics of spike propagation even in randomly connected recurrent networks. Interplay between higher-order synaptic connectivity and the integrative properties of neurons constrains the structure of network dynamics and shapes the routing of information in neocortex. PMID:27542093

  1. An Interactive Network Laboratory for Electronic Engineering Education

    Institute of Scientific and Technical Information of China (English)

    Shao-Chun Fan; Jian-Jun Jiang; Wen-Qing Liu

    2007-01-01

    The advantage of the network laboratory is the better flexibility of lab experiments by allowing remote control from different locations at a freely chosen time. In engineering education, the work should not only be focused on the technical realization of virtual or remote access experiments, but also on the achievement of its pedagogical goals. In this paper, an interactive laboratory is introduced which is based on the online tutoring system, virtual and remote access experiments. It has been piloted in the Department of Electronic Science and Technology, HUST. Some pedagogical issues for electronic engineering laboratory design, the development of a multi-server-based distributed architecture for the reduction of network latency and implementations of the function module are presented. Finally, the system is proved valid by an experiment.

  2. Supply Chain Management: from Linear Interactions to Networked Processes

    Directory of Open Access Journals (Sweden)

    Doina FOTACHE

    2006-01-01

    Full Text Available Supply Chain Management is a distinctive product, with a tremendous impact on the software applications market. SCM applications are back-end solutions intended to link suppliers, manufacturers, distributors and resellers in a production and distribution network, which allows the enterprise to track and consolidate the flows of materials and data trough the process of manufacturing and distribution of goods/services. The advent of the Web as a major means of conducting business transactions and business-tobusiness communications, coupled with evolving web-based supply chain management (SCM technology, has resulted in a transition period from “linear” supply chain models to "networked" supply chain models. The technologies to enable dynamic process changes and real time interactions between extended supply chain partners are emerging and being deployed at an accelerated pace.

  3. Quantum networks with chiral light--matter interaction in waveguides

    CERN Document Server

    Mahmoodian, Sahand; Sørensen, Anders S

    2016-01-01

    We design and analyze a simple on-chip photonic circuit that can form a universal building block of a quantum network. The circuit consists of a single-photon source, and two quantum emitters positioned in two arms of an on-chip Mach-Zehnder interferometer composed of waveguides with chiral light--matter interfaces. The efficient chiral light--matter interaction allows the emitters to act as photon sources to herald internode entanglement, and to perform high-fidelity intranode two-qubit gates within a single chip without any need for reconfiguration. We show that by connecting multiple circuits of this kind into a quantum network, it is possible to perform universal quantum computation with heralded two-qubit gate fidelities ${\\cal F} \\sim 0.998$ achievable in state-of-the-art quantum dot systems.

  4. Adding protein context to the human protein-protein interaction network to reveal meaningful interactions.

    Directory of Open Access Journals (Sweden)

    Martin H Schaefer

    Full Text Available Interactions of proteins regulate signaling, catalysis, gene expression and many other cellular functions. Therefore, characterizing the entire human interactome is a key effort in current proteomics research. This challenge is complicated by the dynamic nature of protein-protein interactions (PPIs, which are conditional on the cellular context: both interacting proteins must be expressed in the same cell and localized in the same organelle to meet. Additionally, interactions underlie a delicate control of signaling pathways, e.g. by post-translational modifications of the protein partners - hence, many diseases are caused by the perturbation of these mechanisms. Despite the high degree of cell-state specificity of PPIs, many interactions are measured under artificial conditions (e.g. yeast cells are transfected with human genes in yeast two-hybrid assays or even if detected in a physiological context, this information is missing from the common PPI databases. To overcome these problems, we developed a method that assigns context information to PPIs inferred from various attributes of the interacting proteins: gene expression, functional and disease annotations, and inferred pathways. We demonstrate that context consistency correlates with the experimental reliability of PPIs, which allows us to generate high-confidence tissue- and function-specific subnetworks. We illustrate how these context-filtered networks are enriched in bona fide pathways and disease proteins to prove the ability of context-filters to highlight meaningful interactions with respect to various biological questions. We use this approach to study the lung-specific pathways used by the influenza virus, pointing to IRAK1, BHLHE40 and TOLLIP as potential regulators of influenza virus pathogenicity, and to study the signalling pathways that play a role in Alzheimer's disease, identifying a pathway involving the altered phosphorylation of the Tau protein. Finally, we provide the

  5. Phase transitions due to interaction between photons and atoms in a cavity system

    CERN Document Server

    Shirai, Tatsuhiko; Miyashita, Seiji

    2012-01-01

    We survey phenomena of a cavity system in which many atoms coherently interact with a single quantized photon mode driven by the AC external field in a dissipative environment. It has been known that a strongly external field causes the so-called optical bistability which is a non-equilibrium phase transition for the balance of excitation and dissipation. On the other hand, a strong interaction causes the Dicke transition, which is a phase transition with a spontaneous appearance of excitations of atoms and photons in the equilibrium system as a consequence of the cooperative phenomena. We study the phenomena in full range of the strength of the interaction and the external field, and present a phase diagram of the stationary state. For the strong interaction region, in order to realize the ground state, appropriate form of the dissipative mechanism in the master equation is necessary instead of the conventional Lindblad form. We provide such an extended master equation. Moreover, the rotating wave approximat...

  6. Atoms in optical networks. A simple tridimensional model; Atomos en redes opticas. Un modelo tridimensional sencillo

    Energy Technology Data Exchange (ETDEWEB)

    Balleza D, E

    2004-07-01

    In the first chapter of this work we will show a detailed analysis of the one cooling Doppler phenomenon that appears when a laser induces a dipolar moment to the atoms in such a way that these may interact with him to transfer moment to the field with the subsequent decrease of kinetic energy that macroscopically it is translated in cooling of the atomic cloud. When the experiments of atomic cooling were carried out it was observed that the temperature was smaller to the one than it predicted the cooling Doppler, this originates the creation of a theory but it dies in which the over simplification is eliminated that the alone atom consists of two energy levels and levels are introduced of it structures fine that are able to explain the extra cooling. To this phenomenon it is called Sisifo effect and it is studied detailedly in the chapter two. The first two chapters talk each other about the atomic cooling, but it stops that the atomic cloud can be manipulated, before being confined, problem that we will expose in the chapter three with experimental solutions that at the moment they are implemented in the laboratories around the world. In particular we will concentrate on the traps FORT (Far Off Resonance Trap, trap very outside of resonance) that confine to the atoms in optic nets. The lasers gaussianos originate a potential sinusoidal along the propagation address and gaussiano in the perpendicular plane to this. In the I surrender four he/she intends a three-dimensional model that substitutes To the variation sinusoidal for a function crenel and he/she makes an approach To first order in the radial dependence to obtain an oscillator potential Harmonic instead of the gaussiano that you taenia. The pattern is solved in a similar way To the pattern unidimensional of bands: they are the functions of wave solution For every period and they are coupled among if so that they satisfy conditions of rhythm, When making this you arrives to a womb that couples the

  7. Interaction-free measurement of the degree of polarization of an atomic ensemble

    International Nuclear Information System (INIS)

    Full text: In the last years, several proposals for quantum information and quantum communication schemes require the use of atomic media together with single photons. Among the possible interactions, much interest has been generated by non destructive techniques, like the quantum non-demolition measurement. We present here instead a characterization of the polarization state of an atomic sample via the non-interaction of our sample with the probe, thus reducing, in principle, the damage to the sample for successful event to zero. The term 'interaction-free' applies to a measurement process where the probe carries information about a system without interacting with it, possible thanks to the quantum nature of the interference process. After the proposal of Elitzur and Vaidman, an experimental demonstration was provided by Kwiat et al.. We have realized an interaction free measurement of the spectrum and polarization state of a hot ensemble of 87Rb by inserting it in a polarization interferometer, where a different optical density for one of the polarization modes is revealed by detection of light at the output dark in the balanced case The probe is a narrowband coherent light, strongly attenuated to the single photon level, with a central frequency that can be scanned by some GHz in the region of the Rb D1 line. The atoms are optically pumped by an intense beam into the mF =1,2 Zeeman substates of the F=2 hyperfine level. Observing the output of the dark port while scanning the probe frequency, the obtained trace presents a peak in correspondence with the transitions involving the hyperfine ground level F=2. The profile of the trace corresponds to the profile of the transition, power broadened by the intense pumping necessary for polarization. The demonstrated scheme suffers from limited statistical efficiency, equal to 1/4 in theory and further reduced because of experimental imperfections. It has been demonstrated that combining the interaction free measurement

  8. Atomic oxygen interactions with protected organic materials on the Long Duration Exposure Facility (LDEF)

    Science.gov (United States)

    Banks, Bruce A.; Degroh, Kim K.; Bucholz, Justine L.; Cales, Michael R.

    1995-01-01

    The Long Duration Exposure Facility (LDEF) has provided an excellent opportunity to understand the nature of directed atomic oxygen interactions with protected polymers and composites. Although there were relatively few samples of materials with protective coatings on their external surfaces on LDEF which were exposed to a high atomic oxygen fluence, analysis of such samples has enabled an examination of the shape of atomic oxygen undercut cavities at defect sites in the protective coatings. Samples of front-surface aluminized (Kapton) polyimide were inspected by scanning electron microscopy to identify and measure crack defects in the aluminum protective coatings. After chemical removal of the aluminum coating, measurements were also made of the width of the oxidized undercut cavities below the crack defects. The LDEF flight undercut cavity geometries were then compared with Monte Carlo computational model undercut cavity predictions. The comparison of the LDEF results and computational modeling indicates agreement in specific undercut cavity geometries for atomic oxygen reaction probabilities dependent upon the 0.68 to 3.0 power of the energy. However, no single energy dependency was adequate to replicate flight results over a variety of aluminum crack widths.

  9. Visualization of protein interaction networks: problems and solutions

    Directory of Open Access Journals (Sweden)

    Agapito Giuseppe

    2013-01-01

    Full Text Available Abstract Background Visualization concerns the representation of data visually and is an important task in scientific research. Protein-protein interactions (PPI are discovered using either wet lab techniques, such mass spectrometry, or in silico predictions tools, resulting in large collections of interactions stored in specialized databases. The set of all interactions of an organism forms a protein-protein interaction network (PIN and is an important tool for studying the behaviour of the cell machinery. Since graphic representation of PINs may highlight important substructures, e.g. protein complexes, visualization is more and more used to study the underlying graph structure of PINs. Although graphs are well known data structures, there are different open problems regarding PINs visualization: the high number of nodes and connections, the heterogeneity of nodes (proteins and edges (interactions, the possibility to annotate proteins and interactions with biological information extracted by ontologies (e.g. Gene Ontology that enriches the PINs with semantic information, but complicates their visualization. Methods In these last years many software tools for the visualization of PINs have been developed. Initially thought for visualization only, some of them have been successively enriched with new functions for PPI data management and PIN analysis. The paper analyzes the main software tools for PINs visualization considering four main criteria: (i technology, i.e. availability/license of the software and supported OS (Operating System platforms; (ii interoperability, i.e. ability to import/export networks in various formats, ability to export data in a graphic format, extensibility of the system, e.g. through plug-ins; (iii visualization, i.e. supported layout and rendering algorithms and availability of parallel implementation; (iv analysis, i.e. availability of network analysis functions, such as clustering or mining of the graph, and the

  10. Upper Secondary Students' Understanding of the Basic Physical Interactions in Analogous Atomic and Solar Systems

    Science.gov (United States)

    Taber, Keith S.

    2013-08-01

    Comparing the atom to a `tiny solar system' is a common teaching analogy, and the extent to which learners saw the systems as analogous was investigated. English upper secondary students were asked parallel questions about the physical interactions between the components of a simple atomic system and a simple solar system to investigate how they understood the forces acting within the two systems. A sample of just over 100 across the 15-18 age range responded to a pencil-and-paper instrument that asked about four aspects of the two systems. It was found that for both systems, about four fifths of students expected forces to decrease with increasing distance; but that only a little over half expected there to be interactions between the minor constituents (electrons and planets). Most students failed to apply Newton's third law to either system. There was a considerable difference in the extent to which respondents were able to identify the type of force acting in the systems (nearly all for the solar system, but only a small proportion in the case of the atom). The findings are considered in terms of both the limitations of students' understanding of the basic physics and possible implications for the use of the teaching analogy.

  11. Direct measurement of the van der Waals interaction between two single atoms

    CERN Document Server

    Béguin, Lucas; Chicireanu, Radu; Lahaye, Thierry; Browaeys, Antoine

    2013-01-01

    We report on the direct measurement of the van der Waals interaction between two isolated, single Rydberg atoms separated by a controlled distance of a few micrometers. By working in a regime where the single-atom Rabi frequency of the laser used for excitation to the Rydberg state is comparable to the interaction energy, we observe a \\emph{partial} Rydberg blockade, whereby the time-dependent populations of the various two-atom states exhibit coherent oscillations with several frequencies. A quantitative comparison of the data with a simple model based on the optical Bloch equations allows us to extract the van der Waals energy, and to observe its characteristic $C_6/R^6$ dependence. The magnitude of the measured $C_6$ coefficient agrees well with an \\emph{ab-initio} theoretical calculation, and we observe its dramatic increase with the principal quantum number $n$ of the Rydberg state. Our results not only allow to test an important physical law, but also demonstrate a degree of experimental control which o...

  12. Opinion dynamics on interacting networks: media competition and social influence

    OpenAIRE

    Quattrociocchi, Walter; Caldarelli, Guido; Scala, Antonio

    2014-01-01

    The inner dynamics of the multiple actors of the informations systems – i.e, T.V., newspapers, blogs, social network platforms, – play a fundamental role on the evolution of the public opinion. Coherently with the recent history of the information system (from few main stream media to the massive diffusion of socio-technical system), in this work we investigate how main stream media signed interaction might shape the opinion space. In particular we focus on how different size (in the number o...

  13. Games as Actors - Interaction, Play, Design, and Actor Network Theory

    DEFF Research Database (Denmark)

    Jessen, Jari Due; Jessen, Carsten

    2014-01-01

    data from a study of board games , computer games, and exergames, we conclude that games are actors that produce experiences by exercising power over the user’ s abilities, for example their cognitive functions. Games are designed to take advantage of the characteristics of the human players......When interacting with computer games, users are forced to follow the rules of the game in return for the excitement, joy, fun, or other pursued experiences. In this paper, we investigate how games a chieve these experiences in the perspective of Actor Network Theory (ANT). Based on a qualitative...

  14. Financial Stability and Interacting Networks of Financial Institutions and Market Infrastructures

    OpenAIRE

    Léon, C.; Berndsen, R.J.; Renneboog, L.D.R.

    2014-01-01

    An interacting network coupling financial institutions’ multiplex (i.e. multi-layer) and financial market infrastructures’ single-layer networks gives an accurate picture of a financial system’s true connective architecture. We examine and compare the main properties of Colombian multiplex and interacting financial networks. Coupling financial institutions’ multiplex networks with financial market infrastructures’ networks removes modularity, which augments financial instability because the n...

  15. STM fingerprint of molecule–adatom interactions in a self-assembled metal–organic surface coordination network on Cu(111)

    OpenAIRE

    Björk, Jonas; Matena, Manfred; Dyer, Matthew S.; Enache, Mihaela; Lobo-Checa, Jorge; Gade, Lutz H.; Jung, Thomas A.; Stöhr, Meike; Persson, Mats

    2010-01-01

    A novel approach of identifying metal atoms within a metal–organic surface coordination network using scanning tunnelling microscopy (STM) is presented. The Cu adatoms coordinated in the porous surface network of 1,3,8,10-tetraazaperopyrene (TAPP) molecules on a Cu(111) surface give rise to a characteristic electronic resonance in STM experiments. Using density functional theory calculations, we provide strong evidence that this resonance is a fingerprint of the interaction between the molecu...

  16. Sum and two-atom dipole squeezing in a system of a two-mode vacuum field interacting with two coupled atoms

    Institute of Scientific and Technical Information of China (English)

    侯邦品; 刘杰; 胡萍

    2002-01-01

    We discuss the effects of the initial atomic coherent factors (including the phase and the distribution parameter)and the dipole-dipole interaction on the sum and two-atom dipole squeezing in the system. The results show thatthe maximum squeezing in both cases is determined by the phase and the distribution parameter, and the duration ofsqueezing becomes longer by strengthening the dipole-dipole interaction. In addition, the comparison of the two typesof squeezing shows that one type of squeezing is obtained at the expense of increased fluctuations in the other squeezingfunction.

  17. Nuclear and Atomic Physics Invited Nuclear medium effects iu' K and R interactions

    International Nuclear Information System (INIS)

    Medium effects in the interaction of K and K' mesons with nucleons are reviewed. Recent K+ nuclear data confirm that conventional multiple scattering models fail to describe the interaction of K mesons for incoming momenta ρL = 400 - 800 MeV/c, suggesting a particular form of density dependence for the K nuclear optical potential. K+- atom strong-interaction data, fitted using a density dependent nuclear optical potential which respects the low-density theorem, require an appreciably stronger attraction than that obtained using a Vopt = tρ form, of order 180 +- 20 MeV at nuclear-matter density. The relationship of this result to the physics of theΛ(1405) KN unstable bound state is clarified, and the prospects of meeting the conditions for K- condensation in high-density matter are discussed

  18. Systematics of ground state multiplets of atomic nuclei in the delta-interaction approach

    Energy Technology Data Exchange (ETDEWEB)

    Imasheva, L. T.; Ishkhanov, B. S.; Stepanov, M. E., E-mail: stepanov@depni.sinp.msu.ru [Moscow State University, Faculty of Physics (Russian Federation); Tretyakova, T. Yu. [Moscow State University, Skobeltsyn Institute of Nuclear Physics (Russian Federation)

    2015-12-15

    Pairing forces between nucleons in an atomic nucleus strongly influence its structure. One of the manifestations of pair interaction is the ground state multiplet (GSM) formation in the spectrum of low-lying excited states of even–even nuclei. The value of GSM splitting is determined by the value of pair interaction of nucleons; for each isotope, it can be estimated on the basis of experimental nuclear masses. The quality of this estimate is characterized by the degree of reproduction of GSM levels in the nucleus. The GSM systematics in even–even nuclei with a pair of identical nucleons in addition to the filled nuclear core is considered on the basis of delta interaction.

  19. Messaging Performance of FIPA Interaction Protocols in Networked Embedded Controllers

    Directory of Open Access Journals (Sweden)

    García JoséAPérez

    2008-01-01

    Full Text Available Abstract Agent-based technologies in production control systems could facilitate seamless reconfiguration and integration of mechatronic devices/modules into systems. Advances in embedded controllers which are continuously improving computational capabilities allow for software modularization and distribution of decisions. Agent platforms running on embedded controllers could hide the complexity of bootstrap and communication. Therefore, it is important to investigate the messaging performance of the agents whose main motivation is the resource allocation in manufacturing systems (i.e., conveyor system. The tests were implemented using the FIPA-compliant JADE-LEAP agent platform. Agent containers were distributed through networked embedded controllers, and agents were communicating using request and contract-net FIPA interaction protocols. The test scenarios are organized in intercontainer and intracontainer communications. The work shows the messaging performance for the different test scenarios using both interaction protocols.

  20. Modeling dark energy through an Ising fluid with network interactions

    CERN Document Server

    Luongo, Orlando

    2013-01-01

    We show that the dark energy effects can be modeled by using an \\emph{Ising perfect fluid} with network interactions, whose low redshift equation of state, i.e. $\\omega_0$, becomes $\\omega_0=-1$ as in the $\\Lambda$CDM model. In our picture, dark energy is characterized by a barotropic fluid on a lattice in the equilibrium configuration. Thus, mimicking the spin interaction by replacing the spin variable with an occupational number, the pressure naturally becomes negative. We find that the corresponding equation of state mimics the effects of a variable dark energy term, whose limiting case reduces to the cosmological constant $\\Lambda$. This permits us to avoid the introduction of a vacuum energy as dark energy source by hand, alleviating the coincidence and fine tuning problems. We find fairly good cosmological constraints, by performing three tests with supernovae Ia, baryonic acoustic oscillation and cosmic microwave background measurements. Finally, we perform the AIC and BIC selection criteria, showing t...

  1. Atomic resolution description of the interaction between the nucleoprotein and phosphoprotein of Hendra virus.

    Directory of Open Access Journals (Sweden)

    Guillaume Communie

    Full Text Available Hendra virus (HeV is a recently emerged severe human pathogen that belongs to the Henipavirus genus within the Paramyxoviridae family. The HeV genome is encapsidated by the nucleoprotein (N within a helical nucleocapsid. Recruitment of the viral polymerase onto the nucleocapsid template relies on the interaction between the C-terminal domain, N(TAIL, of N and the C-terminal X domain, XD, of the polymerase co-factor phosphoprotein (P. Here, we provide an atomic resolution description of the intrinsically disordered N(TAIL domain in its isolated state and in intact nucleocapsids using nuclear magnetic resonance (NMR spectroscopy. Using electron microscopy, we show that HeV nucleocapsids form herringbone-like structures typical of paramyxoviruses. We also report the crystal structure of XD of P that consists of a three-helix bundle. We study the interaction between N(TAIL and XD using NMR titration experiments and provide a detailed mapping of the reciprocal binding sites. We show that the interaction is accompanied by α-helical folding of the molecular recognition element of N(TAIL upon binding to a hydrophobic patch on the surface of XD. Finally, using solution NMR, we investigate the interaction between intact nucleocapsids and XD. Our results indicate that monomeric XD binds to N(TAIL without triggering an additional unwinding of the nucleocapsid template. The present results provide a structural description at the atomic level of the protein-protein interactions required for transcription and replication of HeV, and the first direct observation of the interaction between the X domain of P and intact nucleocapsids in Paramyxoviridae.

  2. Jet atomization and cavitation induced by interactions between focused ultrasound and a water surfacea)

    Science.gov (United States)

    Tomita, Y.

    2014-09-01

    Atomization of a jet produced by the interaction of 1 MHz focused ultrasound with a water surface was investigated using high-speed photography. Viewing various aspects of jet behavior, threshold conditions were obtained necessary for water surface elevation and jet breakup, including drop separation and spray formation. In addition, the position of drop atomization, where a single drop separates from the tip of a jet without spraying, showed good correlation with the jet Weber number. For a set of specified conditions, multiple beaded water masses were formed, moving upwards to produce a vigorous jet. Cavitation phenomena occurred near the center of the primary drop-shaped water mass produced at the leading part of the jet; this was accompanied by fine droplets at the neck between the primary and secondary drop-shaped water masses, due to the collapse of capillary waves.

  3. Ultrastable single-atom gold catalysts with strong covalent metal-support interaction (CMSI)

    Institute of Scientific and Technical Information of China (English)

    Botao Qiao[1; Jin-Xia Liang[3,4; Aiqin Wang[2; Cong-Qiao Xu[3; Jun Li[3; Tao Zhang[2; Jingyue (Jimmy) Liu[1

    2015-01-01

    Supported noble metal nanoparticles (including nanoclusters) are widely used in many industrial catalytic processes. While the finely dispersed nanostructures are highly active, they are usually thermodynamically unstable and tend to aggregate or sinter at elevated temperatures. This scenario is particularly true for supported nanogold catalysts because the gold nanostructures are easily sintered at high temperatures, under reaction conditions, or even during storage at ambient temperature. Here, we demonstrate that isolated Au single atoms dispersed on iron oxide nanocrystallites (Aul/FeOx) are much more sintering- resistant than Au nanostructures, and exhibit extremely high reaction stability for CO oxidation in a wide temperature range. Theoretical studies revealed that the positively charged and surface-anchored Aul atoms with high valent states formed significant covalent metal-support interactions (CMSIs), thus providing the ultra-stability and remarkable catalytic performance. This work may provide insights and a new avenue for fabricating supported Au catalysts with ultra-high stability.

  4. Electron dynamics in the carbon atom induced by spin-orbit interaction

    CERN Document Server

    Rey, H F

    2014-01-01

    We use R-Matrix theory with Time dependence (RMT) to investigate multiphoton ionization of ground-state atomic carbon with initial orbital magnetic quantum number $M_L$=0 and $M_L$=1 at a laser wavelength of 390 nm and peak intensity of 10$^{14}$ W cm$^{-2}$. Significant differences in ionization yield and ejected-electron momentum distribution are observed between the two values for $M_L$. We use our theoretical results to model how the spin-orbit interaction affects electron emission along the laser polarization axis. Under the assumption that an initial C atom is prepared at zero time delay with $M_L=0$, the dynamics with respect to time delay of an ionizing probe pulse modelled using RMT theory is found to be in good agreement with available experimental data.

  5. Dynamics simulation on the interaction of intense laser pulses with atomic clusters

    Institute of Scientific and Technical Information of China (English)

    Du Hong-Chuan; Zhu Peng-Jia; Sun Shao-Hua; Liu Zuo-Ye; Li Lu; Ma Ling-Ling; Hu Bi-Tao

    2009-01-01

    Under classical particle dynamics, the interaction process between intense femtosecond laser pulses and icosahedral noble-gas atomic clusters was studied. Our calculated results show that ionization proceeds mainly through tunnel ionization in the combined field from ions, electrons and laser, rather than the electron-impact ionization. With increasing cluster size, the average and maximum kinetic energy of the product ion increases. According to our calculation, the expansion process of the clusters after laser irradiation is dominated by Coulomb explosion and the expansion scale increases with increasing cluster size. The dependence of average kinetic energy and average charge state of the product ions on laser wavelength is also presented and discussed. The dependence of average kinetic energy on the number of atoms inside the cluster was studied and compared with the experimental data. Our results agree with the experimental results reasonably well.

  6. Well-ordered ZnO nanotube arrays and networks grown by atomic layer deposition

    International Nuclear Information System (INIS)

    Highlights: • ZnO nanotube networks and well-ordered ZnO nanotube arrays are fabricated by ALD. • The wall thickness of the ZnO nanotubes can be well-controlled at the angstrom level. • The fishing net-like networks of ZnO nanotubes with an ultra thin wall thickness are fabricated. • The ZnO nanotube arrays have an aspect ratio as high as 1000:1. - Abstract: Semiconductor ZnO, possessing a large exciton binding energy and wide band gap, has received a great deal of attention because it shows great potential for applications in optoelectronics. Precisely controlling the growth of three-dimensional ZnO nanotube structures with a uniform morphology constitutes an important step forward toward integrating ZnO nanostructures into microelectronic devices. Atomic layer deposition (ALD) technique, featured with self-limiting surface reactions, is an ideal approach to the fabrication of ZnO nanostructures, because it allows for accurate control of the thickness at atomic level and conformal coverage in complex 3D structures. In this work, well-ordered ZnO nanotube arrays and networks are prepared by ALD. The morphology, crystallinity and wall thickness of these nanotube structures are examined for different growth conditions. The microstructure of the ZnO nanotubes is investigated by transmission electron microscopy and X-ray diffraction. The high aspect ratio of ZnO nanotubes provides a large specific area which could enhance the kinetics of chemical reactions taking place between the ZnO and its surroundings, making the potential devices more efficient and compact

  7. Well-ordered ZnO nanotube arrays and networks grown by atomic layer deposition

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yijun [Electronic Materials Research Laboratory, Key Laboratory of the Ministry of Education & International Center for Dielectric Research, Xi’an Jiaotong University, Xi’an 710049 (China); Liu, Ming, E-mail: mingliu@mail.xjtu.edu.cn [Electronic Materials Research Laboratory, Key Laboratory of the Ministry of Education & International Center for Dielectric Research, Xi’an Jiaotong University, Xi’an 710049 (China); Ren, Wei, E-mail: wren@mail.xjtu.edu.cn [Electronic Materials Research Laboratory, Key Laboratory of the Ministry of Education & International Center for Dielectric Research, Xi’an Jiaotong University, Xi’an 710049 (China); Ye, Zuo-Guang, E-mail: zye@sfu.ca [Electronic Materials Research Laboratory, Key Laboratory of the Ministry of Education & International Center for Dielectric Research, Xi’an Jiaotong University, Xi’an 710049 (China); Department of Chemistry and 4D LABS, Simon Fraser University, Burnaby, British Columbia V5A 1S6 (Canada)

    2015-06-15

    Highlights: • ZnO nanotube networks and well-ordered ZnO nanotube arrays are fabricated by ALD. • The wall thickness of the ZnO nanotubes can be well-controlled at the angstrom level. • The fishing net-like networks of ZnO nanotubes with an ultra thin wall thickness are fabricated. • The ZnO nanotube arrays have an aspect ratio as high as 1000:1. - Abstract: Semiconductor ZnO, possessing a large exciton binding energy and wide band gap, has received a great deal of attention because it shows great potential for applications in optoelectronics. Precisely controlling the growth of three-dimensional ZnO nanotube structures with a uniform morphology constitutes an important step forward toward integrating ZnO nanostructures into microelectronic devices. Atomic layer deposition (ALD) technique, featured with self-limiting surface reactions, is an ideal approach to the fabrication of ZnO nanostructures, because it allows for accurate control of the thickness at atomic level and conformal coverage in complex 3D structures. In this work, well-ordered ZnO nanotube arrays and networks are prepared by ALD. The morphology, crystallinity and wall thickness of these nanotube structures are examined for different growth conditions. The microstructure of the ZnO nanotubes is investigated by transmission electron microscopy and X-ray diffraction. The high aspect ratio of ZnO nanotubes provides a large specific area which could enhance the kinetics of chemical reactions taking place between the ZnO and its surroundings, making the potential devices more efficient and compact.

  8. College Chemistry Students' Understanding of Potential Energy in the Context of Atomic-Molecular Interactions

    Science.gov (United States)

    Becker, Nicole M.; Cooper, Melanie M.

    2014-01-01

    Understanding the energy changes that occur as atoms and molecules interact forms the foundation for understanding the macroscopic energy changes that accompany chemical processes. In order to identify ways to scaffold students' understanding of the connections between atomic-molecular and macroscopic energy perspectives, we conducted a…

  9. Upper Secondary Students' Understanding of the Basic Physical Interactions in Analogous Atomic and Solar Systems

    Science.gov (United States)

    Taber, Keith S.

    2013-01-01

    Comparing the atom to a "tiny solar system" is a common teaching analogy, and the extent to which learners saw the systems as analogous was investigated. English upper secondary students were asked parallel questions about the physical interactions between the components of a simple atomic system and a simple solar system to investigate…

  10. A scheme for teleporting Schrdinger-cat states via the dispersive atom-cavity-field interaction

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    A proposal is presented for teleporting Schrding-cat states. The process of the teleportation is achieved through the dispersive atom-cavity-field interaction. In this proposal, only measurement on the cavity field and on the singlet atomic states are used.

  11. Phospho-tyrosine dependent protein–protein interaction network

    Science.gov (United States)

    Grossmann, Arndt; Benlasfer, Nouhad; Birth, Petra; Hegele, Anna; Wachsmuth, Franziska; Apelt, Luise; Stelzl, Ulrich

    2015-01-01

    Post-translational protein modifications, such as tyrosine phosphorylation, regulate protein–protein interactions (PPIs) critical for signal processing and cellular phenotypes. We extended an established yeast two-hybrid system employing human protein kinases for the analyses of phospho-tyrosine (pY)-dependent PPIs in a direct experimental, large-scale approach. We identified 292 mostly novel pY-dependent PPIs which showed high specificity with respect to kinases and interacting proteins and validated a large fraction in co-immunoprecipitation experiments from mammalian cells. About one-sixth of the interactions are mediated by known linear sequence binding motifs while the majority of pY-PPIs are mediated by other linear epitopes or governed by alternative recognition modes. Network analysis revealed that pY-mediated recognition events are tied to a highly connected protein module dedicated to signaling and cell growth pathways related to cancer. Using binding assays, protein complementation and phenotypic readouts to characterize the pY-dependent interactions of TSPAN2 (tetraspanin 2) and GRB2 or PIK3R3 (p55γ), we exemplarily provide evidence that the two pY-dependent PPIs dictate cellular cancer phenotypes. PMID:25814554

  12. Analysing Health Professionals' Learning Interactions in an Online Social Network: A Longitudinal Study.

    Science.gov (United States)

    Li, Xin; Verspoor, Karin; Gray, Kathleen; Barnett, Stephen

    2016-01-01

    This paper summarises a longitudinal analysis of learning interactions occurring over three years among health professionals in an online social network. The study employs the techniques of Social Network Analysis (SNA) and statistical modeling to identify the changes in patterns of interaction over time and test associated structural network effects. SNA results indicate overall low participation in the network, although some participants became active over time and even led discussions. In particular, the analysis has shown that a change of lead contributor results in a change in learning interaction and network structure. The analysis of structural network effects demonstrates that the interaction dynamics slow down over time, indicating that interactions in the network are more stable. The health professionals may be reluctant to share knowledge and collaborate in groups but were interested in building personal learning networks or simply seeking information. PMID:27440295

  13. Emergence of overlap in ensembles of spatial multiplexes and statistical mechanics of spatial interacting networks ensembles

    CERN Document Server

    Halu, Arda; Bianconi, Ginestra

    2013-01-01

    Spatial networks range from the brain networks, to transportation networks and infrastructures. Recently interacting and multiplex networks are attracting great attention because their dynamics and robustness cannot be understood without treating at the same time several networks. Here we present maximal entropy ensembles of spatial multiplex and spatial interacting networks that can be used in order to model spatial multilayer network structures and to build null models of real datasets. We show that spatial multiplex naturally develop a significant overlap of the links, a noticeable property of many multiplexes that can affect significantly the dynamics taking place on them. Additionally, we characterize ensembles of spatial interacting networks and we analyse the structure of interacting airport and railway networks in India, showing the effect of space in determining the link probability.

  14. Evaluation of clustering algorithms for protein-protein interaction networks

    Directory of Open Access Journals (Sweden)

    van Helden Jacques

    2006-11-01

    Full Text Available Abstract Background Protein interactions are crucial components of all cellular processes. Recently, high-throughput methods have been developed to obtain a global description of the interactome (the whole network of protein interactions for a given organism. In 2002, the yeast interactome was estimated to contain up to 80,000 potential interactions. This estimate is based on the integration of data sets obtained by various methods (mass spectrometry, two-hybrid methods, genetic studies. High-throughput methods are known, however, to yield a non-negligible rate of false positives, and to miss a fraction of existing interactions. The interactome can be represented as a graph where nodes correspond with proteins and edges with pairwise interactions. In recent years clustering methods have been developed and applied in order to extract relevant modules from such graphs. These algorithms require the specification of parameters that may drastically affect the results. In this paper we present a comparative assessment of four algorithms: Markov Clustering (MCL, Restricted Neighborhood Search Clustering (RNSC, Super Paramagnetic Clustering (SPC, and Molecular Complex Detection (MCODE. Results A test graph was built on the basis of 220 complexes annotated in the MIPS database. To evaluate the robustness to false positives and false negatives, we derived 41 altered graphs by randomly removing edges from or adding edges to the test graph in various proportions. Each clustering algorithm was applied to these graphs with various parameter settings, and the clusters were compared with the annotated complexes. We analyzed the sensitivity of the algorithms to the parameters and determined their optimal parameter values. We also evaluated their robustness to alterations of the test graph. We then applied the four algorithms to six graphs obtained from high-throughput experiments and compared the resulting clusters with the annotated complexes. Conclusion This

  15. Linear motif-mediated interactions have contributed to the evolution of modularity in complex protein interaction networks.

    Directory of Open Access Journals (Sweden)

    Inhae Kim

    2014-10-01

    Full Text Available The modular architecture of protein-protein interaction (PPI networks is evident in diverse species with a wide range of complexity. However, the molecular components that lead to the evolution of modularity in PPI networks have not been clearly identified. Here, we show that weak domain-linear motif interactions (DLIs are more likely to connect different biological modules than strong domain-domain interactions (DDIs. This molecular division of labor is essential for the evolution of modularity in the complex PPI networks of diverse eukaryotic species. In particular, DLIs may compensate for the reduction in module boundaries that originate from increased connections between different modules in complex PPI networks. In addition, we show that the identification of biological modules can be greatly improved by including molecular characteristics of protein interactions. Our findings suggest that transient interactions have played a unique role in shaping the architecture and modularity of biological networks over the course of evolution.

  16. Novel recurrent neural network for modelling biological networks: oscillatory p53 interaction dynamics.

    Science.gov (United States)

    Ling, Hong; Samarasinghe, Sandhya; Kulasiri, Don

    2013-12-01

    Understanding the control of cellular networks consisting of gene and protein interactions and their emergent properties is a central activity of Systems Biology research. For this, continuous, discrete, hybrid, and stochastic methods have been proposed. Currently, the most common approach to modelling accurate temporal dynamics of networks is ordinary differential equations (ODE). However, critical limitations of ODE models are difficulty in kinetic parameter estimation and numerical solution of a large number of equations, making them more suited to smaller systems. In this article, we introduce a novel recurrent artificial neural network (RNN) that addresses above limitations and produces a continuous model that easily estimates parameters from data, can handle a large number of molecular interactions and quantifies temporal dynamics and emergent systems properties. This RNN is based on a system of ODEs representing molecular interactions in a signalling network. Each neuron represents concentration change of one molecule represented by an ODE. Weights of the RNN correspond to kinetic parameters in the system and can be adjusted incrementally during network training. The method is applied to the p53-Mdm2 oscillation system - a crucial component of the DNA damage response pathways activated by a damage signal. Simulation results indicate that the proposed RNN can successfully represent the behaviour of the p53-Mdm2 oscillation system and solve the parameter estimation problem with high accuracy. Furthermore, we presented a modified form of the RNN that estimates parameters and captures systems dynamics from sparse data collected over relatively large time steps. We also investigate the robustness of the p53-Mdm2 system using the trained RNN under various levels of parameter perturbation to gain a greater understanding of the control of the p53-Mdm2 system. Its outcomes on robustness are consistent with the current biological knowledge of this system. As more

  17. User-Centric Secure Cross-Site Interaction Framework for Online Social Networking Services

    Science.gov (United States)

    Ko, Moo Nam

    2011-01-01

    Social networking service is one of major technological phenomena on Web 2.0. Hundreds of millions of users are posting message, photos, and videos on their profiles and interacting with other users, but the sharing and interaction are limited within the same social networking site. Although users can share some content on a social networking site…

  18. Selective population of ground terms in /sup 14/N atoms after ion-beam--surface interaction at grazing incidence

    Energy Technology Data Exchange (ETDEWEB)

    Winter, H.; Langheim, M.; Schirmacher, A.; Zimny, R.; Andra, H.J.

    1984-04-02

    The orientation of angular momenta in the ground terms of /sup 14/N atoms after the interaction of 350-keV /sup 14/N/sup +/ ions with a solid surface at grazing incidence is investigated by a Zeeman quantum-beat technique. After the ion-solid interaction, a term-selective and highly polarized fast beam of nitrogen atoms is observed. The phenomenon is interpreted in terms of a Pauli-principle--induced selective population.

  19. Quantum entanglement between the two-mode fields and atomic entropy squeezing in the system of a moving atom interacting with two-mode entangled coherent field

    Institute of Scientific and Technical Information of China (English)

    Zou Yan; Li Yong-Ping

    2009-01-01

    This paper investigates the entropy squeezing of a moving two-level atom interacting with the two-mode entangled coherent field via two-photon transition by using an entropic uncertainty relation and the degree of entanglement between the two-mode fields by using quantum relative entropy. The results obtained from numerical calculation indicate that the squeezed period, the duration of entropy squeezing and the maximal squeezing can be controlled by appropriately choosing the intensity of the light field, the atomic motion and the field-mode structure. The atomic motion leads to the periodic recovery of the initial maximal degree of entanglement between the two-mode fields. Moreover, there exists a corresponding relation between the time evolution properties of the atomic entropy squeezing and those of the entanglement between the two-mode fields.

  20. Noise Effects on Entangled Coherent State Generated via Atom-Field Interaction and Beam Splitter

    Science.gov (United States)

    Najarbashi, G.; Mirzaei, S.

    2016-05-01

    In this paper, we introduce a controllable method for producing two and three-mode entangled coherent states (ECS's) using atom-field interaction in cavity QED and beam splitter. The generated states play central roles in linear optics, quantum computation and teleportation. We especially focus on qubit, qutrit and qufit like ECS's and investigate their entanglement by concurrence measure. Moreover, we illustrate decoherence properties of ECS's due to noisy channels, using negativity measure. At the end the effect of noise on monogamy inequality is discussed.

  1. DISLOCATION-SOLUTE ATOM INTERACTION IN ALUMINUM STUDIED BY AMPLITUDE-DEPENDENT INTERNAL FRICTION

    OpenAIRE

    Kosugi, T.; Kino, T.

    1985-01-01

    In order to get the information on the force-distance curve for the interaction between a dislocation and a solute atom, amplitude-dependent internal friction was measured at 1.7 - 30 K on Al-100 at ppm Zn and Al-50 at ppm Zn single crystals. The temperature dependence of applied strain under a constant decrement is the same for two concentrations with high accuracy. The data were analyzed by the thermally assisted break-away model for dislocations assuming several potential forms. In conclus...

  2. Probing molecular interaction between transferrin and anti-transferrin by atomic force microscope

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    The interaction between transferrin (Tf) and its antibody was investigated by atomic force microscope. Tf-antibody was immobilized on the Au-coated glass slide, and the specific combination between antibody and antigen was also characterized by AFM. The results showed that holo-transferrin was jogged with anti-transferrin, and binded anti-tran- sferrin more tightly than apo-transferrin. The force- distance curves revealed that the affinity of anti-trans- ferrin and holo-transferrin was much stronger than that of apo-transferrin.

  3. The interaction between Boron-carbon-nitride heteronanotubes and lithium atoms: Role of composition proportion

    Science.gov (United States)

    Zhong, Rong-Lin; Xu, Hong-Liang; Su, Zhong-Min

    2016-08-01

    A series of Li@BCN models were systematically investigated to explore the physical origin of the interaction between lithium atoms and BCNs. Theoretical results show that the crucial electron population in the BCNs of Li@B-BCN and Li@N-BCN series is dramatically different. As results, the first hyperpolarizability of Li@B-BCN series increases with the increase of carbon proportion whereas that of Li@N-BCN series significantly decreases with the increase of carbon proportion. The results indicate that the physical properties of Li@BCN models are significantly dependent on the different chemical environment of the tube termination.

  4. Molecular ions in ultracold atomic gases: computed electronic interactions for \\MgHion with Rb

    CERN Document Server

    Tacconi, Mario

    2007-01-01

    The electronic structures of the manifold of potential energy surfaces generated in the lower energy range by the interaction of the MgH$^+$(X$^1\\Sigma^+$) cationic molecule with Rb($^2$S), neutral atom are obtained over a broad range of Jacobi coordinates from strongly correlated \\emph{ab initio} calculations which use a Multireference (MR) wavefunction within a Complete Active Space (CAS) approach. The relative features of the lowest five surfaces are analyzed in terms of possible collisional outcomes when employed to model the ultracold dynamics of ionic molecular partners.

  5. Two interacting atoms in a cavity: exact solutions, entanglement and decoherence

    Energy Technology Data Exchange (ETDEWEB)

    Torres, J M; SadurnI, E; Seligman, T H, E-mail: mau@fis.unam.m [Instituto de Ciencias FIsicas, Universidad Nacional Autonoma de Mexico, CP 62210 Cuernavaca, Morelos (Mexico)

    2010-05-14

    We address the problem of two interacting atoms of different species inside a cavity and find the explicit solutions of the corresponding eigenvalues and eigenfunctions using a new variant. This model encompasses various commonly used models. By way of example we obtain closed expressions for concurrence and purity as a function of time for the case where the cavity is prepared in a number state. We discuss the behaviour of these quantities and their relative behaviour in the concurrence-purity plane. (fast track communication)

  6. Visualization of interaction between ribosome-inactivating proteins and supercoiled DNA with an atomic force microscope

    Institute of Scientific and Technical Information of China (English)

    吴晓华; 刘望夷; 欧阳振乾; 李民乾

    1997-01-01

    The interaction between ribosome-inactivating proteins (RIPs) and supercoiled DNA was observed with an atomic force microscope (AFM). It was found that RIPs can bind to both supercoiled DNA and the unwound double stranded loop region in supercoiled DNA. The RIPs hound to the supercoils can induce the conformational change of supercoiled DNA. Furthermore, the supercoiled DNA was relaxed and cleaved into nick or linear form by RIPs. It indicated that RIP seemed to be a supercoil-dependent DNA binding protein and exhibited the activity of su-percoil-dependent DNA endonuclease.

  7. Probing the interaction of individual amino acids with inorganic surfaces using atomic force spectroscopy.

    Science.gov (United States)

    Razvag, Yair; Gutkin, Vitaly; Reches, Meital

    2013-08-13

    This article describes single-molecule force spectroscopy measurements of the interaction between individual amino acid residues and inorganic surfaces in an aqueous solution. In each measurement, there is an amino acid residue, lysine, glutamate, phenylalanine, leucine, or glutamine, and each represents a class of amino acids (positively or negatively charged, aromatic, nonpolar, and polar). Force-distance curves measured the interaction of the individual amino acid bound to a silicon atomic force microscope (AFM) tip with a silcon substrate, cut from a single-crystal wafer, or mica. Using this method, we were able to measure low adhesion forces (below 300 pN) and could clearly determine the strength of interactions between the individual amino acid residues and the inorganic substrate. In addition, we observed how changes in the pH and ionic strength of the solution affected the adsorption of the residues to the substrates. Our results pinpoint the important role of hydrophobic interactions among the amino acids and the substrate, where hydrophobic phenylalanine exhibited the strongest adhesion to a silicon substrate. Additionally, electrostatic interactions also contributed to the adsorption of amino acid residues to inorganic substrates. A change in the pH or ionic strength values of the buffer altered the strength of interactions among the amino acids and the substrate. We concluded that the interplay between the hydrophobic forces and electrostatic interactions will determine the strength of adsorption among the amino acids and the surface. Overall, these results contribute to our understanding of the interaction at the organic-inorganic interface. These results may have implications for our perception of the specificity of peptide binding to inorganic surfaces. Consequently, it would possibly lead to a better design of composite materials and devices.

  8. Amplitude internal friction peaks associated with the interaction between dislocation kinks and solute atoms in aluminium

    International Nuclear Information System (INIS)

    Early in 1950, Ke observed in slightly cold-worked dilute aluminium-copper solid solutions a pronounced low-frequency internal friction peak around room temperature as a function of strain amplitude in which the high-amplitude side of the peak decreases rapidly to a very small value. This paper reviews the experimental results since the work of Ke, with emphasis on cold-worked aluminium containing Cu or Mg as substitutional solute atoms. A dislocation kink dragging and break away model is suggested. The latest results show that this internal friction peak around room temperature consists of two separate peaks. The amplitude peak accompanying the lower temperature peak shifts toward lower amplitudes and that accompanying the higher temperature peak shifts toward higher amplitudes with an increase of temperature of measurement. The former amplitude peak appears at an amplitude range lower than that of the former peak. A mechanism of the double amplitude peaks is suggested in terms of the simultaneous occurrence of longitudinal core diffusion (LCD) and transverse core diffusion (TCD) of the solute atoms during the to and fro sidewise motion of the dislocation kinks. Some conclusions concerning the mechanism of Hasiguti peaks are drawn from the comparison with studies on the internal friction peaks associated with the interaction between dislocation kinks and solute atoms. (orig.)

  9. Regular and chaotic distribution of Bose-Einstein condensed atoms with a space-dependent nonlinear interaction

    International Nuclear Information System (INIS)

    This paper studies the regular and chaotic spatial distribution of Bose-Einstein condensed atoms with a space-dependent nonlinear interaction. There exists a steady atomic current in the system due to the space-dependent phase of condensate. For the system with a positive chemical potential and repulsive interatomic interaction, we construct the general solution of the 1st-order equation, whose boundedness conditions contain the famous Mel'nikov chaotic criterion. When the system doesn't satisfy the perturbation conditions, numerical simulations reveal that increasing the atomic current can destroy the spatial symmetry of the distributional structure of condensed atoms, whether the condensed atoms in a chaotic or regular distribution. (authors)

  10. Phage-bacteria interaction network in human oral microbiome.

    Science.gov (United States)

    Wang, Jinfeng; Gao, Yuan; Zhao, Fangqing

    2016-07-01

    Although increasing knowledge suggests that bacteriophages play important roles in regulating microbial ecosystems, phage-bacteria interaction in human oral cavities remains less understood. Here we performed a metagenomic analysis to explore the composition and variation of oral dsDNA phage populations and potential phage-bacteria interaction. A total of 1,711 contigs assembled with more than 100 Gb shotgun sequencing data were annotated to 104 phages based on their best BLAST matches against the NR database. Bray-Curtis dissimilarities demonstrated that both phage and bacterial composition are highly diverse between periodontally healthy samples but show a trend towards homogenization in diseased gingivae samples. Significantly, according to the CRISPR arrays that record infection relationship between bacteria and phage, we found certain oral phages were able to invade other bacteria besides their putative bacterial hosts. These cross-infective phages were positively correlated with commensal bacteria while were negatively correlated with major periodontal pathogens, suggesting possible connection between these phages and microbial community structure in oral cavities. By characterizing phage-bacteria interaction as networks rather than exclusively pairwise predator-prey relationships, our study provides the first insight into the participation of cross-infective phages in forming human oral microbiota.

  11. Intermittent contact interaction between an atomic force microscope cantilever and a nanowire

    Science.gov (United States)

    Knittel, I.; Ungewitter, L.; Hartmann, U.

    2012-05-01

    We investigate in theory and experiment the intermittent contact interaction between an atomic force microscope (AFM) cantilever and a nanowire under ambient conditions. The nanowire is modeled as a spring reacting instantaneously to any change of the force between the wire and the cantilever. This implies that the cantilever is subject to an "effective" force-distance relation, containing not only the surface forces but also the deflection of the nanowire. Experimentally, CVD-grown tin oxide nanowires and lithographically structured silicon nanowire arrays were investigated by intermittent contact AFM. By comparison of experimental and simulated distance-dependent resonance curves it is found that the nanowires behave like "fast nanosprings" and that the adhesion force is one of the key factors determining distance-dependent resonance curves. The results are fully applicable to a scenario in which a cantilever equipped by a nanowire interacts with a surface.

  12. Multireference configuration interaction calculations of the first six ionization potentials of the uranium atom

    Energy Technology Data Exchange (ETDEWEB)

    Bross, David H.; Parmar, Payal; Peterson, Kirk A., E-mail: kipeters@wsu.edu [Department of Chemistry, Washington State University, Pullman, Washington 99164-4630 (United States)

    2015-11-14

    The first 6 ionization potentials (IPs) of the uranium atom have been calculated using multireference configuration interaction (MRCI+Q) with extrapolations to the complete basis set limit using new all-electron correlation consistent basis sets. The latter was carried out with the third-order Douglas-Kroll-Hess Hamiltonian. Correlation down through the 5s5p5d electrons has been taken into account, as well as contributions to the IPs due to the Lamb shift. Spin-orbit coupling contributions calculated at the 4-component Kramers restricted configuration interaction level, as well as the Gaunt term computed at the Dirac-Hartree-Fock level, were added to the best scalar relativistic results. The final ionization potentials are expected to be accurate to at least 5 kcal/mol (0.2 eV) and thus more reliable than the current experimental values of IP{sub 3} through IP{sub 6}.

  13. P ,T -odd electron-nucleus interaction in atomic systems as an exchange by Higgs bosons

    Science.gov (United States)

    Chubukov, D. V.; Labzowsky, L. N.

    2016-06-01

    Scalar-pseudoscalar P ,T -odd interaction between the electron and the nucleus in atomic systems is constructed within the standard model as an exchange by Higgs boson. The necessary P - and T -violating contribution is obtained at the three-loop level on the basis of Cabibbo-Kobayashi-Maskawa matrix. This contribution, unlike the corresponding contribution to the electron electric dipole moment (EDM), does not vanish since the "Higgs charges" of quarks, contrary to their electric charges, are flavor dependent. Order-of-magnitude estimates of the effect expressed as an "equivalent" electron EDM give the values within the range deeqv˜10-40-10-45e cm , depending on the known different estimates for the electron EDM. This can be compared with the known "benchmark" two-photon P ,T -odd electron-nucleus interaction effect, which provides deeqv˜10-38e cm .

  14. 2012 ATOMIC AND MOLECULAR INTERACTIONS GORDON RESEARCH CONFERENCE AND GORDON RESEARCH SEMINAR, JULY 15-20, 2012

    Energy Technology Data Exchange (ETDEWEB)

    Zwier, Timothy

    2012-07-20

    At the 2012 Atomic and Molecular Interactions Gordon Conference, there will be talks in several broadly defined and partially overlapping areas:  Intramolecular and single-collision reaction dynamics;  Photophysics and photochemistry of excited states;  Clusters, aerosols and solvation;  Interactions at interfaces;  Conformations and folding of large molecules;  Interactions under extreme conditions of temperature and pressure. The theme of the Gordon Research Seminar on Atomic & Molecular Interactions, in keeping with the tradition of the Atomic and Molecular Interactions Gordon Research Conference, is far-reaching and involves fundamental research in the gas and condensed phases along with application of these ideas to practical chemical fields. The oral presentations, which will contain a combination of both experiment and theory, will focus on four broad categories:  Ultrafast Phenomena;  Excited States, Photoelectrons, and Photoions;  Chemical Reaction Dynamics;  Biomolecules and Clusters.

  15. Aspects of the theory of atoms and coherent matter and their interaction with electromagnetic fields

    Energy Technology Data Exchange (ETDEWEB)

    Nilsen, Halvor Moell

    2002-07-01

    In the present work I have outlined and contributed to the time-dependent theory of the interaction between atoms and electromagnetic fields and the theory of Bose-Einstein condensates. New numerical methods and algorithms have been developed and applied in practice. Calculations have exhibited certain new dynamical features. All these calculations are in a regime where the applied field is of the same magnitude as the atomic field. In the case of BEC we have investigated the use of time-dependent methods to calculate the excitation frequencies. We also investigated the possibility of nonlinear coupling for a scissors mode and found no such contributions to damping which is consistent with other studies . Special emphasis has also been paid to the gyroscopic motion of rotating BEC where several models were investigated. Briefly, the main conclusions are: (1) Rydberg wave packets appear for direct excitations of Rydberg atoms for long pulses. (2) The survival of just a few states is decided by symmetry of the Hamiltonian. (3) For few cycle intense pulses classical and quantum mechanics show remarkable similarity. (4) Time-dependent methods for finding excitation frequencies have been shown to be very efficient. (5) New dynamical features is shown in gyroscopic motion of BEC. (6) It was shown that no nonlinear mixing of scissors modes occur in the standard Gross-Pitaevskii regime. As mentioned in the introduction, this work is a part of very active research fields and new progress is constantly reported. Thus, the present work cannot be concluded as a closed loop. The fast development of grid based numerical solutions for atoms in intense fields will surely make great contribution to solve many of today's problems. It is a very important area of research to understand both nonperturbative atomic response and highly nonlinear optics. In the field of Bose-Einstein condensation the new experimental achievements constantly drive the field forward. The new

  16. Nonlinear Dynamics of Cantilever-Sample Interactions in Atomic Force Microscopy

    Science.gov (United States)

    Cantrell, John H.; Cantrell, Sean A.

    2010-01-01

    The interaction of the cantilever tip of an atomic force microscope (AFM) with the sample surface is obtained by treating the cantilever and sample as independent systems coupled by a nonlinear force acting between the cantilever tip and a volume element of the sample surface. The volume element is subjected to a restoring force from the remainder of the sample that provides dynamical equilibrium for the combined systems. The model accounts for the positions on the cantilever of the cantilever tip, laser probe, and excitation force (if any) via a basis set of set of orthogonal functions that may be generalized to account for arbitrary cantilever shapes. The basis set is extended to include nonlinear cantilever modes. The model leads to a pair of coupled nonlinear differential equations that are solved analytically using a matrix iteration procedure. The effects of oscillatory excitation forces applied either to the cantilever or to the sample surface (or to both) are obtained from the solution set and applied to the to the assessment of phase and amplitude signals generated by various acoustic-atomic force microscope (A-AFM) modalities. The influence of bistable cantilever modes of on AFM signal generation is discussed. The effects on the cantilever-sample surface dynamics of subsurface features embedded in the sample that are perturbed by surface-generated oscillatory excitation forces and carried to the cantilever via wave propagation are accounted by the Bolef-Miller propagating wave model. Expressions pertaining to signal generation and image contrast in A-AFM are obtained and applied to amplitude modulation (intermittent contact) atomic force microscopy and resonant difference-frequency atomic force ultrasonic microscopy (RDF-AFUM). The influence of phase accumulation in A-AFM on image contrast is discussed, as is the effect of hard contact and maximum nonlinearity regimes of A-AFM operation.

  17. Extended Bose Hubbard model of interacting bosonic atoms in optical lattices: From superfluidity to density waves

    International Nuclear Information System (INIS)

    For systems of interacting, ultracold spin-zero neutral bosonic atoms, harmonically trapped and subject to an optical lattice potential, we derive an Extended Bose Hubbard (EBH) model by developing a systematic expansion for the Hamiltonian of the system in powers of the lattice parameters and of a scale parameter, the lattice attenuation factor. We identify the dominant terms that need to be retained in realistic experimental conditions, up to nearest-neighbor interactions and nearest-neighbor hoppings conditioned by the on-site occupation numbers. In the mean field approximation, we determine the free energy of the system and study the phase diagram both at zero and at finite temperature. At variance with the standard on site Bose Hubbard model, the zero-temperature phase diagram of the EBH model possesses a dual structure in the Mott insulating regime. Namely, for specific ranges of the lattice parameters, a density wave phase characterizes the system at integer fillings, with domains of alternating mean occupation numbers that are the atomic counterparts of the domains of staggered magnetizations in an antiferromagnetic phase. We show as well that in the EBH model, a zero-temperature quantum phase transition to pair superfluidity is, in principle, possible, but completely suppressed at the lowest order in the lattice attenuation factor. Finally, we determine the possible occurrence of the different phases as a function of the experimentally controllable lattice parameters

  18. Simulated Evolution of Protein-Protein Interaction Networks with Realistic Topology

    OpenAIRE

    G Jack Peterson; Steve Pressé; Peterson, Kristin S.; Dill, Ken A.

    2012-01-01

    We model the evolution of eukaryotic protein-protein interaction (PPI) networks. In our model, PPI networks evolve by two known biological mechanisms: (1) Gene duplication, which is followed by rapid diversification of duplicate interactions. (2) Neofunctionalization, in which a mutation leads to a new interaction with some other protein. Since many interactions are due to simple surface compatibility, we hypothesize there is an increased likelihood of interacting with other proteins in the t...

  19. Density functional theory study of nitrogen atoms and molecules interacting with Fe(1 1 1) surfaces

    Science.gov (United States)

    Nosir, M. A.; Martin-Gondre, L.; Bocan, G. A.; Díez Muiño, R.

    2016-09-01

    We present Density functional theory (DFT) calculations for the investigation of the structural relaxation of Fe(1 1 1), as well as for the study of the interaction of nitrogen atoms and molecules with this surface. We perform spin polarized DFT calculations using VASP (Vienna Ab-initio Simulation Package) code. We use the supercell approach and up to 19 slab layers for the relaxation of the Fe(1 1 1) surface. We find a contraction of the first two interlayer distances with a relative value of Δ12 = - 7.8 % and Δ23 = - 21.7 % with respect to the bulk reference. The third interlayer distance is however expanded with a relative change of Δ34 = 9.7 % . Early experimental studies of the surface relaxation using Low Energy Electron Diffraction (LEED) and Medium Energy Ion Scattering (MEIS) showed contradictory results, even on the relaxation general trend. Our current theoretical results support the LEED conclusions and are consistent qualitatively with other recent theoretical calculations. In addition, we study the interaction energy of nitrogen atoms and molecules on the Fe(1 1 1) surface. The nitrogen atoms are adsorbed in the hollow site of the unit cell, with an adsorption energy consistent with the one found in previous studies. In addition, we find the three molecularly adsorbed states that are observed experimentally. Two of them correspond to the adsorbed molecule oriented normal to the surface and a third one corresponds to the molecule adsorbed parallel to the surface. We conclude that our results are accurate enough to be used to build a full six-dimensional potential energy surface for the N2 system.

  20. Limitations of Gene Duplication Models: Evolution of Modules in Protein Interaction Networks

    OpenAIRE

    Frank Emmert-Streib

    2012-01-01

    It has been generally acknowledged that the module structure of protein interaction networks plays a crucial role with respect to the functional understanding of these networks. In this paper, we study evolutionary aspects of the module structure of protein interaction networks, which forms a mesoscopic level of description with respect to the architectural principles of networks. The purpose of this paper is to investigate limitations of well known gene duplication models by showing that the...

  1. Long-range interactions between a He($2 ^3S$) atom and a He($2 ^3P$) atom for like isotopes

    CERN Document Server

    Zhang, J Y; Sadeghpour, H R; Vrinceanu, D; Yan, Z C; 10.1103/.73.022710

    2006-01-01

    For the interactions between a He($2 ^3S$) atom and a He($2 ^3P$) atom for like isotopes, we report calculations of the coefficients determining the potential energies at large internuclear separations. Using accurate variational wave functions in Hylleraas coordinates we evaluate the coefficient $C_{3}$ of the resonant dipole-dipole energy, and the van der Waals coefficients $C_{6}$, $C_{8}$, and $C_{10}$ of the energies arising from the mutual perturbations of instantaneous electric dipole, quadrupole, and octupole interactions. We establish definitive values including treatment of the finite nuclear mass for the ${}^3$He($2 ^3S$)--${}^3$He($2 ^3P$) and ${}^4$He($2 ^3S$)--${}^4$He($2 ^3P$) interactions.

  2. Drug-Drug Interaction Extraction via Convolutional Neural Networks.

    Science.gov (United States)

    Liu, Shengyu; Tang, Buzhou; Chen, Qingcai; Wang, Xiaolong

    2016-01-01

    Drug-drug interaction (DDI) extraction as a typical relation extraction task in natural language processing (NLP) has always attracted great attention. Most state-of-the-art DDI extraction systems are based on support vector machines (SVM) with a large number of manually defined features. Recently, convolutional neural networks (CNN), a robust machine learning method which almost does not need manually defined features, has exhibited great potential for many NLP tasks. It is worth employing CNN for DDI extraction, which has never been investigated. We proposed a CNN-based method for DDI extraction. Experiments conducted on the 2013 DDIExtraction challenge corpus demonstrate that CNN is a good choice for DDI extraction. The CNN-based DDI extraction method achieves an F-score of 69.75%, which outperforms the existing best performing method by 2.75%. PMID:26941831

  3. Drug-Drug Interaction Extraction via Convolutional Neural Networks.

    Science.gov (United States)

    Liu, Shengyu; Tang, Buzhou; Chen, Qingcai; Wang, Xiaolong

    2016-01-01

    Drug-drug interaction (DDI) extraction as a typical relation extraction task in natural language processing (NLP) has always attracted great attention. Most state-of-the-art DDI extraction systems are based on support vector machines (SVM) with a large number of manually defined features. Recently, convolutional neural networks (CNN), a robust machine learning method which almost does not need manually defined features, has exhibited great potential for many NLP tasks. It is worth employing CNN for DDI extraction, which has never been investigated. We proposed a CNN-based method for DDI extraction. Experiments conducted on the 2013 DDIExtraction challenge corpus demonstrate that CNN is a good choice for DDI extraction. The CNN-based DDI extraction method achieves an F-score of 69.75%, which outperforms the existing best performing method by 2.75%.

  4. Drug-Drug Interaction Extraction via Convolutional Neural Networks

    Directory of Open Access Journals (Sweden)

    Shengyu Liu

    2016-01-01

    Full Text Available Drug-drug interaction (DDI extraction as a typical relation extraction task in natural language processing (NLP has always attracted great attention. Most state-of-the-art DDI extraction systems are based on support vector machines (SVM with a large number of manually defined features. Recently, convolutional neural networks (CNN, a robust machine learning method which almost does not need manually defined features, has exhibited great potential for many NLP tasks. It is worth employing CNN for DDI extraction, which has never been investigated. We proposed a CNN-based method for DDI extraction. Experiments conducted on the 2013 DDIExtraction challenge corpus demonstrate that CNN is a good choice for DDI extraction. The CNN-based DDI extraction method achieves an F-score of 69.75%, which outperforms the existing best performing method by 2.75%.

  5. Moral foundations in an interacting neural networks society

    CERN Document Server

    Vicente, Renato; Jericó, João Pedro; Caticha, Nestor

    2013-01-01

    The moral foundations theory supports that people, across cultures, tend to consider a small number of dimensions when classifying issues on a moral basis. The data also show that the statistics of weights attributed to each moral dimension is related to self-declared political affiliation, which in turn has been connected to cognitive learning styles by recent literature in neuroscience and psychology. Inspired by these data, we propose a simple statistical mechanics model with interacting neural networks classifying vectors and learning from members of their social neighborhood about their average opinion on a large set of issues. The purpose of learning is to reduce dissension among agents even when disagreeing. We consider a family of learning algorithms parametrized by \\delta, that represents the importance given to corroborating (same sign) opinions. We define an order parameter that quantifies the diversity of opinions in a group with homogeneous learning style. Using Monte Carlo simulations and a mean...

  6. Pleistocene megafaunal interaction networks became more vulnerable after human arrival.

    Science.gov (United States)

    Pires, Mathias M; Koch, Paul L; Fariña, Richard A; de Aguiar, Marcus A M; dos Reis, Sérgio F; Guimarães, Paulo R

    2015-09-01

    The end of the Pleistocene was marked by the extinction of almost all large land mammals worldwide except in Africa. Although the debate on Pleistocene extinctions has focused on the roles of climate change and humans, the impact of perturbations depends on properties of ecological communities, such as species composition and the organization of ecological interactions. Here, we combined palaeoecological and ecological data, food-web models and community stability analysis to investigate if differences between Pleistocene and modern mammalian assemblages help us understand why the megafauna died out in the Americas while persisting in Africa. We show Pleistocene and modern assemblages share similar network topology, but differences in richness and body size distributions made Pleistocene communities significantly more vulnerable to the effects of human arrival. The structural changes promoted by humans in Pleistocene networks would have increased the likelihood of unstable dynamics, which may favour extinction cascades in communities facing extrinsic perturbations. Our findings suggest that the basic aspects of the organization of ecological communities may have played an important role in major extinction events in the past. Knowledge of community-level properties and their consequences to dynamics may be critical to understand past and future extinctions. PMID:26336175

  7. Atomic force microscopy study of the interaction of DNA and nanoparticles.

    Science.gov (United States)

    Li, Kungang; Du, Songyan; Van Ginkel, Steven; Chen, Yongsheng

    2014-01-01

    The interaction between nanoparticles (NPs) and DNA plays an important role in the genotoxicity of NPs, and it is imperative to characterize the nano/DNA interactions and explore the underlying chemical mechanisms. In this chapter, we demonstrated systematic experimental approaches based on atomic force microscope (AFM), coupled with modeling computation to probe the binding activity of NPs with DNA and the putative genotoxicity. Using quantum dots (QDs) as a model NP, we examined the binding kinetics, binding isotherm, binding specificity, and binding mechanisms of NPs to DNA with the application of AFM. We further assessed the binding affinity between NPs and DNA by calculating their interaction energy on the basis of Derjaguin-Landau-Verwey-Overbeek (DLVO) models. The modeling results of binding affinity were validated by the NPs/DNA binding images experimentally derived by AFM. The investigation of the relationship between the binding affinity of five NPs ((QDs (+), QDs (-), silver NPs, hematite NPs, and gold NPs) for DNA with their inhibition effects on DNA replication indicated that NPs with a high binding affinity for DNA molecules exhibited higher inhibition on DNA replication. The methodology employed in this study can be extended to study the interaction of other NPs with DNA, which is anticipated to benefit the future design of safe NPs, as well as the toxicological investigations of NPs. PMID:24683029

  8. Interaction forces between silica surfaces in cationic surfactant solutions: an atomic force microscopy study.

    Science.gov (United States)

    Lüderitz, Liset A C; v Klitzing, Regine

    2013-07-15

    The interaction forces between silicon oxide surfaces in the presence of surfactant solutions were studied. Based on the qualitative and quantitative analysis of these interaction forces the correlation with the structure of the aggregates on the surfaces is analyzed. A colloidal probe atomic force microscope (AFM) was used to measure the forces between two colloidal silica particles and between a colloidal particle and a silicon wafer in the presence of hexadecyltrimethylammonium bromide (CTAB) at concentrations between 0.005 mM and 1.2 mM. Different interaction forces were obtained for the silica particle-silica particle system when compared to those for the silica particle-silicon wafer system for the same studied concentration. This indicates that the silica particles and the silicon wafer have different aggregate morphologies on their surfaces. The point of zero charge (pzc) was obtained at 0.05 mM CTAB concentration for the silica particles and at 0.3mM for the silica particle-silicon wafer system. This indicates a higher charge at the silicon wafer than at the silica particles. The observed long range attractions are explained by nanobubbles present at the silicon oxide surfaces and/or by attractive electrostatic interactions between the surfaces, induced by oppositely charged patches at the opposing Si oxide surfaces. PMID:23647691

  9. Pin-Align: A New Dynamic Programming Approach to Align Protein-Protein Interaction Networks

    OpenAIRE

    Farid Amir-Ghiasvand; Abbas Nowzari-Dalini; Vida Momenzadeh

    2014-01-01

    To date, few tools for aligning protein-protein interaction networks have been suggested. These tools typically find conserved interaction patterns using various local or global alignment algorithms. However, the improvement of the speed, scalability, simplification, and accuracy of network alignment tools is still the target of new researches. In this paper, we introduce Pin-Align, a new tool for local alignment of protein-protein interaction networks. Pin-Align accuracy is tested on protein...

  10. Dynamical assessment for evolutions of Atomic-Multinology (AM) in technology innovation using social network theory

    International Nuclear Information System (INIS)

    Highlights: ► The popularity of AM is analyzed by the social network theory. ► The graphical and colorful configurations are used for the meaning of the incident. ► The new industrial field is quantified by dynamical investigations. ► AM can be successfully used in nuclear industry for technology innovation. ► The method could be used for other industries. - Abstract: The technology evolution is investigated. The proposed Atomic Multinology (AM) is quantified by the dynamical method incorporated with Monte-Carlo method. There are three kinds of the technologies as the info-technology (IT), nano-technology (NT), and bio-technology (BT), which are applied to the nuclear technology. AM is initiated and modeled for the dynamic quantifications. The social network algorithm is used in the dynamical simulation for the management of the projects. The result shows that the successfulness of the AM increases, where the 60 years are the investigated period. The values of the dynamical simulation increase in later stage, which means that the technology is matured as time goes on.

  11. MDM2–MDM4 molecular interaction investigated by atomic force spectroscopy and surface plasmon resonance

    Directory of Open Access Journals (Sweden)

    Moscetti I

    2016-08-01

    Full Text Available Ilaria Moscetti,1 Emanuela Teveroni,2,3 Fabiola Moretti,3 Anna Rita Bizzarri,1 Salvatore Cannistraro1 1Biophysics and Nanoscience Centre, Department DEB, Università della Tuscia, Viterbo, Italy; 2Department of Endocrinology and Metabolism, Università Cattolica di Roma, Roma, Italy; 3Institute of Cell Biology and Neurobiology, Consiglio Nazionale delle Ricerche (CNR, Roma, Italy Abstract: Murine double minute 2 (MDM2 and 4 (MDM4 are known as the main negative regulators of p53, a tumor suppressor. They are able to form heterodimers that are much more effective in the downregulation of p53. Therefore, the MDM2–MDM4 complex could be a target for promising therapeutic restoration of p53 function. To this aim, a deeper understanding of the molecular mechanisms underlining the heterodimerization is needed. The kinetic and thermodynamic characterization of the MDM2–MDM4 complex was performed with two complementary approaches: atomic force spectroscopy and surface plasmon resonance. Both techniques revealed an equilibrium dissociation constant (KD in the micromolar range for the MDM2–MDM4 heterodimer, similar to related complexes involved in the p53 network. Furthermore, the MDM2–MDM4 complex is characterized by a relatively high free energy, through a single energy barrier, and by a lifetime in the order of tens of seconds. New insights into the MDM2–MDM4 interaction could be highly important for developing innovative anticancer drugs focused on p53 reactivation. Keywords: MDM2, MDM4, atomic force spectroscopy, surface plasmon resonance

  12. Reconstruction of the Tip-Surface Interaction Potential by Analysis of the Brownian Motion of an Atomic Force Microscope Tip

    NARCIS (Netherlands)

    Willemsen, Oscar H.; Kuipers, Laurens; Werf, van der Kees O.; Grooth, de Bart G.; Greve, Jan

    2000-01-01

    The thermal movement of an atomic force microscope (AFM) tip is used to reconstruct the tip-surface interaction potential. If a tip is brought into the vicinity of a surface, its movement is governed by the sum of the harmonic cantilever potential and the tip-surface interaction potential. By simula

  13. The study of interaction potentials and differential cross sections for collisions between He atoms and hydrogen halide molecules

    Institute of Scientific and Technical Information of China (English)

    孙桂华; 杨向东; 朱俊; 王彩霞

    2002-01-01

    In this paper, we present the uniform interaction potentials for helium atoms and halogen hydride molecules (HF,HC1 and HBr). The differential cross sections are calculated using the above interaction potentials for the He-HF,HCl and HBr systems, respectively, and the results of the calculations are found to be in agreement with the existingtheoretical results and experimental data.

  14. Modeling Ferro- and Antiferromagnetic Interactions in Metal-Organic Coordination Networks

    CERN Document Server

    Faraggi, Marisa N; Stepanow, Sebastian; Tseng, Tzu-Chun; Abdurakhmanova, Nasiba; Kley, Christopher Seiji; Langner, Alexander; Sessi, Violetta; Kern, Klaus; Arnau, Andres

    2014-01-01

    Magnetization curves of two rectangular metal-organic coordination networks formed by the organic ligand TCNQ (7,7,8,8-tetracyanoquinodimethane) and two different (Mn and Ni) 3d transition metal atoms [M(3d)] show marked differences that are explained using first principles density functional theory and model calculations. We find that the existence of a weakly dispersive hybrid band with M(3d) and TCNQ character crossing the Fermi level is determinant for the appearance of ferromagnetic coupling between metal centers, as it is the case of the metallic system Ni-TCNQ but not of the insulating system Mn-TCNQ. The spin magnetic moment localized at the Ni atoms induces a significant spin polarization in the organic molecule; the corresponding spin density being delocalized along the whole system. The exchange interaction between localized spins at Ni centers and the itinerant spin density is ferromagnetic. Based on two different model Hamiltonians, we estimate the strength of exchange couplings between magnetic ...

  15. Opinion dynamics on interacting networks: media competition and social influence.

    Science.gov (United States)

    Quattrociocchi, Walter; Caldarelli, Guido; Scala, Antonio

    2014-01-01

    The inner dynamics of the multiple actors of the informations systems - i.e, T.V., newspapers, blogs, social network platforms, - play a fundamental role on the evolution of the public opinion. Coherently with the recent history of the information system (from few main stream media to the massive diffusion of socio-technical system), in this work we investigate how main stream media signed interaction might shape the opinion space. In particular we focus on how different size (in the number of media) and interaction patterns of the information system may affect collective debates and thus the opinions' distribution. We introduce a sophisticated computational model of opinion dynamics which accounts for the coexistence of media and gossip as separated mechanisms and for their feedback loops. The model accounts also for the effect of the media communication patterns by considering both the simple case where each medium mimics the behavior of the most successful one (to maximize the audience) and the case where there is polarization and thus competition among media memes. We show that plurality and competition within information sources lead to stable configurations where several and distant cultures coexist.

  16. Opinion dynamics on interacting networks: media competition and social influence

    Science.gov (United States)

    Quattrociocchi, Walter; Caldarelli, Guido; Scala, Antonio

    2014-05-01

    The inner dynamics of the multiple actors of the informations systems - i.e, T.V., newspapers, blogs, social network platforms, - play a fundamental role on the evolution of the public opinion. Coherently with the recent history of the information system (from few main stream media to the massive diffusion of socio-technical system), in this work we investigate how main stream media signed interaction might shape the opinion space. In particular we focus on how different size (in the number of media) and interaction patterns of the information system may affect collective debates and thus the opinions' distribution. We introduce a sophisticated computational model of opinion dynamics which accounts for the coexistence of media and gossip as separated mechanisms and for their feedback loops. The model accounts also for the effect of the media communication patterns by considering both the simple case where each medium mimics the behavior of the most successful one (to maximize the audience) and the case where there is polarization and thus competition among media memes. We show that plurality and competition within information sources lead to stable configurations where several and distant cultures coexist.

  17. Entropy evolvement properties in a system of Schr(o)dinger cat state light field interacting with two entangled atoms

    Institute of Scientific and Technical Information of China (English)

    Liu Tang-Kun

    2006-01-01

    The field entropy can be regarded as a measurement of the degree of entanglement between the light field and the atoms of a system which is composed of two-level atoms initially in an entangled state interacting with the Schr(o)dinger cat state. The influences of the strength of light field and the phase angle between the two coherent states on the field entropy are discussed by using numerical calculations. The result shows that when the strength of light field is large enough the field entropy is not zero and the degrees of entanglement between the atoms and the three different states of the light fields are equal. When the strength of the light field is small, the degree of entanglement is maximum in a system of the two entangled atoms interacting with an odd coherent state; it is intermediate for a system of the two entangled atoms interacting with the Yurke-Stoler coherent state, and it is minimum in a system of the two entangled atoms interacting with an even coherent state.

  18. MDM2–MDM4 molecular interaction investigated by atomic force spectroscopy and surface plasmon resonance

    Science.gov (United States)

    Moscetti, Ilaria; Teveroni, Emanuela; Moretti, Fabiola; Bizzarri, Anna Rita; Cannistraro, Salvatore

    2016-01-01

    Murine double minute 2 (MDM2) and 4 (MDM4) are known as the main negative regulators of p53, a tumor suppressor. They are able to form heterodimers that are much more effective in the downregulation of p53. Therefore, the MDM2–MDM4 complex could be a target for promising therapeutic restoration of p53 function. To this aim, a deeper understanding of the molecular mechanisms underlining the heterodimerization is needed. The kinetic and thermodynamic characterization of the MDM2–MDM4 complex was performed with two complementary approaches: atomic force spectroscopy and surface plasmon resonance. Both techniques revealed an equilibrium dissociation constant (KD) in the micromolar range for the MDM2–MDM4 heterodimer, similar to related complexes involved in the p53 network. Furthermore, the MDM2–MDM4 complex is characterized by a relatively high free energy, through a single energy barrier, and by a lifetime in the order of tens of seconds. New insights into the MDM2–MDM4 interaction could be highly important for developing innovative anticancer drugs focused on p53 reactivation. PMID:27621617

  19. Consistent structures and interactions by density functional theory with small atomic orbital basis sets

    Science.gov (United States)

    Grimme, Stefan; Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas

    2015-08-01

    A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of "low-cost" electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT methods

  20. Consistent structures and interactions by density functional theory with small atomic orbital basis sets

    Energy Technology Data Exchange (ETDEWEB)

    Grimme, Stefan, E-mail: grimme@thch.uni-bonn.de; Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas [Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn (Germany)

    2015-08-07

    A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of “low-cost” electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT

  1. VNP: Interactive Visual Network Pharmacology of Diseases, Targets, and Drugs

    OpenAIRE

    Hu, Q-N; Deng, Z.; Tu, W; X. Yang; Meng, Z-B; Deng, Z-X; Liu, J

    2014-01-01

    In drug discovery, promiscuous targets, multifactorial diseases, and “dirty” drugs construct complex network relationships. Network pharmacology description and analysis not only give a systems-level understanding of drug action and disease complexity but can also help to improve the efficiency of target selection and drug design. Visual network pharmacology (VNP) is developed to visualize network pharmacology of targets, diseases, and drugs with a graph network by using disease, target or dr...

  2. Drug-target interaction prediction by random walk on the heterogeneous network.

    Science.gov (United States)

    Chen, Xing; Liu, Ming-Xi; Yan, Gui-Ying

    2012-07-01

    Predicting potential drug-target interactions from heterogeneous biological data is critical not only for better understanding of the various interactions and biological processes, but also for the development of novel drugs and the improvement of human medicines. In this paper, the method of Network-based Random Walk with Restart on the Heterogeneous network (NRWRH) is developed to predict potential drug-target interactions on a large scale under the hypothesis that similar drugs often target similar target proteins and the framework of Random Walk. Compared with traditional supervised or semi-supervised methods, NRWRH makes full use of the tool of the network for data integration to predict drug-target associations. It integrates three different networks (protein-protein similarity network, drug-drug similarity network, and known drug-target interaction networks) into a heterogeneous network by known drug-target interactions and implements the random walk on this heterogeneous network. When applied to four classes of important drug-target interactions including enzymes, ion channels, GPCRs and nuclear receptors, NRWRH significantly improves previous methods in terms of cross-validation and potential drug-target interaction prediction. Excellent performance enables us to suggest a number of new potential drug-target interactions for drug development.

  3. Direct force measurement of single DNA-peptide interactions using atomic force microscopy.

    Science.gov (United States)

    Chung, Ji W; Shin, Dongjin; Kwak, June M; Seog, Joonil

    2013-06-01

    The selective interactions between DNA and miniature (39 residues) engineered peptide were directly measured at the single-molecule level by using atomic force microscopy. This peptide (p007) contains an α-helical recognition site similar to leucine zipper GCN4 and specifically recognizes the ATGAC sequence in the DNA with nanomolar affinity. The average rupture force was 42.1 pN, which is similar to the unbinding forces of the digoxigenin-antidigoxigenin complex, one of the strongest interactions in biological systems. The single linear fit of the rupture forces versus the logarithm of pulling rates showed a single energy barrier with a transition state located at 0.74 nm from the bound state. The smaller koff compared with that of other similar systems was presumably due to the increased stability of the helical structure by putative folding residues in p007. This strong sequence-specific DNA-peptide interaction has a potential to be utilized to prepare well-defined mechanically stable DNA-protein hybrid nanostructures.

  4. Photon Devil’s staircase: photon long-range repulsive interaction in lattices of coupled resonators with Rydberg atoms

    OpenAIRE

    Zhang, Yuanwei; Fan, Jingtao; Liang, J. -Q.; Ma, Jie; Chen, Gang; Jia, Suotang; Nori, Franco

    2015-01-01

    The realization of strong coherent interactions between individual photons is a long-standing goal in science and engineering. In this report, based on recent experimental setups, we derive a strong photon long-range repulsive interaction, by controlling the van der Waals repulsive force between Cesium Rydberg atoms located inside different cavities in extended Jaynes-Cummings-Hubbard lattices. We also find novel quantum phases induced by this photon long-range repulsive interaction. For exam...

  5. Approximate and Conditional Teleportation of an Unknown Atomic State Without Bell-State Measurement with Two-Photon Interaction

    International Nuclear Information System (INIS)

    A scheme for approximately and conditionally teleporting an unknown atomic state via two-photon interaction in cavity QED is proposed. It is the extension of the scheme of Ref. [11] [Phys. Rev. A 69 (2004) 064302], which is based on Jaynes-Cummings model in QED and where only a time point of system evolution and the corresponding fidelity implementing the teleportation are given. In our scheme, the two-photon interaction Jaynes-Cummings model is used to realize the approximate and conditional teleportation. Our scheme does not involve the Bell-state measurement and an additional atom, only requiring two atoms and one single-mode cavity. The fidelity of the scheme is higher than that of Ref. [11]. The scheme may be generalized to not only the teleportation of the state of a cavity mode to another mode by means of a single atom but also the teleportation of the state of a trapped ion.

  6. Approximate and Conditional Teleportation of an Unknown Atomic State Without Bell-State Measurement with Two-Photon Interaction

    Institute of Scientific and Technical Information of China (English)

    CHEN Chang-Yong

    2006-01-01

    A scheme for approximately and conditionally teleporting an unknown atomic state via two-photon interaction in cavity QED is proposed. It is the extension of the scheme of Ref. [11] [Phys. Rev. A 69 (2004) 064302], which is based on Jaynes-Cummings model in QED and where only a time point of system evolution and the corresponding fidelity implementing the teleportation are given. In our scheme, the two-photon interaction Jaynes-Cummings model is used to realize the approximate and conditional teleportation. Our scheme does not involve the Bell-state measurement and an additional atom, only requiring two atoms and one single-mode cavity. The fidelity of the scheme is higher than that of Ref. [11]. The scheme may be generalized to not only the teleportation of the state of a cavity mode to another mode by means of a single atom but also the teleportation of the state of a trapped ion.

  7. Dynamics of gas-surface interactions atomic-level understanding of scattering processes at surfaces

    CERN Document Server

    Díez Muniño, Ricardo

    2013-01-01

    This book gives a representative survey of the state of the art of research on gas-surface interactions. It provides an overview of the current understanding of gas surface dynamics and, in particular, of the reactive and non-reactive processes of atoms and small molecules at surfaces. Leading scientists in the field, both from the theoretical and the experimental sides, write in this book about their most recent advances. Surface science grew as an interdisciplinary research area over the last decades, mostly because of new experimental technologies (ultra-high vacuum, for instance), as well as because of a novel paradigm, the ‘surface science’ approach. The book describes the second transformation which is now taking place pushed by the availability of powerful quantum-mechanical theoretical methods implemented numerically. In the book, experiment and theory progress hand in hand with an unprecedented degree of accuracy and control. The book presents how modern surface science targets the atomic-level u...

  8. Investigation of the Interactions and Bonding between Carbon and Group VIII Metals at the Atomic Scale.

    Science.gov (United States)

    Zoberbier, Thilo; Chamberlain, Thomas W; Biskupek, Johannes; Suyetin, Mikhail; Majouga, Alexander G; Besley, Elena; Kaiser, Ute; Khlobystov, Andrei N

    2016-03-23

    The nature and dynamics of bonding between Fe, Ru, Os, and single-walled carbon nanotubes (SWNTs) is studied by aberration-corrected high-resolution transmission electron microscopy (AC-HRTEM). The metals catalyze a wide variety of different transformations ranging from ejection of carbon atoms from the nanotube sidewall to the formation of hollow carbon shells or metal carbide within the SWNT, depending on the nature of the metal. The electron beam of AC-HRTEM serves the dual purpose of providing energy to the specimen and simultaneously enabling imaging of chemical transformations. Careful control of the electron beam parameters, energy, flux, and dose allowed direct comparison between the metals, demonstrating that their chemical reactions with SWNTs are determined by a balance between the cohesive energy of the metal particles and the strength of the metal-carbon σ- or π-bonds. The pathways of transformations of a given metal can be drastically changed by applying different electron energies (80, 40, or 20 keV), thus demonstrating AC-HRTEM as a new tool to direct and study chemical reactions. The understanding of interactions and bonding between SWNT and metals revealed by AC-HRTEM at the atomic level has important implications for nanotube-based electronic devices and catalysis. PMID:26848826

  9. Interaction of Rydberg atoms in circular states with the alkaline-earth Ca(4s{sup 2}) and Sr(5s{sup 2}) atoms

    Energy Technology Data Exchange (ETDEWEB)

    Mironchuk, E. S.; Narits, A. A.; Lebedev, V. S., E-mail: vlebedev@sci.lebedev.ru [Russian Academy of Sciences, Lebedev Physical Institute (Russian Federation)

    2015-11-15

    The resonant mechanism of interaction of alkaline-earth atoms having a low electron affinity to Rydberg atoms in circular (l = vertical bar m vertical bar = n–1) and near-circular states has been studied. To describe the dynamics of resonant processes accompanied by nonadiabatic transitions between ionic and Rydberg covalent terms of a quasimolecule, an approach based on the integration of coupled equations for the probability amplitudes has been developed taking into account the possibility of the decay of an anion in the Coulomb field of the positive ionic core of a highly excited atom. The approach involves the specific features of the problem associated with the structure of the wavefunction of a Rydberg electron in states with high orbital angular momenta l ∼ n–1. This approach provides a much more accurate description of the dynamics of electronic transitions at collisions between atoms than that within the modified semiclassical Landau–Zener model. In addition, this approach makes it possible to effectively take into account many channels of the problem. The cross sections for resonant quenching of Rydberg states of the Li(nlm) atom with given principal n, orbital l = n–1, and magnetic m quantum numbers at thermal collisions with the Ca(4s{sup 2}) and Sr(5s{sup 2}) atoms have been calculated. The dependences of the results on n, m, and angle α between the relative velocity of the atoms and the normal to the plane of the orbit of the Rydberg electron have been obtained. The influence of orientational effects on the efficiency of the collisional destruction of circular and near-circular states has been studied. The results indicate a higher stability of such states to their perturbations by neutral particles as compared to usually studied nl states with low values of l (l ≪ n)

  10. Entropy squeezing of the field interacting with a nearly degenerate V-type three-level atom

    Institute of Scientific and Technical Information of China (English)

    Zhou Qing-Chun; Zhu Shi-Ning

    2005-01-01

    The position- and momentum-entopic squeezing properties of the optical field in the system of a nearly degenerate three-level atom interacting with a single-mode field are investigated. Calculation results indicate that when the field is initially in the vacuum state, it may lead to squeezing of the position entropy or the momentum entropy of the field if the atom is prepared properly. The effects of initial atomic state and the splitting of the excited levels of the atom on field entropies are discussed in this case. When the initial field is in a coherent state, we find that position-entropy squeezing of the field is present even if the atom is prepared in the ground state. By comparing the variance squeezing and entropy squeezing of the field we confirm that entropy is more sensitive than variance in measuring quantum fluctuations.

  11. The integrated analysis of metabolic and protein interaction networks reveals novel molecular organizing principles

    Directory of Open Access Journals (Sweden)

    Walther Dirk

    2008-11-01

    Full Text Available Abstract Background The study of biological interaction networks is a central theme of systems biology. Here, we investigate the relationships between two distinct types of interaction networks: the metabolic pathway map and the protein-protein interaction network (PIN. It has long been established that successive enzymatic steps are often catalyzed by physically interacting proteins forming permanent or transient multi-enzymes complexes. Inspecting high-throughput PIN data, it was shown recently that, indeed, enzymes involved in successive reactions are generally more likely to interact than other protein pairs. In our study, we expanded this line of research to include comparisons of the underlying respective network topologies as well as to investigate whether the spatial organization of enzyme interactions correlates with metabolic efficiency. Results Analyzing yeast data, we detected long-range correlations between shortest paths between proteins in both network types suggesting a mutual correspondence of both network architectures. We discovered that the organizing principles of physical interactions between metabolic enzymes differ from the general PIN of all proteins. While physical interactions between proteins are generally dissortative, enzyme interactions were observed to be assortative. Thus, enzymes frequently interact with other enzymes of similar rather than different degree. Enzymes carrying high flux loads are more likely to physically interact than enzymes with lower metabolic throughput. In particular, enzymes associated with catabolic pathways as well as enzymes involved in the biosynthesis of complex molecules were found to exhibit high degrees of physical clustering. Single proteins were identified that connect major components of the cellular metabolism and may thus be essential for the structural integrity of several biosynthetic systems. Conclusion Our results reveal topological equivalences between the protein

  12. Atomic and plasma-material interaction data for fusion. V. 5

    International Nuclear Information System (INIS)

    Volume 5 of the supplements on ''atomic and plasma-material interaction data for fusion'' to the journal ''Nuclear Fusion'' is devoted to a critical assessment of the physical and thermo-mechanical properties of presently considered candidate plasma-facing and structural materials for next-generation thermonuclear fusion devices. It contains 9 papers. The subjects are: (i) requirements and selection criteria for plasma-facing materials and components in the ITER EDA (Engineering Design Activities) design; (ii) thermomechanical properties of Beryllium; (iii) material properties data for fusion reactor plasma-facing carbon-carbon composites; (iv) high-Z candidate plasma facing materials; (v) recommended property data for Molybdenum, Niobium and Vanadium alloys; (vi) copper alloys for high heat flux structure applications; (vii) erosion of plasma-facing materials during a tokamak disruption; (viii) runaway electron effects; and (ix) data bases for thermo-hydrodynamic coupling with coolants. Refs, figs, tabs

  13. Shifted Tietz-Wei oscillator for simulating the atomic interaction in diatomic molecules

    CERN Document Server

    Falaye, Babatunde J; Hamzavi, Majid

    2015-01-01

    The shifted Tietz-Wei (sTW) oscillator is as good as traditional Morse potential in simulating the atomic interaction in diatomic molecules. By using the Pekeris-type approximation to deal with the centrifugal term, we obtain the bound-state solutions of the radial Schr\\"odinger equation with this typical molecular model via the exact quantization rule (EQR). The energy spectrum for a set of diatomic molecules ($NO \\left(a^4\\Pi_i\\right)$, $NO \\left(B^2\\Pi_r\\right)$, $NO \\left(L'^2\\phi\\right)$, $NO \\left(b^4\\Sigma^{-}\\right)$, $ICl\\left(X^1\\Sigma_g^{+}\\right)$, $ICl\\left(A^3\\Pi_1\\right)$ and $ICl\\left(A'^3\\Pi_2\\right)$ for arbitrary values of $n$ and $\\ell$ quantum numbers are obtained. For the sake of completeness, we study the corresponding wavefunctions using the formula method.

  14. Three-body bound states in atomic mixtures with resonant p-wave interaction

    CERN Document Server

    Efremov, Maxim A; Ivanov, Misha Yu; Schleich, Wolfgang P

    2013-01-01

    We employ the Born-Oppenheimer approximation to find the effective potential in a three-body system consisting of a light particle and two heavy ones when the heavy-light short-range interaction potential has a resonance corresponding to a non-zero orbital angular momentum. In the case of an exact resonance in the p-wave scattering amplitude, the effective potential is attractive and long-range, namely it decreases as the third power of the inter-atomic distance. Moreover, we show that the range and power of the potential, as well as the number of bound states are determined by the mass ratio of the particles and the parameters of the heavy-light short-range potential.

  15. A Partitioned Correlation Function Interaction approach for describing electron correlation in atoms

    CERN Document Server

    Verdebout, S; Jönsson, P; Gaigalas, G; Fischer, C Froese; Godefroid, M

    2013-01-01

    Traditional multiconfiguration Hartree-Fock (MCHF) and configuration interaction (CI) methods are based on a single orthonormal orbital basis (OB). For atoms with complicated shell structures, a large OB is needed to saturate all the electron correlation effects. The large OB leads to massive configuration state function (CSF) expansions that are difficult to handle. We show that it is possible to relax the orthonormality restriction on the OB and break down the originally large calculations to a set of smaller ones that can be run in parallel. Each calculation determines a partitioned correlation function (PCF) that accounts for a specific correlation effect. The PCFs are built on optimally localized orbital sets and are added to a zero-order multireference (MR) function to form a total wave function. The mixing coefficients of the PCFs are fixed from a small generalized eigenvalue problem. The required matrices are computed using a biorthonormal transformation technique. The new method, called partitioned c...

  16. The thermal Casimir-Polder interaction of an atom with spherical plasma shell

    CERN Document Server

    Khusnutdinov, Nail R

    2012-01-01

    The van der Waals and Casimir-Polder interaction energy of an atom with an infinitely thin sphere with finite conductivity is investigated in the framework of the hydrodynamic approach at finite temperature. The Lifshits approach is used to find the free energy. We find the close expression for the free energy and make the analysis of it for i) high and low temperatures, ii) large radii of sphere and ii) short distance from sphere. At low temperatures the thermal part of the free energy tends to zero as forth power of the temperature while for high temperatures it is proportional to the first degree of the temperature. We show that the entropy of this system is positive for small radii of sphere and it becomes negative at low temperatures and for large radii of the sphere.

  17. Charge transfer in the interactions of partially stripped ions with atoms at intermediate and high energies

    International Nuclear Information System (INIS)

    The Coulomb-Born (CB) approximation has been employed to study charge transfer cross sections in collisions of Cq+, Nq+ and Oq+ (q = 1-5) with atomic hydrogen in ground state in the energy range of 30-200 keV/amu. The interaction of the active electron with the incoming projectile ion has been approximated by a model potential containing both a long-range part and a short-range part. Variations of total capture cross sections with impact energy compare favourable well with the available experimental observations and with other theoretical findings. In addition, sub-shell distributions of total capture cross sections are given in graphical form. However, we are unable to find any oscillation in the charge-state dependence of total capture cross sections. (author)

  18. Relativistic theory of atom-laser interactions at very high laser intensities

    International Nuclear Information System (INIS)

    The high-frequency approximation of Kristic and Mittleman is considered in detail as a basis for the relativistic theory of the atom-laser interactions. The properties of the 3D potentials are discussed. Within a one-dimensional model, similar to that employed by Kylstra, Ermolaev, and Joachain in ab initio calculations on the time-dependent Dirac equation, the electron mass-shift due to dressing by a superstrong laser field is investigated. In the full domain of the laser parameters, frequency ω and the peak field strength Ε0, the 1D bound states exhibit remarkable features. The numerical calculations show the existence of a very wide intermediate range of the field strengths where, in the zeroth-order of the high-frequency approximation, the binding is stabilized by the field

  19. Molecular Architecture of Spinal Cord Injury Protein Interaction Network.

    Directory of Open Access Journals (Sweden)

    Ali Alawieh

    Full Text Available Spinal cord injury (SCI is associated with complex pathophysiological processes that follow the primary traumatic event and determine the extent of secondary damage and functional recovery. Numerous reports have used global and hypothesis-driven approaches to identify protein changes that contribute to the overall pathology of SCI in an effort to identify potential therapeutic interventions. In this study, we use a semi-automatic annotation approach to detect terms referring to genes or proteins dysregulated in the SCI literature and develop a curated SCI interactome. Network analysis of the SCI interactome revealed the presence of a rich-club organization corresponding to a "powerhouse" of highly interacting hub-proteins. Studying the modular organization of the network have shown that rich-club proteins cluster into modules that are specifically enriched for biological processes that fall under the categories of cell death, inflammation, injury recognition and systems development. Pathway analysis of the interactome and the rich-club revealed high similarity indicating the role of the rich-club proteins as hubs of the most prominent pathways in disease pathophysiology and illustrating the centrality of pro-and anti-survival signal competition in the pathology of SCI. In addition, evaluation of centrality measures of single nodes within the rich-club have revealed that neuronal growth factor (NGF, caspase 3, and H-Ras are the most central nodes and potentially an interesting targets for therapy. Our integrative approach uncovers the molecular architecture of SCI interactome, and provide an essential resource for evaluating significant therapeutic candidates.

  20. Nonclasssical Properties in Two-Mode Fields Resonantly Interacting with a Three-Level [Ⅰ]-Type Atom

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Some noclassical properties in electromagnetic Reid are investigated for the interaction of two-modes initially taken in coherent-state representation with the three-level [Ⅰ]-type atom, such as squeezing properties and violation of the Cauchy-Schwartz inequality. The enhancement of Geld squeezing is found by selective atomic measurement. The Cauchy-Schwartz inequality is violated by the application of the classical Geld followed by detection in excited state.

  1. Generation of four-photon GHZ states based on interaction between a four-level atom and two bimodal cavities

    Institute of Scientific and Technical Information of China (English)

    ZHANG Deng-yu; TANG Shi-qing; WANG Xin-wer; XIE Li-jun; ZHAN Xiao-gui; CHEN Yin-hua

    2012-01-01

    A simple scheme is presented for generating four-photon Greenberger-Horne-Zeilinger (GHZ) states with interaction between a four-level atom and two bimodal cavities.In the proposed protocol,the quantum information is encoded on Fock states of the cavity fields.The detection of the atom can collapse the cavity to the desired state.The experimental feasibility of our proposal is also discussed.

  2. Generation of four-photon entangled states based on interaction between a three-level atom and two bimodal cavities

    Institute of Scientific and Technical Information of China (English)

    ZHANG Dengyu; TANG Shiqing; WANG Xinwen; XIE Lijun; ZHAN Xiaogui; CHEN Yinhua

    2011-01-01

    A simple scheme is presented for generating four-photon entangled states with interaction between a three-level atom and two bimodal cavities.In the proposed protocol,the quantum information is encoded on Fock states of the cavity fields.The detection of the atom can collapse the cavity made/wave function to the desired state.The experimental feasibility of our proposal is also discussed.

  3. Laser spectroscopy with nanometric gas cells distance dependence of atom-surface interaction and collisions under confinement

    CERN Document Server

    Hamdi, I; Yarovitski, A; Dutier, G; Maurin, I; Saltiel, S; Li, Y; Lezama, A; Vartapetyan, T; Sarkisyan, D; Gorza, M P; Fichet, M; Bloch, D; Ducloy, M; Hamdi, Ismah\\`{e}ne; Todorov, Petko; Yarovitski, Alexander; Dutier, Gabriel; Maurin, Isabelle; Saltiel, Solomon; Li, Yuanyuan; Lezama, Arturo; Varzhapetyan, Tigran; Sarkisyan, David; Gorza, Marie-Pascale; Fichet, Mich\\`{e}le; Bloch, Daniel; Ducloy, Martial

    2005-01-01

    The high sensitivity of Laser Spectroscopy has made possible the exploration of atomic resonances in newly designed "nanometric" gas cells, whose local thickness varies from 20nm to more than 1000 nm. Following the initial observation of the optical analogous of the coherent Dicke microwave narrowing, the newest prospects include the exploration of long-range atom surface van der Waals interaction with spatial resolution in an unprecedented range of distances, modification of atom dielectric resonant coupling under the influence of the coupling between the two neighbouring dielectric media, and even the possible modification of interatomic collisions processes under the effect of confinement.

  4. The virome: a missing component of biological interaction networks in health and disease.

    Science.gov (United States)

    Handley, Scott A

    2016-01-01

    Host-associated viral populations, viromes, have been understudied relative to their contribution to human physiology. Viruses interact with host gene networks, influencing both health and disease. Analysis of host gene networks in the absence of virome analysis risks missing important network information. PMID:27037032

  5. Fading characterization for context aware body area networks (CABAN) in interactive smart environments

    NARCIS (Netherlands)

    Heaney, S.F.; Scanlon, W.G.; Garcia-Palacios, E.; Cotton, S.L.

    2010-01-01

    Body Area Networks are unique in that the large-scale mobility of users allows the network itself to travel across a diverse range of operating domains. This presents the possibility of creating interactive smart environments where Context Aware Body Area Networks can sense and co-operate with nearb

  6. Some Statistical Properties for Interacting Between a Two Two-Level Atoms and the Electromagnetic Fields in Present of Converter Terms

    Science.gov (United States)

    Ali, S. I.

    2016-01-01

    Two two-level atoms interacting with a finite dimensional four-mode of radiation field is presented. The interaction of the field-field and the atom-field are considered. By using some canonical transformation, an exact solution of the wave function in the Schrodinger picture is obtained. The atomic inversion, the entropy squeezing, variance squeezing and scaled atomic Wehrl entropy phenomena are investigated. All theses phenomena are been controlled by finite state parameters and photon number operators.

  7. Topology association analysis in weighted protein interaction network for gene prioritization

    Science.gov (United States)

    Wu, Shunyao; Shao, Fengjing; Zhang, Qi; Ji, Jun; Xu, Shaojie; Sun, Rencheng; Sun, Gengxin; Du, Xiangjun; Sui, Yi

    2016-11-01

    Although lots of algorithms for disease gene prediction have been proposed, the weights of edges are rarely taken into account. In this paper, the strengths of topology associations between disease and essential genes are analyzed in weighted protein interaction network. Empirical analysis demonstrates that compared to other genes, disease genes are weakly connected with essential genes in protein interaction network. Based on this finding, a novel global distance measurement for gene prioritization with weighted protein interaction network is proposed in this paper. Positive and negative flow is allocated to disease and essential genes, respectively. Additionally network propagation model is extended for weighted network. Experimental results on 110 diseases verify the effectiveness and potential of the proposed measurement. Moreover, weak links play more important role than strong links for gene prioritization, which is meaningful to deeply understand protein interaction network.

  8. Designing finger touch gestures for affective and expressive interaction on mobile social networking sites

    OpenAIRE

    Amoor Pour, Sepehr

    2014-01-01

    This thesis project is an interaction design study, which studies how finger touch gestures can be used as expressive alternatives to text comments on social networking sites. In the study qualitative research methods and a user-centred approach are used. The study collects literature on how emotion is modeled in Human-computer Interaction and how emotion can be expressed through touch. The popular social networking site Facebook is used as a case study of user behavior on social networking s...

  9. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae

    OpenAIRE

    Botstein David; Ho Yuen; Stark Chris; Tong Amy; Oughtred Rose; Friesen Helena; Parsons Ainslie; Myers Chad L; Hon Gary C; Breitkreutz Bobby-Joe; Boucher Lorrie; Breitkreutz Ashton; Reguly Teresa; Andrews Brenda; Boone Charles

    2006-01-01

    Abstract Background The study of complex biological networks and prediction of gene function has been enabled by high-throughput (HTP) methods for detection of genetic and protein interactions. Sparse coverage in HTP datasets may, however, distort network properties and confound predictions. Although a vast number of well substantiated interactions are recorded in the scientific literature, these data have not yet been distilled into networks that enable system-level inference. Results We des...

  10. The correlation between fragility, density, and atomic interaction in glass-forming liquids

    Science.gov (United States)

    Wang, Lijin; Guan, Pengfei; Wang, W. H.

    2016-07-01

    The fragility that controls the temperature-dependent viscous properties of liquids as the glass transition is approached, in various glass-forming liquids with different softness of the repulsive part of atomic interactions at different densities, is investigated by molecular dynamic simulations. We show that the landscape of fragility in purely repulsive systems can be separated into three regions denoted as RI, RII, and RIII, respectively, with qualitatively disparate dynamic behaviors: RI which can be described by "softness makes strong glasses," RII where fragility is independent of softness and can only be tuned by density, and RIII with constant fragility, suggesting that density plays an unexpected role for understanding the repulsive softness dependence of fragility. What is more important is that we unify the long-standing inconsistence with respect to the repulsive softness dependence of fragility by observing that a glass former can be tuned more fragile if nonperturbative attraction is added into it. Moreover, we find that the vastly dissimilar influences of attractive interaction on fragility could be estimated from the structural properties of related zero-temperature glasses.

  11. Visualisation of the interaction between Acidithiobacillus ferrooxidans and oil shale by atomic force microscopy

    Directory of Open Access Journals (Sweden)

    Milić Jelena S.

    2012-01-01

    Full Text Available This study visually documents the mechanical contact and interaction between the bacterial cells of two biogeocenotically different strains of Acidithiobacillus ferrooxidans (At. ferrooxidans and oil shale containing pyrite. Atomic force microscopy (AFM imaging was used to visualise initial interaction between the microorganisms and the surface minerals of an oil shale and to evaluate bacterial effects in the first hours of the bioleaching process. Acidithiobacillus ferrooxidans was attached to the shale surface already after 2 h, and after 48 h, numerous cells covered the surface with a biofilm. After 5 day incubation with At. ferrooxidans, AFM imaging revealed ellipsoid etched pits that represent footprints left by detached cells. Combining AFM surface imaging and leaching analysis following bacterial colonisation of oil shale layers demonstrates that an initial attachment to the surface is necessary for the leaching and that later on, once a sufficient concentration of Fe2+ ions in the solution is achieved, cells detach to become free cells, and leaching occurs primarily by the Fe3+. This experiment confirmed that microorganisms isolated from sites in which a particular substrate is found will demonstrate stronger binding to that substrate.

  12. Spin filtering and switching action in a diamond network with magnetic-nonmagnetic atomic distribution

    Science.gov (United States)

    Pal, Biplab; Dutta, Paramita

    2016-09-01

    We propose a simple model quantum network consisting of diamond-shaped plaquettes with deterministic distribution of magnetic and non-magnetic atoms in presence of a uniform external magnetic flux in each plaquette and predict that such a simple model can be a prospective candidate for spin filter as well as flux driven spintronic switch. The orientations and the amplitudes of the substrate magnetic moments play a crucial role in the energy band engineering of the two spin channels which essentially gives us a control over the spin transmission leading to a spin filtering effect. The externally tunable magnetic flux plays an important role in inducing a switch on-switch off effect for both the spin states indicating the behavior like a spintronic switch. Even a correlated disorder configuration in the on-site potentials and in the magnetic moments may lead to disorder-induced spin filtering phenomenon where one of the spin channel gets entirely blocked leaving the other one transmitting over the entire allowed energy regime. All these features are established by evaluating the density of states and the two terminal transmission probabilities using the transfer-matrix formalism within a tight-binding framework. Experimental realization of our theoretical study may be helpful in designing new spintronic devices.

  13. Spin filtering and switching action in a diamond network with magnetic-nonmagnetic atomic distribution.

    Science.gov (United States)

    Pal, Biplab; Dutta, Paramita

    2016-01-01

    We propose a simple model quantum network consisting of diamond-shaped plaquettes with deterministic distribution of magnetic and non-magnetic atoms in presence of a uniform external magnetic flux in each plaquette and predict that such a simple model can be a prospective candidate for spin filter as well as flux driven spintronic switch. The orientations and the amplitudes of the substrate magnetic moments play a crucial role in the energy band engineering of the two spin channels which essentially gives us a control over the spin transmission leading to a spin filtering effect. The externally tunable magnetic flux plays an important role in inducing a switch on-switch off effect for both the spin states indicating the behavior like a spintronic switch. Even a correlated disorder configuration in the on-site potentials and in the magnetic moments may lead to disorder-induced spin filtering phenomenon where one of the spin channel gets entirely blocked leaving the other one transmitting over the entire allowed energy regime. All these features are established by evaluating the density of states and the two terminal transmission probabilities using the transfer-matrix formalism within a tight-binding framework. Experimental realization of our theoretical study may be helpful in designing new spintronic devices. PMID:27600958

  14. Cancer risk at low doses of ionizing radiation: artificial neural networks inference from atomic bomb survivors.

    Science.gov (United States)

    Sasaki, Masao S; Tachibana, Akira; Takeda, Shunichi

    2014-05-01

    Cancer risk at low doses of ionizing radiation remains poorly defined because of ambiguity in the quantitative link to doses below 0.2 Sv in atomic bomb survivors in Hiroshima and Nagasaki arising from limitations in the statistical power and information available on overall radiation dose. To deal with these difficulties, a novel nonparametric statistics based on the 'integrate-and-fire' algorithm of artificial neural networks was developed and tested in cancer databases established by the Radiation Effects Research Foundation. The analysis revealed unique features at low doses that could not be accounted for by nominal exposure dose, including (i) the presence of a threshold that varied with organ, gender and age at exposure, and (ii) a small but significant bumping increase in cancer risk at low doses in Nagasaki that probably reflects internal exposure to (239)Pu. The threshold was distinct from the canonical definition of zero effect in that it was manifested as negative excess relative risk, or suppression of background cancer rates. Such a unique tissue response at low doses of radiation exposure has been implicated in the context of the molecular basis of radiation-environment interplay in favor of recently emerging experimental evidence on DNA double-strand break repair pathway choice and its epigenetic memory by histone marking. PMID:24366315

  15. Influence of Halide Solutions on Collagen Networks: Measurements of Physical Properties by Atomic Force Microscopy

    Science.gov (United States)

    Kempe, André; Lackner, Maximilian

    2016-01-01

    The influence of aqueous halide solutions on collagen coatings was tested. The effects on resistance against indentation/penetration on adhesion forces were measured by atomic force microscopy (AFM) and the change of Young's modulus of the coating was derived. Comparative measurements over time were conducted with halide solutions of various concentrations. Physical properties of the mesh-like coating generally showed large variability. Starting with a compact set of physical properties, data disperse after minutes. A trend of increase in elasticity and permeability was found for all halide solutions. These changes were largest in NaI, displaying a logical trend with ion size. However a correlation with concentration was not measured. Adhesion properties were found to be independent of mechanical properties. The paper also presents practical experience for AFM measurements of soft tissue under liquids, particularly related to data evaluation. The weakening in physical strength found after exposure to halide solutions may be interpreted as widening of the network structure or change in the chemical properties in part of the collagen fibres (swelling). In order to design customized surface coatings at optimized conditions also for medical applications, halide solutions might be used as agents with little impact on the safety of patients.

  16. Evaluating the spatio-temporal factors that structure network parameters of plant-herbivore interactions.

    Directory of Open Access Journals (Sweden)

    Antonio López-Carretero

    Full Text Available Despite the dynamic nature of ecological interactions, most studies on species networks offer static representations of their structure, constraining our understanding of the ecological mechanisms involved in their spatio-temporal stability. This is the first study to evaluate plant-herbivore interaction networks on a small spatio-temporal scale. Specifically, we simultaneously assessed the effect of host plant availability, habitat complexity and seasonality on the structure of plant-herbivore networks in a coastal tropical ecosystem. Our results revealed that changes in the host plant community resulting from seasonality and habitat structure are reflected not only in the herbivore community, but also in the emergent properties (network parameters of the plant-herbivore interaction network such as connectance, selectiveness and modularity. Habitat conditions and periods that are most stressful favored the presence of less selective and susceptible herbivore species, resulting in increased connectance within networks. In contrast, the high degree of selectivennes (i.e. interaction specialization and modularity of the networks under less stressful conditions was promoted by the diversification in resource use by herbivores. By analyzing networks at a small spatio-temporal scale we identified the ecological factors structuring this network such as habitat complexity and seasonality. Our research offers new evidence on the role of abiotic and biotic factors in the variation of the properties of species interaction networks.

  17. Simulated evolution of protein-protein interaction networks with realistic topology.

    Science.gov (United States)

    Peterson, G Jack; Pressé, Steve; Peterson, Kristin S; Dill, Ken A

    2012-01-01

    We model the evolution of eukaryotic protein-protein interaction (PPI) networks. In our model, PPI networks evolve by two known biological mechanisms: (1) Gene duplication, which is followed by rapid diversification of duplicate interactions. (2) Neofunctionalization, in which a mutation leads to a new interaction with some other protein. Since many interactions are due to simple surface compatibility, we hypothesize there is an increased likelihood of interacting with other proteins in the target protein's neighborhood. We find good agreement of the model on 10 different network properties compared to high-confidence experimental PPI networks in yeast, fruit flies, and humans. Key findings are: (1) PPI networks evolve modular structures, with no need to invoke particular selection pressures. (2) Proteins in cells have on average about 6 degrees of separation, similar to some social networks, such as human-communication and actor networks. (3) Unlike social networks, which have a shrinking diameter (degree of maximum separation) over time, PPI networks are predicted to grow in diameter. (4) The model indicates that evolutionarily old proteins should have higher connectivities and be more centrally embedded in their networks. This suggests a way in which present-day proteomics data could provide insights into biological evolution.

  18. Simulated evolution of protein-protein interaction networks with realistic topology.

    Directory of Open Access Journals (Sweden)

    G Jack Peterson

    Full Text Available We model the evolution of eukaryotic protein-protein interaction (PPI networks. In our model, PPI networks evolve by two known biological mechanisms: (1 Gene duplication, which is followed by rapid diversification of duplicate interactions. (2 Neofunctionalization, in which a mutation leads to a new interaction with some other protein. Since many interactions are due to simple surface compatibility, we hypothesize there is an increased likelihood of interacting with other proteins in the target protein's neighborhood. We find good agreement of the model on 10 different network properties compared to high-confidence experimental PPI networks in yeast, fruit flies, and humans. Key findings are: (1 PPI networks evolve modular structures, with no need to invoke particular selection pressures. (2 Proteins in cells have on average about 6 degrees of separation, similar to some social networks, such as human-communication and actor networks. (3 Unlike social networks, which have a shrinking diameter (degree of maximum separation over time, PPI networks are predicted to grow in diameter. (4 The model indicates that evolutionarily old proteins should have higher connectivities and be more centrally embedded in their networks. This suggests a way in which present-day proteomics data could provide insights into biological evolution.

  19. Functional organization and its implication in evolution of the human protein-protein interaction network

    OpenAIRE

    Zhao Yiqiang; Mooney Sean D

    2012-01-01

    Abstract Background Based on the distinguishing properties of protein-protein interaction networks such as power-law degree distribution and modularity structure, several stochastic models for the evolution of these networks have been purposed, motivated by the idea that a validated model should reproduce similar topological properties of the empirical network. However, being able to capture topological properties does not necessarily mean it correctly reproduces how networks emerge and evolv...

  20. HKC: An Algorithm to Predict Protein Complexes in Protein-Protein Interaction Networks

    OpenAIRE

    Xiaomin Wang; Zhengzhi Wang; Jun Ye

    2011-01-01

    With the availability of more and more genome-scale protein-protein interaction (PPI) networks, research interests gradually shift to Systematic Analysis on these large data sets. A key topic is to predict protein complexes in PPI networks by identifying clusters that are densely connected within themselves but sparsely connected with the rest of the network. In this paper, we present a new topology-based algorithm, HKC, to detect protein complexes in genome-scale PPI networks. HKC mainly use...