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. An Atomic Force Microscopy Study of the Interactions Involving Polymers and Silane Networks

    Directory of Open Access Journals (Sweden)

    Rodrigo L. Oréfice

    1998-12-01

    Full Text Available ABSTRACT: Silane coupling agents have been frequently used as interfacial agents in polymer composites to improve interfacial strength and resistance to fluid migration. Although the capability of these agents in improving properties and performance of composites has been reported, there are still many uncertainties regarding the processing-structure-property relationships and the mechanisms of coupling developed by silane agents. In this work, an Atomic Force Microscope (AFM was used to measure interactions between polymers and silica substrates, where silane networks with a series of different structures were processed. The influence of the structure of silane networks on the interactions with polymers was studied and used to determine the mechanisms involved in the coupling phenomenon. The AFM results showed that phenomena such as chain penetration, entanglements, intersegment bonding, chain conformation in the vicinities of rigid surfaces were identified as being relevant for the overall processes of adhesion and adsorption of polymeric chains within a silane network. AFM adhesion curves showed that penetration of polymeric chains through a more open silane network can lead to higher levels of interactions between polymer and silane agents.

  3. 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

  4. 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.

  5. Interaction networks in protein folding via atomic-resolution experiments and long-time-scale molecular dynamics simulations

    DEFF Research Database (Denmark)

    Sborgi, Lorenzo; Verma, Abhinav; Piana, Stefano;

    2015-01-01

    to investigate the folding of gpW, a protein with two-state-like, fast folding dynamics and cooperative equilibrium unfolding behavior. Experiments and simulations expose a remarkably complex pattern of structural changes that occur at the atomic level and from which the detailed network of residue...

  6. 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...

  7. Interaction Networks in Protein Folding via Atomic-Resolution Experiments and Long-Time-Scale Molecular Dynamics Simulations.

    Science.gov (United States)

    Sborgi, Lorenzo; Verma, Abhinav; Piana, Stefano; Lindorff-Larsen, Kresten; Cerminara, Michele; Santiveri, Clara M; Shaw, David E; de Alba, Eva; Muñoz, Victor

    2015-05-27

    The integration of atomic-resolution experimental and computational methods offers the potential for elucidating key aspects of protein folding that are not revealed by either approach alone. Here, we combine equilibrium NMR measurements of thermal unfolding and long molecular dynamics simulations to investigate the folding of gpW, a protein with two-state-like, fast folding dynamics and cooperative equilibrium unfolding behavior. Experiments and simulations expose a remarkably complex pattern of structural changes that occur at the atomic level and from which the detailed network of residue-residue couplings associated with cooperative folding emerges. Such thermodynamic residue-residue couplings appear to be linked to the order of mechanistically significant events that take place during the folding process. Our results on gpW indicate that the methods employed in this study are likely to prove broadly applicable to the fine analysis of folding mechanisms in fast folding proteins. PMID:25924808

  8. Interaction Networks in Protein Folding via Atomic-Resolution Experiments and Long-Time-Scale Molecular Dynamics Simulations

    OpenAIRE

    Sborgi, Lorenzo; Verma, Abhinav; Piana, Stefano; Lindorff-Larsen, Kresten; Cerminara, Michele; Santiveri, Clara M.; Shaw, David E.; de Alba, Eva; Muñoz, Victor

    2015-01-01

    The integration of atomic-resolution experimental and computational methods offers the potential for elucidating key aspects of protein folding that are not revealed by either approach alone. Here, we combine equilibrium NMR measurements of thermal unfolding and long molecular dynamics simulations to investigate the folding of gpW, a protein with two-state-like, fast folding dynamics and cooperative equilibrium unfolding behavior. Experiments and simulations expose a remarkably complex patter...

  9. 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.

  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. 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.

  13. 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

  14. 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.

  15. 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

  16. 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...

  17. Enhancing Light-Atom Interactions via Atomic Bunching

    CERN Document Server

    Schmittberger, Bonnie L

    2014-01-01

    There is a broad interest in enhancing the strength of light-atom interactions to the point where injecting a single photon induces a nonlinear material response. Here, we show theoretically that sub-Doppler-cooled, two-level atoms that are spatially organized by weak optical fields give rise to a nonlinear material response that is greatly enhanced beyond that attainable in a homogeneous gas. Specifically, in the regime where the intensity of the applied optical fields is much less than the off-resonant saturation intensity, we show that the third-order nonlinear susceptibility scales inversely with atomic temperature and, due to this scaling, can be two orders of magnitude larger than that of a homogeneous gas for typical experimental parameters. As a result, we predict that spatially bunched two-level atoms can exhibit single-photon nonlinearities. Our model is valid for all atomic temperature regimes and simultaneously accounts for the back-action of the atoms on the optical fields. Our results agree with...

  18. 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 of...... Netherlands. Networking appears to be mediated by policy and regulatory imperatives.......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 of...... `street-level' employment services staff for the impacts of this. Contrary to expectations, networking has generally declined over the last decade. There are signs of path dependence in networking patterns within each country, but also a convergence of patterns for the UK and Australia, but not The...

  19. 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.

  20. Atom slowing via dispersive optical interactions

    Science.gov (United States)

    Hamamda, M.; Boustimi, M.; Correia, F.; Baudon, J.; Taillandier-Loize, T.; Dutier, G.; Perales, F.; Ducloy, M.

    2012-02-01

    A promising technique of atom slowing is proposed. It is based upon the dispersive interaction of atoms with optical potential pulses generated by a far-off-resonance standing wave modulated in time. Each pulse reduces the velocity by a small amount. By repeating the process thousands of times, the velocity can be lowered from several hundreds of meters per second down to almost zero, over a path as short as 20cm. In the absence of any random recoil process, the initial characteristics of the beam are preserved.

  1. 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

  2. Dynamic and interacting complex networks

    Science.gov (United States)

    Dickison, Mark E.

    This thesis employs methods of statistical mechanics and numerical simulations to study some aspects of dynamic and interacting complex networks. The mapping of various social and physical phenomena to complex networks has been a rich field in the past few decades. Subjects as broad as petroleum engineering, scientific collaborations, and the structure of the internet have all been analyzed in a network physics context, with useful and universal results. In the first chapter we introduce basic concepts in networks, including the two types of network configurations that are studied and the statistical physics and epidemiological models that form the framework of the network research, as well as covering various previously-derived results in network theory that are used in the work in the following chapters. In the second chapter we introduce a model for dynamic networks, where the links or the strengths of the links change over time. We solve the model by mapping dynamic networks to the problem of directed percolation, where the direction corresponds to the time evolution of the network. We show that the dynamic network undergoes a percolation phase transition at a critical concentration pc, that decreases with the rate r at which the network links are changed. The behavior near criticality is universal and independent of r. We find that for dynamic random networks fundamental laws are changed: i) The size of the giant component at criticality scales with the network size N for all values of r, rather than as N2/3 in static network, ii) In the presence of a broad distribution of disorder, the optimal path length between two nodes in a dynamic network scales as N1/2, compared to N1/3 in a static network. The third chapter consists of a study of the effect of quarantine on the propagation of epidemics on an adaptive network of social contacts. For this purpose, we analyze the susceptible-infected-recovered model in the presence of quarantine, where susceptible

  3. 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.

  4. 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...

  5. 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...

  6. 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 ...

  7. 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.

  8. 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).

  9. 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...

  10. Network biomarkers, interaction networks and dynamical network biomarkers in respiratory diseases

    OpenAIRE

    Wu, Xiaodan; Chen, Luonan; Wang, Xiangdong

    2014-01-01

    Identification and validation of interaction networks and network biomarkers have become more critical and important in the development of disease-specific biomarkers, which are functionally changed during disease development, progression or treatment. The present review headlined the definition, significance, research and potential application for network biomarkers, interaction networks and dynamical network biomarkers (DNB). Disease-specific interaction networks, network biomarkers, or DNB...

  11. 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.

  12. Strong interaction studies with kaonic atoms

    Science.gov (United States)

    Marton, J.; Bazzi, M.; 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.; Levi Sandri, P.; Okada, S.; Pietreanu, D.; Piscicchia, K.; Ponta, T.; Quaglia, R.; Romero Vidal, A.; Sbardella, E.; Scordo, A.; Shi, H.; Sirghi, D. L.; Sirghi, F.; Tatsuno, H.; Vazquez Doce, O.; Widmann, E.; Zmeskal, J.

    2016-03-01

    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 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 ɛ1s 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.

  13. Statistical Mechanics of Temporal and Interacting Networks

    Science.gov (United States)

    Zhao, Kun

    In the last ten years important breakthroughs in the understanding of the topology of complexity have been made in the framework of network science. Indeed it has been found that many networks belong to the universality classes called small-world networks or scale-free networks. Moreover it was found that the complex architecture of real world networks strongly affects the critical phenomena defined on these structures. Nevertheless the main focus of the research has been the characterization of single and static networks. Recently, temporal networks and interacting networks have attracted large interest. Indeed many networks are interacting or formed by a multilayer structure. Example of these networks are found in social networks where an individual might be at the same time part of different social networks, in economic and financial networks, in physiology or in infrastructure systems. Moreover, many networks are temporal, i.e. the links appear and disappear on the fast time scale. Examples of these networks are social networks of contacts such as face-to-face interactions or mobile-phone communication, the time-dependent correlations in the brain activity and etc. Understanding the evolution of temporal and multilayer networks and characterizing critical phenomena in these systems is crucial if we want to describe, predict and control the dynamics of complex system. In this thesis, we investigate several statistical mechanics models of temporal and interacting networks, to shed light on the dynamics of this new generation of complex networks. First, we investigate a model of temporal social networks aimed at characterizing human social interactions such as face-to-face interactions and phone-call communication. Indeed thanks to the availability of data on these interactions, we are now in the position to compare the proposed model to the real data finding good agreement. Second, we investigate the entropy of temporal networks and growing networks , to provide

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Interaction of rare gas metastable atoms

    International Nuclear Information System (INIS)

    The physical and chemical properties of metastable rare gas atoms are discussed and summarized. This is followed by a detailed examination of the various possible pathways whereby the metastable's excess electronic energy can be dissipated. The phenomenon of chemi-ionization is given special emphasis, and a theoretical treatment based on the use of complex (optical) potential is presented. This is followed by a discussion on the unique advantages offered by elastic differential cross section measurements in the apprehension of the fundamental forces governing the ionization process. The methodology generally adopted to extract information about the interaction potential for scattering data is also systematically outlined. Two widely studied chemi-ionization systems are then closely examined in the light of accurate differential cross section measurements obtained in this work. The first system is He(23S) + Ar for which one can obtain an interaction potential which is in good harmony with the experimental results of other investigators. The validity of using the first-order semiclassical approximation for the phase shifts calculation in the presence of significant opacities is also discussed. The second reaction studied is He*+D2 for which measurements were made on both spin states of the metastable helium. A self-consistent interaction potential is obtained for the triplet system, and reasons are given for not being able to do likewise for the singlet system. The anomalous hump proposed by a number of laboratories is analyzed. Total elastic and ionization cross sections as well as rate constants are calculated for the triplet case. Good agreement with experimental data is found. Finally, the construction and operation of a high power repetitively pulsed nitrogen laser pumped dye laser system is described in great details. Details for the construction and operation of a flashlamp pumped dye laser are likewise given

  1. 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.

  2. 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.

  3. 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.

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

    CERN Document Server

    Perreault, J D; 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 caused by atom-surface interactions. The magnitude of the phase shift is in agreement with that predicted by quantum electrodynamics for a non-retarded van der Waals interaction. This experiment also demonstrates that atom-waves can retain their coherence even when atom-surface distances are as small as 10 nm.

  5. Observation of Atom Wave Phase Shifts Induced by Van Der Waals Atom-Surface Interactions

    International Nuclear Information System (INIS)

    The development of nanotechnology and atom optics relies on understanding how atoms behave and interact with their environment. Isolated atoms can exhibit wavelike (coherent) behavior 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 caused by atom-surface interactions. The magnitude of the phase shift is in agreement with that predicted by Lifshitz theory for a nonretarded van der Waals interaction. This experiment also demonstrates that atom waves can retain their coherence even when atom-surface distances are as small as 10 nm

  6. 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...... dynamics simulations, complemented by extensive comparison to experimental data. The discussion is divided into four sections. The first part investigates the properties of one-component SM bilayers and compares them to bilayers with phosphatidylcholine (PC), the focus being on a detailed analysis of the...... hydrogen bonding network in the two bilayers. The second part deals with binary mixtures of sterols with either SM or PC. The results show how the membrane properties may vary substantially depending on the sterol and SM type available, the membrane order and interdigitation being just two of the many...

  7. 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.

  8. 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.

  9. Evolution, Interactions, and Biological Networks

    OpenAIRE

    Weitz, Joshua S.; Benfey, Philip N.; Wingreen, Ned S.

    2007-01-01

    Shifting the perspective of the questions we ask will ensure that network theory continues to excite the network theorists, but more importantly, that it remains vital to progress in biological research.

  10. 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...

  11. Interaction between atoms and slow light: a design study

    CERN Document Server

    Zang, Xiaorun; Faggiani, Rémi; Gill, Christopher; Petrov, Plamen G; Hugonin, Jean-Paul; Bernon, Simon; Bouyer, Philippe; Boyer, Vincent; Lalanne, Philippe

    2015-01-01

    The emerging field of on-chip integration of nanophotonic devices and cold atoms offers extremely-strong and pure light-matter interaction schemes, which may have profound impact on quantum information science. In this context, a longstanding obstacle is to achieve strong interaction between single atoms and single photons, while at the same time trap atoms in vacuum at large separation distances from dielectric surfaces. In this letter, we study new waveguide geometries that challenge these conflicting objectives. The designed photonic crystal waveguide is expected to offer a good compromise, which additionally allow for easy manipulation of atomic clouds around the structure.

  12. 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.

  13. Low Earth Orbital Atomic Oxygen Interactions With Materials

    Science.gov (United States)

    Banks, Bruce A.; Miller, Sharon K.; deGroh, Kim K.

    2004-01-01

    Atomic oxygen is formed in the low Earth orbital environment (LEO) by photo dissociation of diatomic oxygen by short wavelength (improved durability to atomic oxygen attack, as well as atomic oxygen protective coatings, have been employed with varying degrees of success to improve durability of polymers in the LEO environment. Atomic oxygen can also oxidize silicones and silicone contamination to produce non-volatile silica deposits. Such contaminants are present on most LEO missions and can be a threat to performance of optical surfaces. The LEO atomic oxygen environment, its interactions with materials, results of space testing, computational modeling, mitigation techniques, and ground laboratory simulation procedures and issues are presented.

  14. 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

  15. From Atomism to Networks in Social Systems

    Science.gov (United States)

    Snowden, David

    2005-01-01

    Purpose: The purpose of this article is to focus on the role of networks in organizations as a critical aspect of knowledge management and learning processes. Design/methodology/approach: The article has built on an established technique, namely SNA, by shifting from individuals to identities and then to abstractions. Findings: By making the…

  16. 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...

  17. Quantum optics and cavity QED Quantum network with individual atoms and photons

    Directory of Open Access Journals (Sweden)

    Rempe G.

    2013-08-01

    Full Text Available Quantum physics allows a new approach to information processing. A grand challenge is the realization of a quantum network for long-distance quantum communication and large-scale quantum simulation. This paper highlights a first implementation of an elementary quantum network with two fibre-linked high-finesse optical resonators, each containing a single quasi-permanently trapped atom as a stationary quantum node. Reversible quantum state transfer between the two atoms and entanglement of the two atoms are achieved by the controlled exchange of a time-symmetric single photon. This approach to quantum networking is efficient and offers a clear perspective for scalability. It allows for arbitrary topologies and features controlled connectivity as well as, in principle, infinite-range interactions. Our system constitutes the largest man-made material quantum system to date and is an ideal test bed for fundamental investigations, e.g. quantum non-locality.

  18. Entanglement distillation for quantum communication network with atomic-ensemble memories.

    Science.gov (United States)

    Li, Tao; Yang, Guo-Jian; Deng, Fu-Guo

    2014-10-01

    Atomic ensembles are effective memory nodes for quantum communication network due to the long coherence time and the collective enhancement effect for the nonlinear interaction between an ensemble and a photon. Here we investigate the possibility of achieving the entanglement distillation for nonlocal atomic ensembles by the input-output process of a single photon as a result of cavity quantum electrodynamics. We give an optimal entanglement concentration protocol (ECP) for two-atomic-ensemble systems in a partially entangled pure state with known parameters and an efficient ECP for the systems in an unknown partially entangled pure state with a nondestructive parity-check detector (PCD). For the systems in a mixed entangled state, we introduce an entanglement purification protocol with PCDs. These entanglement distillation protocols have high fidelity and efficiency with current experimental techniques, and they are useful for quantum communication network with atomic-ensemble memories. PMID:25321967

  19. 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...

  20. 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)

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

    CERN Document Server

    Hood, J D; Asenjo-Garcia, A; Lu, M; Yu, S -P; Chang, D E; Kimble, H J

    2016-01-01

    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 crossover from propagating fields $E(x) \\propto e^{\\pm ik_x x}$ outside the bandgap to localized fields $E(x) \\propto e^{-\\kappa_x |x|}$ 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 for the first time by shifting the band edge frequency of the PCW relative to the $\\rm D_1$ line of atomic cesium for $\\bar{N}=3.0\\pm 0.5$ atoms trapped along the PCW. Our results are the initial demonstration of this new paradigm for coherent atom-atom interactions with low dissipation into the guided mode.

  2. 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

  3. Tailoring the chiral magnetic interaction between two individual atoms

    Science.gov (United States)

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

    2016-01-01

    Chiral magnets are a promising route towards 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 tunnelling 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. PMID:26902332

  4. Two-electron processes in atom-photon interactions

    International Nuclear Information System (INIS)

    Two-electron processes in atom-photon interactions have been studied. Various mechanisms of double photoionization, angular correlations, total cross sections, energy distributions and results for non-Helium like systems are discussed

  5. 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...

  6. 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)

  7. 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)

  8. Direct observation of atomic network migration in glass

    International Nuclear Information System (INIS)

    Many physical properties of glasses are still far from being understood at the atomic level. The lack of experimental methods capable of studying glassy dynamics at this scale has impeded the development of a complete model for atomic transport processes. Here we apply the new technique of atomic-scale x-ray photon correlation spectroscopy to directly observe single atomic motion in lead silicate glass. We show that dynamics change significantly depending on the glass composition, from single jump processes between inhomogeneous regions to multiple jump processes along network paths and through voids. Up until now, such measurements were far out of reach for temperatures below the glass transition. Our findings suggest that the method and the model introduced here will also help understanding atomic diffusion in a wide range of other glass systems. (paper)

  9. 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)

  10. 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.)

  11. 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

  12. 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.

  13. Social networks and interactions in cities

    OpenAIRE

    Robert W. Helsley; Zenou, Yves

    2011-01-01

    We examine how interaction choices depend on the interplay of social and physical distance, and show that agents who are more central in the social network, or are located closer to the geographic center of interaction, choose higher levels of interactions in equilibrium. As a result, the level of interactivity in the economy as a whole will rise with the density of links in the social network and with the degree to which agents are clustered in physical space. When agents can choose geograph...

  14. 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.

  15. Evolution of a protein domain interaction network

    International Nuclear Information System (INIS)

    In this paper, we attempt to understand complex network evolution from the underlying evolutionary relationship between biological organisms. Firstly, we construct a Pfam domain interaction network for each of the 470 completely sequenced organisms, and therefore each organism is correlated with a specific Pfam domain interaction network; secondly, we infer the evolutionary relationship of these organisms with the nearest neighbour joining method; thirdly, we use the evolutionary relationship between organisms constructed in the second step as the evolutionary course of the Pfam domain interaction network constructed in the first step. This analysis of the evolutionary course shows: (i) there is a conserved sub-network structure in network evolution; in this sub-network, nodes with lower degree prefer to maintain their connectivity invariant, and hubs tend to maintain their role as a hub is attached preferentially to new added nodes; (ii) few nodes are conserved as hubs; most of the other nodes are conserved as one with very low degree; (iii) in the course of network evolution, new nodes are added to the network either individually in most cases or as clusters with relative high clustering coefficients in a very few cases. (general)

  16. 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...

  17. 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.

  18. 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...

  19. 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...

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Nanofiber-Mediated Interaction of Light with Cold Atoms

    Science.gov (United States)

    Sheremet, A. S.; Gauraud, B.; Corzo-Trejo, N.; Laurat, J.; Kupriyanov, D. V.

    2015-09-01

    Light-matter interaction processes are extremely attractive for quantum information problems, where one of the main goals consists in a quantum state of light mapping into a collective atomic state. By analogy with the Purcell effect, which exhibits in the presence of a resonator, enhancement of light-matter interaction can be achieved by using a nanofiber [1-2]. In this work we present a theoretical description of light interaction with a cold atomic ensemble mediated the nanofiber, which lies in a base of the experimental realization of a quantum memory protocol [3].

  5. 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.

  6. 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.

  7. 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...

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

    Science.gov (United States)

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

    2016-05-01

    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 C3 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.

  9. Atom-pair kinetics with strong electric-dipole interactions

    CERN Document Server

    Thaicharoen, N; Raithel, G

    2016-01-01

    Rydberg-atom ensembles are switched from a weakly- into a strongly-interacting regime via adiabatic transformation of the atoms from an approximately non-polar 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.

  10. A simple model for studying interacting networks

    Science.gov (United States)

    Liu, Wenjia; Jolad, Shivakumar; Schmittmann, Beate; Zia, R. K. P.

    2011-03-01

    Many specific physical networks (e.g., internet, power grid, interstates), have been characterized in considerable detail, but in isolation from each other. Yet, each of these networks supports the functions of the others, and so far, little is known about how their interactions affect their structure and functionality. To address this issue, we consider two coupled model networks. Each network is relatively simple, with a fixed set of nodes, but dynamically generated set of links which has a preferred degree, κ . In the stationary state, the degree distribution has exponential tails (far from κ), an attribute which we can explain. Next, we consider two such networks with different κ 's, reminiscent of two social groups, e.g., extroverts and introverts. Finally, we let these networks interact by establishing a controllable fraction of cross links. The resulting distribution of links, both within and across the two model networks, is investigated and discussed, along with some potential consequences for real networks. Supported in part by NSF-DMR-0705152 and 1005417.

  11. Interaction of Interpolating Number-Coherent States with Atomic Systems

    CERN Document Server

    Feng, Y; Solomon, A I; Feng, Yinqi; Fu, Hongchen

    1999-01-01

    Interpolating number-coherent states are new states of the radiation field which interpolate between number and coherent states, to which they reduce in appropriate limits. We study some fundamental features of the interaction of these new states with a atomic system in the framework of the Jaynes-Cummings model(JCM). The dynamical evolution of atomic population inversion, field entropy, the Q-function and photon number distribution properties are investigated in detail.

  12. 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...

  13. 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.

  14. Systematic computational prediction of protein interaction networks

    International Nuclear Information System (INIS)

    Determining the network of physical protein associations is an important first step in developing mechanistic evidence for elucidating biological pathways. Despite rapid advances in the field of high throughput experiments to determine protein interactions, the majority of associations remain unknown. Here we describe computational methods for significantly expanding protein association networks. We describe methods for integrating multiple independent sources of evidence to obtain higher quality predictions and we compare the major publicly available resources available for experimentalists to use

  15. Systematic computational prediction of protein interaction networks.

    Science.gov (United States)

    Lees, J G; Heriche, J K; Morilla, I; Ranea, J A; Orengo, C A

    2011-06-01

    Determining the network of physical protein associations is an important first step in developing mechanistic evidence for elucidating biological pathways. Despite rapid advances in the field of high throughput experiments to determine protein interactions, the majority of associations remain unknown. Here we describe computational methods for significantly expanding protein association networks. We describe methods for integrating multiple independent sources of evidence to obtain higher quality predictions and we compare the major publicly available resources available for experimentalists to use. PMID:21572181

  16. 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).

  17. Using atomic diffraction of Na from material gratings to measure atom-surface interactions

    International Nuclear Information System (INIS)

    In atom optics a material structure is commonly regarded as an amplitude mask for atom waves. However, atomic diffraction patterns formed using material gratings indicate that material structures also operate as phase masks. In this study a well collimated beam of sodium atoms is used to illuminate a silicon nitride grating with a period of 100 nm. During passage through the grating slots atoms acquire a phase shift due to the van der Waals (vdW) interaction with the grating walls. As a result the relative intensities of the matter-wave diffraction peaks deviate from those expected for a purely absorbing grating. Thus a complex transmission function is required to explain the observed diffraction envelopes. An optics perspective to the theory of atomic diffraction from material gratings is put forth in the hopes of providing a more intuitive picture concerning the influence of the vdW potential. The van der Waals coefficient C3=2.7±0.8 meV nm3 is determined by fitting a modified Fresnel optical theory to the experimental data. This value of C3 is consistent with a van der Waals interaction between atomic sodium and a silicon nitride surface

  18. 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 ...

  19. 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

  20. 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.

  1. Scattering of atoms by coherent interaction with light

    Science.gov (United States)

    Grinchuk, V. A.; Kuzin, E. F.; Nagaeva, M. L.; Riabenko, G. A.; Kazantsev, A. P.

    1985-11-01

    A theoretical and experimental study is presented of the effect of stimulated radiation pressure (SRP) under the conditions of strong saturation of the resonance transition when the interaction times between the atom and the field are short (shorter than the radiative lifetime). An experimental method for studying the scattering of an atomic beam by the field of a standing light wave is described. The measured dependence of the scattering efficiency on the electric field and the detuning from resonance are reported. Experimental relationshps are compared with theoretical calculations based on the quasi-classical description of the motion of atoms in the field of a light wave, using an effective potential. It is shown that the efficiency of scattering of atoms by SRP forces is of the order of unity in relatively weak (100-1000-V/cm) laser fields.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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

  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)

    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.

  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)

    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.

  10. Inferring microbial interaction networks based on consensus similarity network fusion.

    Science.gov (United States)

    Jiang, XingPeng; Hu, XiaoHua

    2014-11-01

    With the rapid accumulation of high-throughput metagenomic sequencing data, it is possible to infer microbial species relations in a microbial community systematically. In recent years, some approaches have been proposed for identifying microbial interaction network. These methods often focus on one dataset without considering the advantage of data integration. In this study, we propose to use a similarity network fusion (SNF) method to infer microbial relations. The SNF efficiently integrates the similarities of species derived from different datasets by a cross-network diffusion process. We also introduce consensus k-nearest neighborhood (Ck-NN) method instead of k-NN in the original SNF (we call the approach CSNF). The final network represents the augmented species relationships with aggregated evidence from various datasets, taking advantage of complementarity in the data. We apply the method on genus profiles derived from three microbiome datasets and we find that CSNF can discover the modular structure of microbial interaction network which cannot be identified by analyzing a single dataset. PMID:25326827

  11. 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...

  12. 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

  13. 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.

  14. 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

  15. Using Atomic Diffraction of Na from Material Gratings to Measure Atom-Surface Interactions

    CERN Document Server

    Perreault, J D; Savas, T A; Perreault, John D.; Cronin, Alexander D.

    2003-01-01

    In atom optics a material structure is commonly regarded as an amplitude mask for atom waves. However, atomic diffraction patterns formed using material gratings indicate that material structures also operate as phase masks. In this study a well collimated beam of sodium atoms is used to illuminate a silicon nitride grating with a period of 100 nm. During passage through the grating slots atoms acquire a phase shift due to the van der Waals interaction with the grating walls. As a result the relative intensities of the matter-wave diffraction peaks deviate from those expected for a purely absorbing grating. Thus a complex transmission function is required to explain the observed diffraction envelopes. An optics perspective to the theory of atomic diffraction from material gratings is put forth in the hopes of providing a more intuitive picture concerning the influence of the vdW potential. The van der Waals coefficient $C_{3} = 2.7\\pm 0.8{meV nm}^{3}$ is determined by fitting a modified Fresnel optical theory...

  16. A Waveguide Platform for Collective Light-Atom Interaction

    DEFF Research Database (Denmark)

    Sørensen, Heidi Lundgaard

    is compared against a prediction derived from a numerical model build upon an easy experimental calibration of the viscosity profile within the heater. Very good agreement between the modeled and measured fiber shape is found. We next study the coherent back-scattering off atoms confined as two one......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......-dimensional strings in the evanescent field of a tapered optical fiber. By applying a near-resonant standing wave field, the atoms are arranged into a periodic Bragg structure in close analogy to a photo-refractive medium with a refractive index grating. We observe more than 10% power reflection off about 1000...

  17. The long-range interaction of relativistic hydrogen atoms

    International Nuclear Information System (INIS)

    A treatment is given of long-range interatomic forces that exhibits the following features: (a) the result is valid both at small separations and in the retarded (long range) regime, (b) all atomic multipole moments are taken into account and (c) the treatment includes relativistic effects up to any desired order. The third requirement can be met for hydrogen atoms of which electrons are described by the relativistic Dirac theory. The interaction energy of two such atoms is broken up in a retarded dispersion energy and a nonretarded induction energy using a multipole expansion in the spherical-tensor formalism which contain orbital and spin contributions. Fourth order perturbation theory is used, and special attention is paid to the asymptotic behavior of the dispersion energy at very large interatomic separations. Finally, semi and nonrelativistic approximations are discussed

  18. 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.

  19. 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

  20. Resonance interaction between cold Rb atoms and a frequency comb

    International Nuclear Information System (INIS)

    Full text: A long life time of atoms in a magneto-optical trap (MOT) makes it a powerful tool to study interactions with optical fields processing small cross sections. Since the life time in MOT can reach a few seconds, even processes with characteristic rates of 1 -s1 can be easily analyzed if they result in losses of trapped atoms. We have investigated the interaction of laser-cooled 87Rb atoms in a MOT with a femtosecond (fs) laser radiation in the spectral region 760-820 nm. We show that in a wide range of average intensities of the fs laser field (2) the dominating process is the cascade ionization. In this case the femtosecond radiation interacts with the atomic ensemble both as spectrally-narrow components (a frequency comb) and as a powerful ionizing laser field. Atoms excited by a single mode of a frequency comb from the 5P3/2(F = 3) to the 5D5/2(F = 2, 3, 4) hyperfine sublevels are consequently ionized by a full power of the fs laser from the 5D level to the continuum. By tuning the repetition rate frep of the fs laser we observe the periodic spectrum in the MOT luminescence at 780 nm (the cooling transition) reproducing the hyperfine structure of the 5D level. We have quantitatively analyzed the ionization of the 5D5/2 level by monitoring the loading rate of the MOT at different powers of the fs laser radiation using an auxiliary cw laser locked to the 5P3/2(F = 3) → 5D5/2(F = 4) at 776 nm. A sensitive method allowing accurate determination of the 5/2 5D level population is developed. (author)

  1. 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.

  2. 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.

  3. 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

  4. Kaon-nucleon strong interaction in kaonic atoms

    International Nuclear Information System (INIS)

    The SIDDHARTA experiment (SIlicon Drift Detector for Hadronic Atom Research by Timing Application) aims to perform a precise measurement of the X-ray K-series of kaonic hydrogen and the first-ever measurement of kaonic deuterium, to obtain the strong-interaction energy-level shifts and widths of the lowest lying atomic states. The measurements will allow the determination of the isospin-dependent kaon-nucleon (KN) scattering lengths, directly connected to the physics of the KN interaction. The experiment uses the low-energy kaon beam generated at DAΦNE collider, high-density cryogenic targets and fast, large area X-ray spectroscopic detectors. In addition to the kaonic hydrogen and kaonic deuterium, the collaboration performed measurements of the kaonic Helium transitions to the 2p level (L-lines). Kaonic Helium 4 was measured for the first time in a gaseous target while the kaonic Helium 3 was measured for the first time ever.

  5. High energy neutral atoms from high intensity laser plasma interaction

    International Nuclear Information System (INIS)

    Interaction of a high intensity laser with solid targets leads to acceleration of ions from the surface of the target. Ion acceleration is governed by electron dynamics at the target vacuum interface setting up a charge separation. This electron cloud near the target interface can also provide a neutralizing background for ions that have been accelerated. The accelerated ions are thus detected as a high energy neutral atom on a detector. Further, due to the inherent contrast profile of high intensity lasers a pre-plasma is almost always formed and neutral atoms can be detected. The ion and neutral atom energies are measured by a Thomson parabola spectrometer coupled with a 'time of flight' measurement. The neutral atom energies are obtained from the time of flight. The TIFR 20TW laser with an intensity contrast 10-5 was used to carry out the experiment. Defocusing the target led to a 2 fold increase in the neutral atom yield suggesting the role of the pre-plasma. Using a high contrast laser we attempt to tune the recombination dynamics for efficient neutralization of ions by using a controlled pre-plasma. (author)

  6. 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...

  7. Dynamics of interacting information waves in networks.

    Science.gov (United States)

    Mirshahvalad, A; Esquivel, A V; Lizana, L; Rosvall, M

    2014-01-01

    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: lagging waves die out and only leading waves survive. As a result, and in contrast to models with noninteracting 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 the path redundancy and the effective dimension of the system. In general, the decay of the information wave frequency as a function of distance from the source follows a power-law distribution with an exponent between -0.2 for a two-dimensional system with high path redundancy and -0.5 for a tree-like system with no path redundancy. We found that the real spatial networks provide an infrastructure for information spreading that lies in between these two extremes. Finally, to better understand the mechanics behind the scaling results, we provide analytical calculations of the scaling for a one-dimensional system. PMID:24580283

  8. Elucidating Common Structural Features of Human Pathogenic Variations Using Large-Scale Atomic-Resolution Protein Networks

    Science.gov (United States)

    Das, Jishnu; Lee, Hao Ran; Sagar, Adithya; Fragoza, Robert; Liang, Jin; Wei, Xiaomu; Wang, Xiujuan; Mort, Matthew; Stenson, Peter D.; Cooper, David N.; Yu, Haiyuan

    2016-01-01

    With the rapid growth of structural genomics, numerous protein crystal structures have become available. However, the parallel increase in knowledge of the functional principles underlying biological processes, and more specifically the underlying molecular mechanisms of disease, has been less dramatic. This notwithstanding, the study of complex cellular networks has made possible the inference of protein functions on a large scale. Here, we combine the scale of network systems biology with the resolution of traditional structural biology to generate a large-scale atomic-resolution interactome-network comprising 3,398 interactions between 2,890 proteins with a well-defined interaction interface and interface residues for each interaction. Within the framework of this atomic-resolution network, we have explored the structural principles underlying variations causing human-inherited disease. We find that in-frame pathogenic variations are enriched at both the interface and in the interacting domain, suggesting that variations not only at interface “hot-spots,” but in the entire interacting domain can result in alterations of interactions. Further, the sites of pathogenic variations are closely related to the biophysical strength of the interactions they perturb. Finally, we show that biochemical alterations consequent to these variations are considerably more disruptive than evolutionary changes, with the most significant alterations at the protein interaction interface. PMID:24599843

  9. 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.

  10. 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)

  11. A general approach to the Bose-einstein condensation of neutral atoms with repellent interaction

    International Nuclear Information System (INIS)

    A general approach to the Bose-Einstein condensation of neutral atoms with repellent interaction is presented. Especially in the case of free atoms (V = 0) with repellent interaction, an exact solution for the atom's wave function can be derived, and therefore the calculation of atom's Bose-Einstein condensation is completed

  12. 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.

  13. 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

  14. Bose-Einstein atoms in atomic traps with predominantly attractive two-body interactions

    International Nuclear Information System (INIS)

    Using the Perron-Frobenius theorem, we prove that the results by Wilkin, Gunn, and Smith [Phys. Rev. Lett. 80, 2265 (1998)] for the ground states at angular momentum L of N harmonically trapped Bose atoms, interacting via weak attractive δ2(r) forces, are valid for a broad class of predominantly attractive interactions V(r), not necessarily attractive for any r. This class is described by sufficient conditions on the two-body matrix elements of the potential V(r). It includes, in particular, the Gaussian attraction of arbitrary radius, -1/r-Coulomb and log(r)-Coulomb forces, as well as all the short-range interactions satisfying inequality ∫d2r-vectorV(r)<0. In the precollapse regime, the angular momentum L is concentrated in the collective 'center-of-mass' mode, and there is no condensation at high L

  15. 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.

  16. Financial interaction networks inferred from traded volumes

    International Nuclear Information System (INIS)

    In order to use the advanced inference techniques available for Ising models, we transform complex data (real vectors) into binary strings, using local averaging and thresholding. This transformation introduces parameters, which must be varied to characterize the behaviour of the system. The approach is illustrated on financial data, using three inference methods—equilibrium, synchronous and asynchronous inference—to construct functional connections between stocks. We show that the traded volume information is enough to obtain well-known results about financial markets that use, however, presumably richer price information: collective behaviour (‘market mode’) and strong interactions within industry sectors. Synchronous and asynchronous Ising inference methods give results that are coherent with equilibrium ones and are more detailed since the obtained interaction networks are directed. (paper)

  17. Attractive interaction between an atom and a surface

    International Nuclear Information System (INIS)

    Using a general self-energy formalism we examine the interaction between an atom and a surface. Considered in detail are deviations from the Van der Waals force due to recoil and finite velocity of the particle. Calculations for positronium near a metal surface show that for such systems recoil and velocity effects are significant even at very low energies. We also examine the mechanisms for energy exchange with the surface and calculations show that single quantum events do not always dominate the exchange rates. 8 references, 2 figures

  18. APIPIS: the Atomic Physics Ion-Photon Interaction System

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, B.M.; Jones, K.W.; Meron, M.; Kostroun, V.O.

    1985-01-01

    A proposed new facility for the study of highly charged heavy ions is described. The basic elements of APIPIS, the Atomic Physics Ion-Photon Interaction System, are: (1) a source of multiply-charged ions; (2) a linear accelerator; (3) a synchrotron storage ring; and (4) a source of high brightness x rays. The placement of a heavy ion storage ring at the x-ray ring of the National Synchrotron Light Source will provide unique opportunities for the study of photo-excitation of heavy ions.

  19. 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...

  20. 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 $\\beta$...

  1. Interaction of atomic hydrogen with charcoal at 77 K

    International Nuclear Information System (INIS)

    Charcoal is a working material of sorption cryopumps in the ITER project. The interaction of thermal hydrogen molecules and atoms with charcoal has been analyzed by TDS (77-300 K) and sorption measurements at 77 K. A stream quartz reactor with an H2 RF discharge was used for the production of H atoms. The ratio of H and H2 in the gas mixture in the afterglow zone was ∼10-4, hydrogen flow and inlet pressure were 6.9 sccm and 30 Pa, respectively. After exposure in the H/H2 mixture during 1 hour the marked change in the shape of the TD spectra and decrease of the charcoal sorption capacity for hydrogen and nitrogen were detected. A wide spectrum of hydrocarbon fragments formed at 77 K was registered by mass-spectrometry at charcoal heating up to 700 K. The specific adsorption volume of charcoal, which was measured by N2 adsorption at 77 K, decreased directly as amount of H atoms passed through the section with charcoal. (author)

  2. 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...

  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. 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...

  5. 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...

  6. Kaon-nucleon strong interaction in kaonic atoms

    Energy Technology Data Exchange (ETDEWEB)

    Iliescu, M., E-mail: mihai@lnf.infn.i [INFN, Laboratori Nazionali di Frascati, via E. Fermi 40, 00044 Frascati (Roma) (Italy); Bazzi, M. [INFN, Laboratori Nazionali di Frascati, via E. Fermi 40, 00044 Frascati (Roma) (Italy); Beer, G. [Dep. of Phys. and Astro., Univ. of Victoria, Victoria B.C. (Canada); Bombelli, L. [Politecnico di Milano, Sez. di Elettronica, Milano (Italy); Bragadireanu, A.M. [INFN, Laboratori Nazionali di Frascati, via E. Fermi 40, 00044 Frascati (Roma) (Italy); IFIN-HH, Magurele, Bucharest (Romania); Cargnelli, M. [Stefan-Meyer-Institut fuer subatomare Physik, Vienna (Austria); Corradi, G.; Curceanu, C.; D' Uffizi, A. [INFN, Laboratori Nazionali di Frascati, via E. Fermi 40, 00044 Frascati (Roma) (Italy); Fiorini, C.; Frizzi, T. [Politecnico di Milano, Sez. di Elettronica, Milano (Italy); Ghio, F.; Girolami, B. [INFN Sez. di Roma I and Inst. Superiore di Sanita, Roma (Italy); Guaraldo, C. [INFN, Laboratori Nazionali di Frascati, via E. Fermi 40, 00044 Frascati (Roma) (Italy); Hayano, R.S. [Univ. of Tokyo, Tokyo (Japan); Ishiwatari, T. [Stefan-Meyer-Institut fuer subatomare Physik, Vienna (Austria); Iwasaki, M. [RIKEN, The Inst. of Phys. and Chem. Research, Saitama (Japan); Kienle, P. [Stefan-Meyer-Institut fuer subatomare Physik, Vienna (Austria); Tech. Univ. Muenchen, Physik Dep., Garching (Germany); Sandri, P.Levi [INFN, Laboratori Nazionali di Frascati, via E. Fermi 40, 00044 Frascati (Roma) (Italy); Longoni, A. [Politecnico di Milano, Sez. di Elettronica, Milano (Italy)

    2010-10-15

    The SIDDHARTA experiment (SIlicon Drift Detector for Hadronic Atom Research by Timing Application) aims to perform a precise measurement of the X-ray K-series of kaonic hydrogen and the first-ever measurement of kaonic deuterium, to obtain the strong-interaction energy-level shifts and widths of the lowest lying atomic states. The measurements will allow the determination of the isospin-dependent kaon-nucleon (KN) scattering lengths, directly connected to the physics of the KN interaction. The experiment uses the low-energy kaon beam generated at DA{Phi}NE collider, high-density cryogenic targets and fast, large area X-ray spectroscopic detectors. In addition to the kaonic hydrogen and kaonic deuterium, the collaboration performed measurements of the kaonic Helium transitions to the 2p level (L-lines). Kaonic Helium 4 was measured for the first time in a gaseous target while the kaonic Helium 3 was measured for the first time ever.

  7. 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.

  8. 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 be e...

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

    International Nuclear Information System (INIS)

    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 C6, C8 and C10 atom–atom interactions for the dimers formed from any of these atoms and ions, and we present tables covering all of these combinations

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

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Jun, E-mail: phyjiang@yeah.net [Key Laboratory of Atomic and Molecular Physics and Functional Materials of Gansu Province, College of Physics and Electronic Engineering, Northwest Normal University, Lanzhou 730070 (China); School of Engineering, Charles Darwin University, Darwin, Northern Territory, 0909 (Australia); Mitroy, J. [School of Engineering, Charles Darwin University, Darwin, Northern Territory, 0909 (Australia); Cheng, Yongjun, E-mail: cyj83mail@gmail.com [School of Engineering, Charles Darwin University, Darwin, Northern Territory, 0909 (Australia); Academy of Fundamental and Interdisciplinary Science, Harbin Institute of Technology, Harbin 150080 (China); Bromley, M.W.J., E-mail: brom@physics.uq.edu.au [School of Mathematics and Physics, The University of Queensland, Brisbane, Queensland 4075 (Australia)

    2015-01-15

    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{sub 6}, C{sub 8} and C{sub 10} atom–atom interactions for the dimers formed from any of these atoms and ions, and we present tables covering all of these combinations.

  11. 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.

  12. 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.

  13. The kinetochore interaction network (KIN) of ascomycetes.

    Science.gov (United States)

    Freitag, Michael

    2016-05-01

    Chromosome segregation relies on coordinated activity of a large assembly of proteins, the kinetochore interaction network (KIN). How conserved the underlying mechanisms driving the epigenetic phenomenon of centromere and kinetochore assembly and maintenance are remains unclear, even though various eukaryotic models have been studied. More than 50 different proteins, many in multiple copies, comprise the KIN or are associated with fungal centromeres and kinetochores. Proteins isolated from immune sera recognized centromeric regions on chromosomes and thus were named centromere proteins (CENPs). CENP-A, sometimes called centromere-specific H3 (CenH3), is incorporated into nucleosomes within or near centromeres. The constitutive centromere-associated network (CCAN) assembles on this specialized chromatin, likely based on specific interactions with and requiring presence of CENP-C. The outer kinetochore comprises the Knl1-Mis12-Ndc80 (KMN) protein complexes that connect CCAN to spindles, accomplished by binding and stabilizing microtubules (MTs) and in the process generating load-bearing assemblies for chromatid segregation. In most fungi the Dam1/DASH complex connects the KMN complexes to MTs. Fungi present a rich resource to investigate mechanistic commonalities but also differences in kinetochore architecture. While ascomycetes have sets of CCAN and KMN proteins that are conserved with those of budding yeast or metazoans, searching other major branches of the fungal kingdom revealed that CCAN proteins are poorly conserved at the primary sequence level. Several conserved binding motifs or domains within KMN complexes have been described recently, and these features of ascomycete KIN proteins are shared with most metazoan proteins. In addition, several ascomycete-specific domains have been identified here. PMID:26908646

  14. Atomic and plasma-material interaction data for fusion. V.4

    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 volume is exclusively devoted to cross sections for collisions of hydrogen atoms with electron, protons and multiply charged ions

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

    OpenAIRE

    Bogdan Raducanu; Sergio Escalera; Xavier Baró; Petia Radeva; Jordi Vitrià

    2012-01-01

    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 ...

  16. Two-dimensional noncommutative atom gas with the Anandan interaction

    Energy Technology Data Exchange (ETDEWEB)

    Yu Xiaomin [Hangzhou Dianzi University, Hangzhou, 310018 (China); Li Kang [Department of Physics, Hangzhou Normal University, Hangzhou, 310036 (China)

    2011-09-15

    Landau-like quantization of the Anandan system in a special electromagnetic field is studied. Unlike the cases of the Aharonov-Casher (AC) system and the He-McKellar-Wilkens (HMW) system, the torques of the system on the magnetic dipole and the electric dipole do not vanish. By constructing Heisenberg algebra, the Landau analog levels and eigenstates on commutative space, noncommutative (NC) space, and NC phase space are obtained, respectively. By using the coherent state method, some statistical properties of such free-atom gas are studied and the expressions of some thermodynamic quantities related to revolution direction are obtained. Two particular cases of temperature are discussed and the more simple expressions of the free energy on the three spaces are obtained. We give the relation between the value of {sigma} and revolution direction clearly and find Landau like levels of the Anandan system are invariant and the levels between the AC system and the HMW system are interchanged each other under Maxwell dual transformations on the three spaces. The two sets of eigenstates labeled by {sigma} can be related by a supersymmetry transformation on commutative space, but the phenomenon do not occur on NC situation. We emphasize that some results relevant to Anandan interaction are suitable for the cases of AC interaction and HMW interaction under special conditions.

  17. 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.

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. 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

  3. Atomic scale insights into urea-peptide interactions in solution.

    Science.gov (United States)

    Steinke, Nicola; Gillams, Richard J; Pardo, Luis Carlos; Lorenz, Christian D; McLain, Sylvia E

    2016-02-01

    The mechanism by which proteins are denatured by urea is still not well understood, especially on the atomic scale where these interactions occur in vivo. In this study, the structure of the peptide GPG has been investigated in aqueous urea solutions in order to understand the combination of roles that both urea and water play in protein unfolding. Using a combination of neutron diffraction enhanced by isotopic substitution and computer simulations, it was found, in opposition with previous simulations studies, that urea is preferred over water around polar and charged portions of the peptides. Further, it appears that while urea directly replaces water around the nitrogen groups on GPG that urea and water occupy different positions around the peptide bond carbonyl groups. This suggests that urea may in fact weaken the peptide bond, disrupting the peptide backbone, thus ultimately causing denaturation. PMID:26764567

  4. 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.

  5. Properties of atoms under pressure: bonded interactions of the atoms in three perovskites.

    Science.gov (United States)

    Gibbs, G V; Wang, D; Hin, C; Ross, N L; Cox, D F; Crawford, T D; Spackman, M A; Angel, R J

    2012-10-28

    The crystal structures for the three perovskites, CaSnO(3), YAlO(3), and LaAlO(3), were geometry optimized at the density functional theory level for a wide range of simulated isotropic pressures up to 80 GPa. The connections between the geometry optimized bond lengths, R(M-O), the values of the electron density, ρ(r(c)), the local kinetic, G(r(c)), potential, V(r(c)), energy densities, H(r(c)), and the Laplacian, ∇(2)(r(c)), at the bond critical points, r(c), for the M-O nonequivalent bonded interactions were examined. With increasing pressure, ρ(r(c)) increases along four distinct trends when plotted in terms of the Al-O, Ca-O, Sn-O, Y-O, and La-O bond lengths, but when the bond lengths were plotted in terms of ρ(r(c))/r where r is the periodic table row number of the M atoms, the data scatter along a single trend modeled by the power law regression expression R(M-O) = 1.41(ρ(r(c))/r)(-0.21), an expression that is comparable with that obtained for the bonded interactions for a large number of silicate and oxides crystals, R(M-O) = 1.46(ρ(r(c))/r)(-0.19) and that obtained for a relatively large number of hydroxyacid molecules R(M-O) = 1.39(s/r)(-0.22) where s is the Pauling bond strength of a bonded interaction. The similarity of the expressions determined for the perovskites, silicate and oxides crystals, and hydroxyacid molecules suggest that the bonded interactions in molecules and crystal are not only similar and comparable. The close correspondence of the expressions for the perovskites, the silicate and oxide crystals, and the molecules indicates that Pauling bond strength and ρ(r(c)) are comparable measures of the bonded interactions, the larger the accumulation of the electron density between the bonded atoms the larger the value of s, the shorter the bond lengths. It also indicates that the bonded interactions that govern the bond length variations behave as if largely short ranged. Like ρ(r(c))/r, the values of G(r(c))/r, V(r(c))/r, ∇(2)(r

  6. 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.

  7. WebInterViewer: visualizing and analyzing molecular interaction networks

    OpenAIRE

    Han, Kyungsook; Ju, Byong-Hyon; Jung, Haemoon

    2004-01-01

    Molecular interaction networks, such as those involving protein–protein and protein–DNA interactions, often consist of thousands of nodes or even more, which severely limits the usefulness of many graph drawing tools because they become too slow for interactive analysis of the networks and because they produce cluttered drawings with many edge crossings. We present a new, fast-layout algorithm and its implementation called WebInterViewer for visualizing large-scale molecular interaction netwo...

  8. 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.

  9. 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.

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

    International Nuclear Information System (INIS)

    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. (paper)

  11. 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.

  12. 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.

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

    International Nuclear Information System (INIS)

    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 the wall material. The obtained results are important for the theoretical interpretation of experiments on quantum reflection and Bose-Einstein condensation

  14. 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.

  15. Group Interaction Method Based on Wireless Sensor Network

    Directory of Open Access Journals (Sweden)

    Wu Qun

    2013-06-01

    Full Text Available This paper presents a group interaction method based on Wireless Sensor Network which supplies new attempts and ideas for human-computer interaction. Firstly, analyze group interaction framework that is different from the monomer interaction, then integrate data language of group interaction based on user’s purpose so that the Wireless Sensor Network technology and methods are applied to the system of group interaction. Finally, group interaction toys based on Wireless Sensor Network are developed. Each of toy monomers is compactly filled with sensors, wireless communication devices, LED lights. The Wireless Sensor Network which is composed of many monomers makes interface function come true in virtual. The users not only act on the physical object but also act directly on the "data" when they use the device. Currently the functions including light transmission and light color blending have been accomplished and developing.

  16. PhIN: A Protein Pharmacology Interaction Network Database

    OpenAIRE

    Wang, Z.; Li, J.; Dang, R; Liang, L; J. Lin

    2015-01-01

    Network pharmacology is a new and hot concept in drug discovery for its ability to investigate the complexity of polypharmacology, and becomes more and more important in drug development. Here we report a protein pharmacology interaction network database (PhIN), aiming to assist multitarget drug discovery by providing comprehensive and flexible network pharmacology analysis. Overall, PhIN contains 1,126,060 target–target interaction pairs in terms of shared compounds and 3,428,020 pairs in te...

  17. 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

  18. 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.

  19. Topological aspects of the human protein interaction network

    OpenAIRE

    Wiebringhaus, Thomas

    2008-01-01

    It is currently widely accepted that the understanding of complex cell functions depends on an integrated network theoretical approach and not on an isolated view of the different molecular agents. Aim of this thesis was the examination of topological properties that mirror known biological aspects by depicting the human protein network with methods from graph- and network theory. The presented network is a partial human interactome of 9222 proteins and 36324 interactions, consisting of singl...

  20. 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.

  1. Atomic switch networks-nanoarchitectonic design of a complex system for natural computing.

    Science.gov (United States)

    Demis, E C; Aguilera, R; Sillin, H O; Scharnhorst, K; Sandouk, E J; Aono, M; Stieg, A Z; Gimzewski, J K

    2015-05-22

    Self-organized complex systems are ubiquitous in nature, and the structural complexity of these natural systems can be used as a model to design new classes of functional nanotechnology based on highly interconnected networks of interacting units. Conventional fabrication methods for electronic computing devices are subject to known scaling limits, confining the diversity of possible architectures. This work explores methods of fabricating a self-organized complex device known as an atomic switch network and discusses its potential utility in computing. Through a merger of top-down and bottom-up techniques guided by mathematical and nanoarchitectonic design principles, we have produced functional devices comprising nanoscale elements whose intrinsic nonlinear dynamics and memorization capabilities produce robust patterns of distributed activity and a capacity for nonlinear transformation of input signals when configured in the appropriate network architecture. Their operational characteristics represent a unique potential for hardware implementation of natural computation, specifically in the area of reservoir computing-a burgeoning field that investigates the computational aptitude of complex biologically inspired systems. PMID:25912970

  2. Convergence of configuration-interaction single-center calculations of positron-atom interactions

    International Nuclear Information System (INIS)

    The configuration interaction (CI) method using orbitals centered on the nucleus has recently been applied to calculate the interactions of positrons interacting with atoms. Computational investigations of the convergence properties of binding energy, phase shift, and annihilation rate with respect to the maximum angular momentum of the orbital basis for the e+Cu and PsH bound states, and the e+-H scattering system were completed. The annihilation rates converge very slowly with angular momentum, and moreover the convergence with radial basis dimension appears to be slower for high angular momentum. A number of methods of completing the partial wave sum are compared; an approach based on a ΔXJ=a(J+(1/2))-n+b(J+(1/2))-(n+1) form [with n=4 for phase shift (or energy) and n=2 for the annihilation rate] seems to be preferred on considerations of utility and underlying physical justification

  3. Kaonic atoms – studies of the strong interaction with strangeness

    Directory of Open Access Journals (Sweden)

    Marton J.

    2014-01-01

    Full Text Available The strong interaction of charged antikaons (K− with nucleons and nuclei in the low-energy regime is a fascinating topic. The antikaon plays a peculiar role in hadron physics due to the strong attraction antikaon-nucleon which is a key question for possible kaonic nuclear bound states. A rather direct experimental access to the antikaon-nucleon scattering lengths is provided by precision X-ray spectroscopy of transitions to low-lying states in light kaonic atoms like kaonic hydrogen and deuterium. After the successful completion of precision measurements on kaonic hydrogen and helium isotopes by SIDDHARTA at DAΦNE/LNF, new X-ray studies with the focus on kaonic deuterium are in preparation (SIDDHARTA2. In the future with kaonic deuterium data the antikaon-nucleon isospin-dependent scattering lengths can be extracted for the first time. An overview of the experimental results of SIDDHARTA and an outlook to future perspectives in the SIDDHARTA2 experiments in this frontier research field will be given.

  4. Kaonic atoms - studies of the strong interaction with strangeness

    Science.gov (United States)

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

    2014-11-01

    The strong interaction of charged antikaons (K-) with nucleons and nuclei in the low-energy regime is a fascinating topic. The antikaon plays a peculiar role in hadron physics due to the strong attraction antikaon-nucleon which is a key question for possible kaonic nuclear bound states. A rather direct experimental access to the antikaon-nucleon scattering lengths is provided by precision X-ray spectroscopy of transitions to low-lying states in light kaonic atoms like kaonic hydrogen and deuterium. After the successful completion of precision measurements on kaonic hydrogen and helium isotopes by SIDDHARTA at DAΦNE/LNF, new X-ray studies with the focus on kaonic deuterium are in preparation (SIDDHARTA2). In the future with kaonic deuterium data the antikaon-nucleon isospin-dependent scattering lengths can be extracted for the first time. An overview of the experimental results of SIDDHARTA and an outlook to future perspectives in the SIDDHARTA2 experiments in this frontier research field will be given.

  5. 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 ...

  6. 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...

  7. 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.

  8. Interaction mechanisms between ceramic particles and atomized metallic droplets

    Science.gov (United States)

    Wu, Yue; Lavernia, Enrique J.

    1992-10-01

    The present study was undertaken to provide insight into the dynamic interactions that occur when ceramic particles are placed in intimate contact with a metallic matrix undergoing a phase change. To that effect, Al-4 wt pct Si/SiCp composite droplets were synthesized using a spray atomization and coinjection approach, and their solidification microstructures were studied both qualitatively and quantitatively. The present results show that SiC particles (SiCp) were incor- porated into the matrix and that the extent of incorporation depends on the solidification con- dition of the droplets at the moment of SiC particle injection. Two factors were found to affect the distribution and volume fraction of SiC particles in droplets: the penetration of particles into droplets and the entrapment and/or rejection of particles by the solidification front. First, during coinjection, particles collide with the atomized droplets with three possible results: they may penetrate the droplets, adhere to the droplet surface, or bounce back after impact. The extent of penetration of SiC particles into droplets was noted to depend on the kinetic energy of the particles and the magnitude of the surface energy change in the droplets that occurs upon impact. In liquid droplets, the extent of penetration of SiC particles was shown to depend on the changes in surface energy, ΔEs, experienced by the droplets. Accordingly, large SiC particles encoun- tered more resistance to penetration relative to small ones. In solid droplets, the penetration of SiC particles was correlated with the dynamic pressure exerted by the SiC particles on the droplets during impact and the depth of the ensuing crater. The results showed that no pene- tration was possible in such droplets. Second, once SiC particles have penetrated droplets, their final location in the microstructure is governed by their interactions with the solidification front. As a result of these interactions, both entrapment and rejection of

  9. 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.

  10. Study of the interaction of very slow hollow atoms with a solid

    International Nuclear Information System (INIS)

    The behavior of very slow hollow atoms traveling inside a solid is presented. The radiative electron capture of the target conduction electrons by these ions has been observed owing to the infrared divergence cross section of this process. The very specific properties of the hollow atoms are used to study their interaction in the first mono-atomic layers below the surface. (orig.)

  11. 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 ...

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. Atomic and plasma-material interaction data for fusion. V. 3

    International Nuclear Information System (INIS)

    This volume of Atomic and Plasma-Material Interaction Data for Fusion is devoted to atomic collision processes of helium atoms and of beryllium and boron atoms and ions in fusion plasmas. Most of the articles included in this volume are extended versions of the contributions presented at the IAEA experts' meetings on Atomic Data for Helium Beam Fusion Alpha Particle Diagnostics and on the Atomic Database for Beryllium and Boron, held in June 1991 at the IAEA headquarters in Vienna, or have resulted from the cross-section data analyses and evaluations performed by the working groups of these meetings. Refs, figs and tabs

  19. 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.)

  20. 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].

  1. 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].

  2. 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.

  3. 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.

  4. 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.

  5. Inter-network interactions: impact of connections between oscillatory neuronal networks on oscillation frequency and pattern.

    Directory of Open Access Journals (Sweden)

    Oscar J Avella Gonzalez

    Full Text Available Oscillations in electrical activity are a characteristic feature of many brain networks and display a wide variety of temporal patterns. A network may express a single oscillation frequency, alternate between two or more distinct frequencies, or continually express multiple frequencies. In addition, oscillation amplitude may fluctuate over time. The origin of this complex repertoire of activity remains unclear. Different cortical layers often produce distinct oscillation frequencies. To investigate whether interactions between different networks could contribute to the variety of oscillation patterns, we created two model networks, one generating on its own a relatively slow frequency (20 Hz; slow network and one generating a fast frequency (32 Hz; fast network. Taking either the slow or the fast network as source network projecting connections to the other, or target, network, we systematically investigated how type and strength of inter-network connections affected target network activity. For high inter-network connection strengths, we found that the slow network was more effective at completely imposing its rhythm on the fast network than the other way around. The strongest entrainment occurred when excitatory cells of the slow network projected to excitatory or inhibitory cells of the fast network. The fast network most strongly imposed its rhythm on the slow network when its excitatory cells projected to excitatory cells of the slow network. Interestingly, for lower inter-network connection strengths, multiple frequencies coexisted in the target network. Just as observed in rat prefrontal cortex, the target network could express multiple frequencies at the same time, alternate between two distinct oscillation frequencies, or express a single frequency with alternating episodes of high and low amplitude. Together, our results suggest that input from other oscillating networks may markedly alter a network's frequency spectrum and may partly

  6. 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

  7. Dominant couplings in qubit networks with controlled interactions

    International Nuclear Information System (INIS)

    Systems evolving under the influence of competing two- and three-body interactions are of particular interest in exploring the stability of the equilibrium states of a strongly interacting many-body system. We present a solvable model based on qubit networks, which allows us to investigate the intricate influence of these couplings on the possible asymptotic equilibrium states. We study the asymptotic evolution of finite qubit networks under two- and three-qubit interactions. As representatives of three-qubit interactions we choose controlled unitary interactions (cu-interactions) with one and two control qubits. It is shown that networks with purely three-qubit interactions exhibit different asymptotic dynamics depending on whether we deal with interactions controlled by one or two qubits. However, when we allow three-qubit interactions next to two-qubit interactions, the asymptotics is dictated by two-qubit interactions only. Finally, we prove that the simultaneous presence of two types of three-qubit interactions results in the asymptotic dynamics characteristic for two-qubit cu-interactions. (paper)

  8. Analysing health professionals' learning interactions in online social networks: A social network analysis approach

    OpenAIRE

    Li, Xin; Gray, Kathleen; Verspoor, Karin; Barnett, Stephen

    2016-01-01

    Online Social Networking may be a way to support health professionals' need for continuous learning through interaction with peers and experts. Understanding and evaluating such learning is important but difficult, and Social Network Analysis (SNA) offers a solution. This paper demonstrates how SNA can be used to study levels of participation as well as the patterns of interactions that take place among health professionals in a large online professional learning network. Our analysis has sho...

  9. 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.

  10. 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.

  11. 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...

  12. 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),…

  13. 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.

  14. 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.

  15. 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...

  16. 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.

  17. 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

    2016-01-01

    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. PMID:27174162

  18. 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.

  19. 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

    2016-01-01

    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. PMID:27174162

  20. Theory of light-matter interactions in cascade and diamond type atomic ensembles

    CERN Document Server

    Jen, Hsiang-Hua

    2011-01-01

    In this thesis, we investigate the quantum mechanical interaction of light with matter in the form of a gas of ultracold atoms: the atomic ensemble. We present a theoretical analysis of two problems, which involve the interaction of quantized electromagnetic fields (called signal and idler) with the atomic ensemble (i) cascade two-photon emission in an atomic ladder configuration, and (ii) photon frequency conversion in an atomic diamond configuration. The motivation of these studies comes from potential applications in long-distance quantum communication where it is desirable to generate quantum correlations between telecommunication wavelength light fields and ground level atomic coherences. We develop a theory of correlated signal-idler pair correlation. The analysis is complicated by the possible generation of multiple excitations in the atomic ensemble. An analytical treatment is given in the limit of a single excitation assuming adiabatic laser excitations. The analysis predicts superradiant timescales ...

  1. 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

  2. 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...

  3. 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...

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

    OpenAIRE

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

    2016-01-01

    Low-mass (sub-eV) spin-0 dark matter particles, which form a coherently oscillating classical field $\\phi = \\phi_0 \\cos(m_\\phi t)$, 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 $\\phi$ with the Higgs boson, on atomic and molecular transitions. Using recent atomic clock spectroscopy measurements, we derive new limits on ...

  5. Perfect state transfer over interacting boson networks associated with group schemes

    CERN Document Server

    Jafarizadeh, M A; Azimia, M; Fama, F Eghbali

    2010-01-01

    It is shown how to perfectly transfer an arbitrary qudit state in interacting boson networks. By defining a family of Hamiltonians related to Bose-Hubbard model, we describe a possible method for state transfer through bosonic atoms trapped in these networks with different kinds of coupling strengths between them. Particularly, by taking the underlying networks of so called group schemes as interacting boson networks, we show how choose suitable coupling strengths between the nodes, in order that an arbitrary qudit state be transferred from one node to its antipode, perfectly. In fact, by employing the group theory properties of these networks, an explicit formula for suitable coupling strengths has been given in order that perfect state transfer (PST) be achieved. Finally, as examples, PST on the underlying networks associated with cyclic group C2m, dihedral group D2n, Clifford group CL(n), and the groups U6n and V8n has been considered in details. Keywords: Bose-Hubbard Hamiltonian, Interacting boson networ...

  6. 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.

  7. Covalent bond orders for non-bonded atoms: The case for carbon-carbon interactions

    International Nuclear Information System (INIS)

    The Cioslowski-Mixon (CM) covalent bond order and the atoms-in-molecules (AIM) delocalization index can be used to study bonding characteristics between atoms not bonded in the conventional chemical sense. In particular, the bond orders between atoms (AIM basins) with one intervening atom evolve in a predictable manner and are related to the bond orders of conventionally bonded species. The CM approach shows that it is the tails of the incompletely localized orbitals that provide for such interactions. Single, multiple, and resonant bond effects are seen which are physically meaningful and useful as an additional characterization of molecular bonding. The important case of carbon-carbon interactions is studied here.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Interaction of a deuterium atomic beam with a palladium membrane

    Energy Technology Data Exchange (ETDEWEB)

    Livshits, A.I.; Metter, I.M.; Samartsev, A.A.

    1976-07-01

    It is suggested that under certain conditions the permeability of a solid membrane of the usual thickness for gases can be comparable to the permeability of an aperture in a thin wall. Experiments are carried out to test this suggestion. A study is made of the penetration of deuterium from a thermal atomic beam with a flux density of 10/sup 11/--10/sup 12/ atoms/cm/sup 2/xsec) through an ''inactive'' palladium membrane (i.e., which is comparatively impenetrable for molecular hydrogen). The probability for the penetration of deuterium atoms in a single collision with the membrane over the temperature range 20--520degreeC is independent of the temperature and is equal to 0.1 (i.e., a value of the same order of magnitude as the sticking probability for hydrogen atoms on metals). It is shown experimentally that the desorption is of second order in the concentration of the desolved gas. It is suggested that each atom which recombines at the membrane is first absorbed and then reaches the opposite boundary.

  14. Experimental Study on Interactions Between H Atoms and Organic Haze

    Science.gov (United States)

    Sekine, Y.; Imanaka, H.; Khare, B. N.; Bakes, E. L. O.; McKay, C. P.; Sugita, S.; Matsui, T.

    2005-01-01

    In Titan s atmosphere composed of N2 and CH4, irradiations of both solar ultraviolet light and charged particles induce active chemical reactions. In the processes of these reactions, a large amount of hydrogen (H) atoms are expected to be formed by dissociation of CH4 and other hydrocarbons [e.g., 1, 2]. Theoretical models suggest that these active H atoms need to be converted to stable hydrogen molecules (H2) efficiently to maintain unsaturated hydrocarbons and organic haze in Titan s atmosphere [e.g., 1]. Furthermore, molecular hydrogen is an important greenhouse effect gas in Titan s atmosphere, and small variation in its abundance strongly affects Titan s surface temperature [3]. Thus, the formation of H2 molecules from H atoms is a key reaction for both the atmospheric chemistry and the surface environment of Titan. Although several numerical calculations have been conducted to investigate the atmospheric chemistry of Titan with hypothesized recombination reactions of H atoms, such as catalytic scheme of C4H2 [e.g., 1, 2], it is still unclear what chemical reaction is responsible for the conversion of H atoms to H2 molecules in Titan s atmosphere.

  15. 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.

  16. Recurrent interactions in spiking networks with arbitrary topology.

    Science.gov (United States)

    Pernice, Volker; Staude, Benjamin; Cardanobile, Stefano; Rotter, Stefan

    2012-03-01

    The population activity of random networks of excitatory and inhibitory leaky integrate-and-fire neurons has been studied extensively. In particular, a state of asynchronous activity with low firing rates and low pairwise correlations emerges in sparsely connected networks. We apply linear response theory to evaluate the influence of detailed network structure on neuron dynamics. It turns out that pairwise correlations induced by direct and indirect network connections can be related to the matrix of direct linear interactions. Furthermore, we study the influence of the characteristics of the neuron model. Interpreting the reset as self-inhibition, we examine its influence, via the spectrum of single-neuron activity, on network autocorrelation functions and the overall correlation level. The neuron model also affects the form of interaction kernels and consequently the time-dependent correlation functions. We find that a linear instability of networks with Erdös-Rényi topology coincides with a global transition to a highly correlated network state. Our work shows that recurrent interactions have a profound impact on spike train statistics and provides tools to study the effects of specific network topologies. PMID:22587132

  17. 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

  18. 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".

  19. 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

  20. 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).

  1. 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.

  2. 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.

  3. 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.

  4. 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…

  5. 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.

  6. Scattering approach to dispersive atom-surface interactions

    Energy Technology Data Exchange (ETDEWEB)

    Dalvit, Diego [Los Alamos National Laboratory; Messina, Riccardo [LAB KASTLER BROSSEL; Maia Neto, Paulo [INSTITUTO DE FISICA UFRJ; Lambrecht, Astrid [LAB KASTLER BROSSEL; Reynaud, Serge [LAB KASTLER BROSSEL

    2009-01-01

    We develop the scattering approach for the dispersive force on a ground state atom on top of a corrugated surface. We present explicit results to first order in the corrugation amplitude. A variety of analytical results are derived in different limiting cases, including the van der Waals and Casimir-Polder regimes. We compute numerically the exact first-order dispersive potential for arbitrary separation distances and corrugation wavelengths, for a Rubidium atom on top of a silicon or gold corrugated surface. We consider in detail the correction to the proximity force approximation, and present a very simple approximation algorithm for computing the potential.

  7. 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...

  8. 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.

  9. 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 ...

  10. 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.

  11. 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.

  12. 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...

  13. Pairwise interaction pattern in the weighted communication network

    CERN Document Server

    Xu, Xiao-Ke; Wu, Ye; Small, Michael

    2012-01-01

    Although recent studies show that both topological structures and human dynamics can strongly affect information spreading on social networks, the complicated interplay of the two significant factors has not yet been clearly described. In this work, we find a strong pairwise interaction based on analyzing the weighted network generated by the short message communication dataset within a Chinese tele-communication provider. The pairwise interaction bridges the network topological structure and human interaction dynamics, which can promote local information spreading between pairs of communication partners and in contrast can also suppress global information (e.g., rumor) cascade and spreading. In addition, the pairwise interaction is the basic pattern of group conversations and it can greatly reduce the waiting time of communication events between a pair of intimate friends. Our findings are also helpful for communication operators to design novel tariff strategies and optimize their communication services.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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...

  19. 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...

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

    International Nuclear Information System (INIS)

    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. (paper)

  1. Microbial interaction networks in soil and in silico

    Science.gov (United States)

    Vetsigian, Kalin

    2012-02-01

    Soil harbors a huge number of microbial species interacting through secretion of antibiotics and other chemicals. What patterns of species interactions allow for this astonishing biodiversity to be sustained, and how do these interactions evolve? I used a combined experimental-theoretical approach to tackle these questions. Focusing on bacteria from the genus Steptomyces, known for their diverse secondary metabolism, I isolated 64 natural strains from several individual grains of soil and systematically measured all pairwise interactions among them. Quantitative measurements on such scale were enabled by a novel experimental platform based on robotic handling, a custom scanner array and automatic image analysis. This unique platform allowed the simultaneous capturing of ˜15,000 time-lapse movies of growing colonies of each isolate on media conditioned by each of the other isolates. The data revealed a rich network of strong negative (inhibitory) and positive (stimulating) interactions. Analysis of this network and the phylogeny of the isolates, together with mathematical modeling of microbial communities, revealed that: 1) The network of interactions has three special properties: ``balance'', ``bi- modality'' and ``reciprocity''; 2) The interaction network is fast evolving; 3) Mathematical modeling explains how rapid evolution can give rise to the three special properties through an interplay between ecology and evolution. These properties are not a result of stable co-existence, but rather of continuous evolutionary turnover of strains with different production and resistance capabilities.

  2. Bose-Einstein condensation of trapped atoms with dipole interactions

    OpenAIRE

    Nho, Kwangsik; Landau, D. P.

    2005-01-01

    The path integral Monte Carlo method is used to simulate dilute trapped Bose gases and to investigate the equilibrium properties at finite temperatures. The quantum particles have a long-range dipole-dipole interaction and a short-range s-wave interaction. Using an anisotropic pseudopotential for the long-range dipolar interaction and a hard-sphere potential for the short-range s-wave interaction, we calculate the energetics and structural properties as a function of temperature and the numbe...

  3. 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

  4. 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.``

  5. Weak Interactions in Atoms and Nuclei: The Standard Model and Beyond

    OpenAIRE

    Ramsey-Musolf, M. J.; Secrest, J.

    2003-01-01

    Studies in nuclear and atomic physics have played an important role in developing our understanding of the Standard Model of electroweak interactions. We review the basic ingredients of the Standard Model, and discuss some key nuclear and atomic physics experiments used in testing these ideas. We also summarize the conceptual issues of the Standard Model that motivate the search for new physics.

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. A constructive model potential method for atomic interactions

    Science.gov (United States)

    Bottcher, C.; Dalgarno, A.

    1974-01-01

    A model potential method is presented that can be applied to many electron single centre and two centre systems. The development leads to a Hamiltonian with terms arising from core polarization that depend parametrically upon the positions of the valence electrons. Some of the terms have been introduced empirically in previous studies. Their significance is clarified by an analysis of a similar model in classical electrostatics. The explicit forms of the expectation values of operators at large separations of two atoms given by the model potential method are shown to be equivalent to the exact forms when the assumption is made that the energy level differences of one atom are negligible compared to those of the other.

  11. 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}...

  12. Long-range dispersion interactions. I. Formalism for two heteronuclear atoms

    International Nuclear Information System (INIS)

    A general procedure for systematically evaluating the long-range dispersion interaction between two heteronuclear atoms in arbitrary states is outlined. The C6 dispersion parameter can always be written in terms of sum rules involving oscillator strengths only and formulas for a number of symmetry cases are given. The dispersion coefficients for excited alkali-metal atoms interacting with the ground-state H and He are tabulated

  13. 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...

  14. Control of Wannier orbitals for generating tunable Ising interactions of ultracold atoms in an optical lattice

    Energy Technology Data Exchange (ETDEWEB)

    Inaba, Kensuke; Tamaki, Kiyoshi; Igeta, Kazuhiro; Yamashita, Makoto [NTT Basic Research Laboratories, NTT Corporation, Atsugi 243-0198, Japan and JST, CREST, Chiyoda-ku, Tokyo 102-0075 (Japan); Tokunaga, Yuuki [NTT Secure Platform Laboratories, NTT Corporation, Musashino 180-8585, Japan and JST, CREST, Chiyoda-ku, Tokyo 102-0075 (Japan)

    2014-12-04

    In this study, we propose a method for generating cluster states of atoms in an optical lattice. By utilizing the quantum properties of Wannier orbitals, we create an tunable Ising interaction between atoms without inducing the spin-exchange interactions. We investigate the cause of errors that occur during entanglement generations, and then we propose an error-management scheme, which allows us to create high-fidelity cluster states in a short time.

  15. 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.

  16. 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...

  17. Hydrogen internal friction and interaction of solute atoms in niobium- and vanadium-based alloys

    International Nuclear Information System (INIS)

    A computer model has been proposed to be used to calculate the internal friction spectrum, caused by the ''diffusion under stress'' of hydrogen atoms in a solid solution with a b.c.c. lattice containing substitutional atoms. The model takes into account the long-range pair interaction of dissolved atoms. It is suggested that such interaction acts on diffusion by producing short-range order of mobile hydrogen atoms and by changing their energy. These changes occur in the tetrahedral (before the jump) as well as in the octahedral (at the saddle point of the diffusion barrier) interstitial sites and, therefore, produce local changes of the hydrogen diffusion activation energy (the activation energy of internal friction). The relaxation strength is calculated from the local fields of atomic displacements around every atom that participates in diffusion. The model has been used to study the nature of hydrogen relaxation in Ti- and Zr-containing Nb- and V-based alloys and to calculate the ''chemical'' interaction energy of the H(D)-Ti(Zr) pairs. It was shown that the hydrogen relaxation mechanism in Nb(V)-Ti(Zr)-H(D) alloys consists in diffusion under stress of hydrogen or deuterium atoms in the vicinity of single substitutional atoms at low concentration of substitutional atoms and high hydrogen or deuterium concentration, and in the vicinity of substitutional pairs - at high concentration of substitutional atoms and low hydrogen or deuterium concentration. The ''chemical'' interaction H(D)-Ti(Zr) in niobium and vanadium is stronger or is of the same order, as the strain-induced (elastic) interaction. (orig.)

  18. 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.

  19. Effects of dipole-dipole interaction between cigar-shaped BECs of cold alkali atoms: Towards inverse-squared interactions

    OpenAIRE

    Yu, Yue; Luo, Zhuxi; Wang, Ziqiang

    2011-01-01

    We show that the dipole-dipole coupling between Wannier modes in cigar-shaped Bose-Einstein condensates (BECs) is significantly enhanced while the short-range coupling strongly suppressed. As a result, the dipole-dipole interaction can become the dominant interaction between ultracold alkali Bose atoms. In the long length limit of a cigar-shaped BEC, the resulting effective one-dimensional models possess an effective inverse squared interacting potential, the Calogero-Sutherland potential, wh...

  20. 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...

  1. Digital Ecology: Coexistence and Domination among Interacting Networks

    OpenAIRE

    Kaj-Kolja Kleineberg; Marián Boguñá

    2015-01-01

    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 concer...

  2. 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...

  3. 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.

  4. 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.

  5. 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...

  6. Atoms

    International Nuclear Information System (INIS)

    Completed by recent contributions on various topics (atoms and the Brownian motion, the career of Jean Perrin, the evolution of atomic physics since Jean Perrin, relationship between scientific atomism and philosophical atomism), this book is a reprint of a book published at the beginning of the twentieth century in which the author addressed the relationship between atomic theory and chemistry (molecules, atoms, the Avogadro hypothesis, molecule structures, solutes, upper limits of molecular quantities), molecular agitation (molecule velocity, molecule rotation or vibration, molecular free range), the Brownian motion and emulsions (history and general features, statistical equilibrium of emulsions), the laws of the Brownian motion (Einstein's theory, experimental control), fluctuations (the theory of Smoluchowski), light and quanta (black body, extension of quantum theory), the electricity atom, the atom genesis and destruction (transmutations, atom counting)

  7. 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.

  8. 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

  9. 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.

  10. Bose-Einstein condensation of trapped atoms with dipole interactions

    International Nuclear Information System (INIS)

    The path-integral Monte Carlo method is used to simulate dilute trapped Bose gases and to investigate the equilibrium properties at finite temperatures. The quantum particles have a long-range dipole-dipole interaction and a short-range s-wave interaction. Using an anisotropic pseudopotential for the long-range dipolar interaction and a hard-sphere potential for the short-range s-wave interaction, we calculate the energetics and structural properties as a function of temperature and the number of particles. Also, in order to determine the effects of dipole-dipole forces and the influence of the trapping field on the dipolar condensate, we use two cylindrically symmetric harmonic confinements (a cigar-shaped trap and a disk-shaped trap). We find that the net effect of dipole-dipole interactions is governed by the trapping geometry. For a cigar-shaped trap, the net contribution of dipolar interactions is attractive and the shrinking of the density profiles is observed. For a disk-shaped trap, the net effect of long-range dipolar forces is repulsive and the density profiles expand

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

    DEFF Research Database (Denmark)

    Volosniev, A. G.; Petrosyan, D.; Valiente, M.; Fedorov, D. V.; Jensen, A. S.; Zinner, Nikolaj Thomas

    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...... find that bosonic atoms offer more flexibility for tuning independently the parameters of the spin Hamiltonian through interatomic (intra-species) interaction which is absent for fermions due to the Pauli exclusion principle. Our formalism can have important implications for control and manipulation of...

  12. 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...

  13. 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).

  14. 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.

  15. 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.

  16. Spatial assignment of symmetry adapted perturbation theory interaction energy components: The atomic SAPT partition

    Science.gov (United States)

    Parrish, Robert M.; Sherrill, C. David

    2014-07-01

    We develop a physically-motivated assignment of symmetry adapted perturbation theory for intermolecular interactions (SAPT) into atom-pairwise contributions (the A-SAPT partition). The basic precept of A-SAPT is that the many-body interaction energy components are computed normally under the formalism of SAPT, following which a spatially-localized two-body quasiparticle interaction is extracted from the many-body interaction terms. For electrostatics and induction source terms, the relevant quasiparticles are atoms, which are obtained in this work through the iterative stockholder analysis (ISA) procedure. For the exchange, induction response, and dispersion terms, the relevant quasiparticles are local occupied orbitals, which are obtained in this work through the Pipek-Mezey procedure. The local orbital atomic charges obtained from ISA additionally allow the terms involving local orbitals to be assigned in an atom-pairwise manner. Further summation over the atoms of one or the other monomer allows for a chemically intuitive visualization of the contribution of each atom and interaction component to the overall noncovalent interaction strength. Herein, we present the intuitive development and mathematical form for A-SAPT applied in the SAPT0 approximation (the A-SAPT0 partition). We also provide an efficient series of algorithms for the computation of the A-SAPT0 partition with essentially the same computational cost as the corresponding SAPT0 decomposition. We probe the sensitivity of the A-SAPT0 partition to the ISA grid and convergence parameter, orbital localization metric, and induction coupling treatment, and recommend a set of practical choices which closes the definition of the A-SAPT0 partition. We demonstrate the utility and computational tractability of the A-SAPT0 partition in the context of side-on cation-π interactions and the intercalation of DNA by proflavine. A-SAPT0 clearly shows the key processes in these complicated noncovalent interactions, in

  17. XSAMS: XML schema for atomic and molecular data and particle solid interaction. Summary report of an IAEA consultants' meeting

    International Nuclear Information System (INIS)

    Advanced developments in computer technologies offer exciting opportunities for new distribution tools and applications in various fields of physics. The convenient and reliable exchange of data is clearly an important component of such applications. Therefore, in 2003, the A and M Data Unit initiated within the collaborative efforts of the DCN (Data Centres Network) a new standard for atomic, molecular and particle surface interaction data exchange (AM/PSI) based on XML (eXtensible Markup Language). The schema is named XSAMS which stands for 'XML Schema for Atoms Molecules and Solids'. A working group composed of staff from the IAEA, NIST, ORNL and Observatoire Paris-Meudon meets biannually to discuss progress made on XSAMS, and to foresee new developments and actions to be taken to promote this standard for AM/PSI data exchange. Such a meeting was held on 27 October 2008, and the discussions and progress made in the schema are considered within this report. (author)

  18. Casimir-Polder interaction between an atom and a cylinder with application to nanosystems

    International Nuclear Information System (INIS)

    Recently, the Lifshitz theory of dispersion forces was extended for the case of an atom (molecule) interacting with a plane surface of a uniaxial crystal or with a long solid cylinder or cylindrical shell made of isotropic material or uniaxial crystal. The obtained results are applicable to nanosystems. In particular, we investigate the Casimir-Polder interaction between hydrogen atoms (molecules) and multi-wall carbon nanotubes. It is demonstrated that the hydrogen atoms located inside multiwall carbon nanotubes have a lower free energy compared to those located outside. We also perform comparison studies of the interaction of hydrogen atoms between themselves and with multi-wall carbon nanotube. The obtained results are important for the problem of hydrogen storage

  19. 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.

  20. 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.

  1. From Casimir-Polder Force to Dicke Physics: Interaction between Atoms and a Topological Insulator

    Science.gov (United States)

    Fuchs, Sebastian; Buhmann, Stefan

    We apply the theory of macroscopic quantum electrodynamics in dispersing and absorbing media to study the Casimir-Polder force between an atom and a topological insulator. The electromagnetic response of a topological insulator surface leads to a mixing of electric and magnetic fields, breaking the time-reversal symmetry. The coupling of these fields to an atom causes shifts of the atom's eigenenergies and modified decay rates near the surface of the topological insulator. Energy shifts and modified decay rates cannot only be triggered by the presence of a material, but can be caused by other atoms in close proximity as well. The collective dynamics of atoms (Dicke Physics) leads to a superradiant burst. Combining macroscopic QED and Dicke physics opens the door to the investigation of cooperative atom-surface interactions.

  2. FENDL/E-2.0. Evaluated nuclear data library of neutron-nucleus interaction cross sections and photon production cross sections and photon-atom interaction cross sections for fusion applications. Version 1, March 1997. Summary documentation

    International Nuclear Information System (INIS)

    This document presents the description of a physical tape containing the basic evaluated nuclear data library of neutron-nucleus interaction cross sections, photon production cross sections and photon-atom interaction cross sections for fusion applications. It is part of the evaluated nuclear data library for fusion applications FENDL-2. The data are available cost-free from the Nuclear Data Section upon request. The data can also be retrieved by the user via online access through international computer networks. (author)

  3. 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).

  4. The Kinetochore Interaction Network (KIN) of ascomycetes

    Science.gov (United States)

    Freitag, Michael

    2016-01-01

    Chromosome segregation relies on coordinated activity of a large assembly of proteins, the “Kinetochore Interaction Network” (KIN). How conserved the underlying mechanisms driving the epigenetic phenomenon of centromere and kinetochore assembly and maintenance are remains unclear, even though various eukaryotic models have been studied. More than 50 different proteins, many in multiple copies, comprise the KIN or are associated with fungal centromeres and kinetochores. Proteins isolated from immune sera recognized centromeric regions on chromosomes and were thus named centromere proteins (“CENPs”). CENP-A, sometimes called “centromere-specific H3” (CenH3), is incorporated into nucleosomes within or near centromeres. The “constitutive centromere-associated network” (CCAN) assembles on this specialized chromatin, likely based on specific interactions with and requiring presence of CENP-C. The outer kinetochore comprises the Knl1-Mis12-Ndc80 (“KMN”) protein complexes that connect the CCAN to spindles, accomplished by binding and stabilizing microtubules (MTs) and in the process generating load-bearing assemblies for chromatid segregation. In most fungi the Dam1/DASH complex connects the KMN complexes to MTs. Fungi present a rich resource to investigate mechanistic commonalities but also differences in kinetochore architecture. While ascomycetes have sets of CCAN and KMN proteins that are conserved with those of either budding yeast or metazoans, searching other major branches of the fungal kingdom revealed that CCAN proteins are poorly conserved at the primary sequence level. Several conserved binding motifs or domains within KMN complexes have been described recently, and these features of ascomycete KIN proteins are shared with most metazoan proteins. In addition, several ascomycete-specific domains have been identified here. PMID:26908646

  5. 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

  6. First principles investigation of interaction between impurity atom (Si, Ge, Sn) and carbon atom in diamond-like carbon system

    International Nuclear Information System (INIS)

    The interaction between impurity atom (Si, Ge, and Sn) and carbon atom in diamond-like carbon (DLC) system was investigated by the first principles simulation method based on the density functional theory. The tetrahedral configuration was selected as the calculation model for simplicity. When the bond angle varied in a range of 90°–130° from the equivalent state of 109.471°, the distortion energy and the electronic structures including charge density of the highest occupied molecular orbital (HOMO) and partial density of state (PDOS) in the different systems were calculated. The results showed that the addition of Si, Ge and Sn atom into amorphous carbon matrix significantly decreased the distortion energy of the system as the bond angles deviated from the equilibrium one. Further studies of the HOMO and PDOS indicated that the weak covalent bond between Si(Ge, Sn) and C atoms was formed with the decreased strength and directionality, which were influenced by the electronegative difference. These results implied that the electron transfer behavior at the junction of carbon nano-devices could be tailored by the impurity element, and the compressive stress in DLC films could be reduced by the incorporation of Si, Ge and Sn because of the formation of weaker covalent bonds. - Highlights: ►Distortion energy after bond angle distortion was decreased comparing with C-C unit. ►The weak covalent bond was formed between impurity atoms and corner carbon atoms. ►Observed electron transfer behavior affected the strength and directionality of bond. ►Reduction of strength and directionality of bond contributed to small energy change.

  7. Epidemic spreading in networks with nonrandom long-range interactions

    Science.gov (United States)

    Estrada, Ernesto; Kalala-Mutombo, Franck; Valverde-Colmeiro, Alba

    2011-09-01

    An “infection,” understood here in a very broad sense, can be propagated through the network of social contacts among individuals. These social contacts include both “close” contacts and “casual” encounters among individuals in transport, leisure, shopping, etc. Knowing the first through the study of the social networks is not a difficult task, but having a clear picture of the network of casual contacts is a very hard problem in a society of increasing mobility. Here we assume, on the basis of several pieces of empirical evidence, that the casual contacts between two individuals are a function of their social distance in the network of close contacts. Then, we assume that we know the network of close contacts and infer the casual encounters by means of nonrandom long-range (LR) interactions determined by the social proximity of the two individuals. This approach is then implemented in a susceptible-infected-susceptible (SIS) model accounting for the spread of infections in complex networks. A parameter called “conductance” controls the feasibility of those casual encounters. In a zero conductance network only contagion through close contacts is allowed. As the conductance increases the probability of having casual encounters also increases. We show here that as the conductance parameter increases, the rate of propagation increases dramatically and the infection is less likely to die out. This increment is particularly marked in networks with scale-free degree distributions, where infections easily become epidemics. Our model provides a general framework for studying epidemic spreading in networks with arbitrary topology with and without casual contacts accounted for by means of LR interactions.

  8. 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.

  9. 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...

  10. 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 must...

  11. Regular structure of low-lying states for atomic nuclei under random interactions

    International Nuclear Information System (INIS)

    In this paper we review regularities of low-lying states for many-body systems, in particular, atomic nuclei, under random interactions. We shall discuss the famous problem of spin zero ground state dominance, positive parity dominance, collective motion, odd-even staggering, average energies, etc., in the presence of random interactions. (author)

  12. [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

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. 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...

  18. 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.

  19. 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

  20. 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.

  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. 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.

  4. 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.

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

    CERN Document Server

    Stadnik, Y V

    2016-01-01

    Low-mass (sub-eV) spin-0 dark matter particles, which form a coherently oscillating classical field $\\phi = \\phi_0 \\cos(m_\\phi t)$, 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 $\\phi$ with the Higgs boson, on atomic and molecular transitions. Using recent atomic clock spectroscopy measurements, we derive new limits on the linear interaction of $\\phi$ with the Higgs boson, as well as its quadratic interactions with the photon and light quarks. For the linear interaction of $\\phi$ with the Higgs boson, our derived limits improve on existing constraints by up to $2-3$ orders of magnitude.

  6. Effects of dipole–dipole interaction between cigar-shaped BECs of cold alkali atoms: towards inverse-squared interactions

    International Nuclear Information System (INIS)

    We show that the dipole–dipole coupling between Wannier modes in cigar-shaped Bose–Einstein condensates (BECs) is significantly enhanced while the short-range coupling is strongly suppressed. As a result, the dipole–dipole interaction can become the dominant interaction between ultracold alkali Bose atoms. In the long length limit of a cigar-shaped BEC, the resulting effective one-dimensional models possess an effective inverse squared interacting potential, the Calogero–Sutherland potential, which plays a fundamental role in many fields of contemporary physics; but its direct experimental realization has been a challenge for a long time. We propose to realize the Calogero–Sutherland model in ultracold alkali Bose atoms and study the effects of the dipole–dipole interaction. (paper)

  7. Effects of dipole-dipole interaction between cigar-shaped BECs of cold alkali atoms: towards inverse-squared interactions

    Science.gov (United States)

    Yu, Yue; Luo, Zhuxi; Wang, Ziqiang

    2014-07-01

    We show that the dipole-dipole coupling between Wannier modes in cigar-shaped Bose-Einstein condensates (BECs) is significantly enhanced while the short-range coupling is strongly suppressed. As a result, the dipole-dipole interaction can become the dominant interaction between ultracold alkali Bose atoms. In the long length limit of a cigar-shaped BEC, the resulting effective one-dimensional models possess an effective inverse squared interacting potential, the Calogero-Sutherland potential, which plays a fundamental role in many fields of contemporary physics; but its direct experimental realization has been a challenge for a long time. We propose to realize the Calogero-Sutherland model in ultracold alkali Bose atoms and study the effects of the dipole-dipole interaction.

  8. 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)

  9. 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 ...

  10. 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.

  11. 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...

  12. 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.

  13. Casimir-Polder interaction energy between two atoms moving with uniform acceleration

    CERN Document Server

    Noto, Antonio

    2013-01-01

    We consider the interatomic Casimir-Polder interaction energy between two neutral ground-state atoms moving in the vacuum space with the same uniform acceleration. We assume the acceleration orthogonal to their separation, so that their mutual distance remains constant. Using a model of the Casimir-Polder interaction based on the interaction between the instantaneous atomic dipole moments, which are induced and correlated by the zero-point field fluctuations, we evaluate the interaction energy between the two accelerating atoms in terms of quantities expressed in the laboratory reference frame. We find that the dependence of the Casimir-Polder interaction between the atoms from the distance is different with respect to the case of atoms at rest, and the relation of our results with the Unruh effect is discussed. We show that in the near zone a new term proportional to $R^{-5}$ adds to the usual $R^{-6}$ behavior, and in the far zone a term proportional to $R^{-6}$ adds to the usual $R^{-7}$ behavior, making t...

  14. 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.

  15. Visualizing Gene - Interactions within the Rice and Maize Network

    Science.gov (United States)

    Sampong, A.; Feltus, A.; Smith, M.

    2014-12-01

    The purpose of this research was to design a simpler visualization tool for comparing or viewing gene interaction graphs in systems biology. This visualization tool makes it possible and easier for a researcher to visualize the biological metadata of a plant and interact with the graph on a webpage. Currently available visualization software like Cytoscape and Walrus are difficult to interact with and do not scale effectively for large data sets, limiting the ability to visualize interactions within a biological system. The visualization tool developed is useful for viewing and interpreting the dataset of a gene interaction network. The graph layout drawn by this visualization tool is an improvement from the previous method of comparing lines of genes in two separate data files to, now having the ability to visually see the layout of the gene networks and how the two systems are related. The graph layout presented by the visualization tool draws a graph of the sample rice and maize gene networks, linking the common genes found in both plants and highlighting the functions served by common genes from each plant. The success of this visualization tool will enable Dr. Feltus to continue his investigations and draw conclusions on the biological evolution of the sorghum plant as well. REU Funded by NSF ACI Award 1359223 Vetria L. Byrd, PI

  16. 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

  17. Fragmentation of phosphorylated and singly charged peptide ions via interaction with metastable atoms.

    Science.gov (United States)

    Berkout, Vadym D; Doroshenko, Vladimir M

    2008-12-01

    Fragmentation of phosphorylated peptide ions via interaction with electronically excited metastable argon atoms was studied in a linear trap - time-of-flight mass spectrometer. Doubly charged ions of phosphorylated peptides from an Enolase digest were produced by electrospray ionization and subjected to a metastable atom beam in the linear trap. The metastable argon atoms were generated using a glow-discharge source. An intensive series of c- and z- ions were observed in all cases, with the phosphorylation group intact. The formation of molecular radical cations with reduced charge indicated that an electron transfer from a highly excited metastable state of argon to the peptide cation occurred. Additionally, singly charged Bradykinin, Substance P and Fibrinopeptide A molecular ions were fragmented via interaction with electronically excited metastable helium atoms. The fragmentation mechanism was different in this case and involved Penning ionization. PMID:19956340

  18. Emergence of overlap in ensembles of spatial multiplexes and statistical mechanics of spatial interacting networks ensembles

    OpenAIRE

    Halu, Arda; Mukherjee, Satyam; 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 ...

  19. 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

  20. Engineering and Characterization of Collagen Networks Using Wet Atomic Force Microscopy and Environmental Scanning Electron Microscopy

    Science.gov (United States)

    Osborn, Jenna; Coffey, Tonya; Conrad, Brad; Burris, Jennifer; Hester, Brooke

    2014-03-01

    Collagen is an abundant protein and its monomers covalently crosslink to form fibrils which form fibers which contribute to forming macrostructures like tendon or bone. While the contribution is well understood at the macroscopic level, it is not well known at the fibril level. We wish to study the mechanical properties of collagen for networks of collagen fibers that vary in size and density. We present here a method to synthesize collagen networks from monomers and that allows us to vary the density of the networks. By using biotynilated collagen and a surface that is functionalized with avidin, we generate two-dimensional collagen networks across the surface of a silicon wafer. During network synthesis, the incubation time is varied from 30 minutes to 3 hours or temperature is varied from 25°C to 45°C. The two-dimensional collagen network created in the process is characterized using environmental atomic force microscopy (AFM) and scanning electron microscopy (SEM). The network density is measured by the number of strands in one frame using SPIP software. We expect that at body temperature (37°C) and with longer incubation times, the network density should increase.

  1. 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.

  2. The collapse and revival of Bell-nonlocality of two macroscopic fields interacting with resonant atoms

    Science.gov (United States)

    Luo, Cheng-Li; Liao, Chang-Geng; Chen, Zi-Hong

    2010-08-01

    We investigate the nonlocality dynamics of two initially entangled macroscopic fields each interacting with a resonant two-level atom. The nonlocality of macroscopic field is characterized by the extent to which the Bell Clauser-Horne-Shimony-Holt (CHSH)'s inequality for continuous-variable states is violated. We show that the collapse and revival of the Bell-nonlocality are similar to the collapse and revival of the atomic population inversion of the Jaynes-Cummings model (JCM).

  3. Molecular dynamics simulation of gaseous atomic hydrogen interactions with hydrocarbon grains

    OpenAIRE

    Papoular, Renaud

    2004-01-01

    Semi-empirical molecular dynamics is used to simulate several gaseous atomic hydrogen interactions with hydrocarbon grains in space: recoil, adsorption, diffusion, chemisorption and recombination into molecular hydrogen. Their probabilities are determined by multiple numerical experiments, as a function of initial velocity of gas atoms. The equilibrium hydrogen coverage of free grains is then derived. These data can be used in calculations of material and energy balance as well as rates of hy...

  4. Inelastic transitions of atoms and molecules induced by van der Waals interaction with a surface

    Science.gov (United States)

    Baudon, J.; Hamamda, M.; Boustimi, M.; Bocvarski, V.; Taillandier-Loize, T.; Dutier, G.; Perales, F.; Ducloy, M.

    2012-05-01

    Inelastic processes occuring in thermal-velocity metastable atoms and molecules passing at a mean distance (1-100 nm) are investigated. These processes are caused by the quadrupolar part of the van der Waals interaction: fine-structure transitions in atoms (Ar∗, Kr∗), rovibrational transitions in N2∗(3Σu+), transitions among magnetic sub-levels in the presence of a magnetic field.

  5. Dynamics of two three-level atoms interacting with two modes of radiation

    International Nuclear Information System (INIS)

    The system of two 3-level atoms in interaction with 2-modes of the radiation field is investigated. The (Ξ cascade) configuration for the two identical atoms is taken and exact resonance is considered. The wave function is calculated and the phenomena of collapses and revivals, sub-poissonian statistics, and two-mode anticorrelation are discussed. Subrevivals are noted for these phenomena. (author). 26 refs, 5 figs

  6. 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.

  7. 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

  8. Graph theory and stability analysis of protein complex interaction networks.

    Science.gov (United States)

    Huang, Chien-Hung; Chen, Teng-Hung; Ng, Ka-Lok

    2016-04-01

    Protein complexes play an essential role in many biological processes. Complexes can interact with other complexes to form protein complex interaction network (PCIN) that involves in important cellular processes. There are relatively few studies on examining the interaction topology among protein complexes; and little is known about the stability of PCIN under perturbations. We employed graph theoretical approach to reveal hidden properties and features of four species PCINs. Two main issues are addressed, (i) the global and local network topological properties, and (ii) the stability of the networks under 12 types of perturbations. According to the topological parameter classification, we identified some critical protein complexes and validated that the topological analysis approach could provide meaningful biological interpretations of the protein complex systems. Through the Kolmogorov-Smimov test, we showed that local topological parameters are good indicators to characterise the structure of PCINs. We further demonstrated the effectiveness of the current approach by performing the scalability and data normalization tests. To measure the robustness of PCINs, we proposed to consider eight topological-based perturbations, which are specifically applicable in scenarios of targeted, sustained attacks. We found that the degree-based, betweenness-based and brokering-coefficient-based perturbations have the largest effect on network stability. PMID:26997661

  9. 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

  10. 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...

  11. Double-atom excitation in heavy-particle collisions induced by the electron-electron interaction

    International Nuclear Information System (INIS)

    We present an analytical method for rapid calculation of matrix elements for double-atom excitation induced by the electron-electron interaction. The method is applied to calculation of probabilities and cross sections for double-atom n = 2 excitation in H(1s)-H(1s) and various A(Zp-1)+(1s)-H(1s) collisions at intermediate and high projectile energies. Based on first-order perturbation theory an empirical scaling rule for the double-atom excitation cross sections is derived. The calculated cross sections are shown to be in good agreement with this scaling relation. (author)

  12. 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.

  13. 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...

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

    CERN Document Server

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

    2015-01-01

    Largely motivated by a number of applications, the dispersion ($C_3$) coefficients for the interaction of a Cs atom with different material media such as Au (metal), Si (semiconductor) and various dielectric surfaces like SiO$_2$, SiN$_{\\rm{x}}$, 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 coefficients 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 devise a simple working functional fitting form for the retarded coefficients in terms of two parameters that are quoted for each medium.

  15. 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.

  16. Fluctuation-induced forces between atoms and surfaces: the Casimir-Polder interaction

    CERN Document Server

    Intravaia, F; Antezza, M

    2010-01-01

    Electromagnetic fluctuation-induced forces between atoms and surfaces are generally known as Casimir-Polder interactions. The exact knowledge of these forces is rapidly becoming important in modern experimental set-ups and for technological applications. Recent theoretical and experimental investigations have shown that such an interaction is tunable in strength and sign, opening new perspectives to investigate aspects of quantum field theory and condensed-matter physics. In this Chapter we review the theory of fluctuation-induced interactions between atoms and a surface, paying particular attention to the physical characterization of the system. We also survey some recent developments concerning the role of temperature, situations out of thermal equilibrium, and measurements involving ultra-cold atoms.

  17. 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

  18. 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.

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

    OpenAIRE

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

    2016-01-01

    We show that for ultra-cold 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 pair-wise 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...

  20. 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.

  1. 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...

  2. 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.

  3. Permutation invariant polynomial neural network approach to fitting potential energy surfaces. II. Four-atom systems

    International Nuclear Information System (INIS)

    A rigorous, general, and simple method to fit global and permutation invariant potential energy surfaces (PESs) using neural networks (NNs) is discussed. This so-called permutation invariant polynomial neural network (PIP-NN) method imposes permutation symmetry by using in its input a set of symmetry functions based on PIPs. For systems with more than three atoms, it is shown that the number of symmetry functions in the input vector needs to be larger than the number of internal coordinates in order to include both the primary and secondary invariant polynomials. This PIP-NN method is successfully demonstrated in three atom-triatomic reactive systems, resulting in full-dimensional global PESs with average errors on the order of meV. These PESs are used in full-dimensional quantum dynamical calculations

  4. 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...

  5. 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...

  6. 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

  7. 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

  8. 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

  9. 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.

  10. Reconstruction and Application of Protein–Protein Interaction Network

    Directory of Open Access Journals (Sweden)

    Tong Hao

    2016-06-01

    Full Text Available The protein-protein interaction network (PIN is a useful tool for systematic investigation of the complex biological activities in the cell. With the increasing interests on the proteome-wide interaction networks, PINs have been reconstructed for many species, including virus, bacteria, plants, animals, and humans. With the development of biological techniques, the reconstruction methods of PIN are further improved. PIN has gradually penetrated many fields in biological research. In this work we systematically reviewed the development of PIN in the past fifteen years, with respect to its reconstruction and application of function annotation, subsystem investigation, evolution analysis, hub protein analysis, and regulation mechanism analysis. Due to the significant role of PIN in the in-depth exploration of biological process mechanisms, PIN will be preferred by more and more researchers for the systematic study of the protein systems in various kinds of organisms.

  11. Quantum state swapping via a qubit network with Hubbard interactions

    International Nuclear Information System (INIS)

    We study the quantum state transfer (QST) in a class of qubit networks with on-site Coulomb interaction, which are described by the generalized Hubbard model with engineered hopping strengths. It is proved that the N-site system of two electrons with opposite spins can be rigorously reduced into N one dimensional engineered single Bloch electron models with central potential barrier. With this observation, we find that such system can perform a perfect QST, the quantum swapping between two distant electrons with opposite spins. Numerical results show that such QST and the resonant tunneling occur for the optimal on-site repulsive interaction

  12. Graphics processing unit-based alignment of protein interaction networks.

    Science.gov (United States)

    Xie, Jiang; Zhou, Zhonghua; Ma, Jin; Xiang, Chaojuan; Nie, Qing; Zhang, Wu

    2015-08-01

    Network alignment is an important bridge to understanding human protein-protein interactions (PPIs) and functions through model organisms. However, the underlying subgraph isomorphism problem complicates and increases the time required to align protein interaction networks (PINs). Parallel computing technology is an effective solution to the challenge of aligning large-scale networks via sequential computing. In this study, the typical Hungarian-Greedy Algorithm (HGA) is used as an example for PIN alignment. The authors propose a HGA with 2-nearest neighbours (HGA-2N) and implement its graphics processing unit (GPU) acceleration. Numerical experiments demonstrate that HGA-2N can find alignments that are close to those found by HGA while dramatically reducing computing time. The GPU implementation of HGA-2N optimises the parallel pattern, computing mode and storage mode and it improves the computing time ratio between the CPU and GPU compared with HGA when large-scale networks are considered. By using HGA-2N in GPUs, conserved PPIs can be observed, and potential PPIs can be predicted. Among the predictions based on 25 common Gene Ontology terms, 42.8% can be found in the Human Protein Reference Database. Furthermore, a new method of reconstructing phylogenetic trees is introduced, which shows the same relationships among five herpes viruses that are obtained using other methods. PMID:26243827

  13. 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...

  14. Modeling of Interaction of Hydraulic Fractures in Complex Fracture Networks

    Science.gov (United States)

    Kresse, O. 2; Wu, R.; Weng, X.; Gu, H.; Cohen, C.

    2011-12-01

    A recently developed unconventional fracture model (UFM) is able to simulate complex fracture network propagation in a formation with pre-existing natural fractures. Multiple fracture branches can propagate at the same time and intersect/cross each other. Each open fracture exerts additional stresses on the surrounding rock and adjacent fractures, which is often referred to as "stress shadow" effect. The stress shadow can cause significant restriction of fracture width, leading to greater risk of proppant screenout. It can also alter the fracture propagation path and drastically affect fracture network patterns. It is hence critical to properly model the fracture interaction in a complex fracture model. A method for computing the stress shadow in a complex hydraulic fracture network is presented. The method is based on an enhanced 2D Displacement Discontinuity Method (DDM) with correction for finite fracture height. The computed stress field is compared to 3D numerical simulation in a few simple examples and shows the method provides a good approximation for the 3D fracture problem. This stress shadow calculation is incorporated in the UFM. The results for simple cases of two fractures are presented that show the fractures can either attract or expel each other depending on their initial relative positions, and compares favorably with an independent 2D non-planar hydraulic fracture model. Additional examples of both planar and complex fractures propagating from multiple perforation clusters are presented, showing that fracture interaction controls the fracture dimension and propagation pattern. In a formation with no or small stress anisotropy, fracture interaction can lead to dramatic divergence of the fractures as they tend to repel each other. However, when stress anisotropy is large, the fracture propagation direction is dominated by the stress field and fracture turning due to fracture interaction is limited. However, stress shadowing still has a strong effect

  15. 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...

  16. 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.

  17. 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...

  18. 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...

  19. 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

  20. Electron density of KNiF3: analysis of the atomic interactions

    Science.gov (United States)

    Tsirelson; Ivanov; Zhurova; Zhurov; Tanaka

    2000-04-01

    The topological analysis of the electron density in the perovskite KNiF3, potassium nickel trifluoride, based on the accurate X-ray diffraction data, has been performed. The topological picture of the atomic interactions differs from that resulting from the classic crystal chemistry consideration. The shapes of atoms in KNiF3 defined by zero-flux surfaces in the electron density are, in general, far from spherical. At the same time, their asphericity in the close-packed layer is very small. The topological coordination numbers of K and Ni are the same as the geometrical ones, whereas topological coordination for the F atom (6) differs from the geometrical value. The latter results from a specific shape of the Ni-atom basin preventing the bond-path formation between F atoms in the same atomic close-packed layer, in spite of the fact that the closest F-F distance is the same as K-F. Judging by the electron density value and curvature at the bond critical points, the K-F interaction in KNiF3 can be considered ionic, while the Ni-F bond belongs to the polar covalent type. No correlation of the topological ionic radii with crystal or ionic radii was found in KNiF3. Critical points in the electrostatic potential have also been studied. PMID:10794272

  1. 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)

  2. Photon-photon interaction in strong-coupling cavity-atom system

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Jian; Kwiat, Paul G. [Department of Physics, University of Illinois at Urbana-Champaign (United States)

    2014-12-04

    We study photon-photon interactions mediated by a cavity-atom system in the strongcoupling regime of cavity quantum electrodynamics (QED). Different temporal shapes of the incident photons have been explored via numerical calculations. Especially, time-reversed photons can be in the cavity simultaneously and potentially acquire strong interaction with each other, advancing quantum information applications, e.g., quantum non-demolition (QND) measurement.

  3. 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

  4. Strongly Resilient Non-Interactive Key Predistribution For Hierarchical Networks

    CERN Document Server

    Chen, Hao

    2010-01-01

    Key establishment is the basic necessary tool in the network security, by which pairs in the network can establish shared keys for protecting their pairwise communications. There have been some key agreement or predistribution schemes with the property that the key can be established without the interaction (\\cite{Blom84,BSHKY92,S97}). Recently the hierarchical cryptography and the key management for hierarchical networks have been active topics(see \\cite{BBG05,GHKRRW08,GS02,HNZI02,HL02,Matt04}. ). Key agreement schemes for hierarchical networks were presented in \\cite{Matt04,GHKRRW08} which is based on the Blom key predistribution scheme(Blom KPS, [1]) and pairing. In this paper we introduce generalized Blom-Blundo et al key predistribution schemes. These generalized Blom-Blundo et al key predistribution schemes have the same security functionality as the Blom-Blundo et al KPS. However different and random these KPSs can be used for various parts of the networks for enhancing the resilience. We also presentk...

  5. 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.

  6. 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.

  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 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.

  9. A quantum sensor for atom-surface interactions below 10 $\\mu$m

    CERN Document Server

    Sorrentino, F; Ferrari, G; Ivanov, V V; Poli, N; Schioppo, M; Tino, G M

    2008-01-01

    We report about the realization of a quantum device for force sensing at micrometric scale. We trap an ultracold $^{88}$Sr atomic cloud with a 1-D optical lattice, then we place the atomic sample close to a test surface using the same optical lattice as an elevator. We demonstrate precise positioning of the sample at the $\\mu$m scale. By observing the Bloch oscillations of atoms into the 1-D optical standing wave, we are able to measure the total force on the atoms along the lattice axis, with a spatial resolution of few microns. We also demonstrate a technique for transverse displacement of the atoms, allowing to perform measurements near either transparent or reflective test surfaces. In order to reduce the minimum distance from the surface, we compress the longitudinal size of the atomic sample by means of an optical tweezer. Such system is suited for studies of atom-surface interaction at short distance, such as measurement of Casimir force and search for possible non-Newtonian gravity effects.

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

    Science.gov (United States)

    Litinskaya, Marina; Tignone, Edoardo; Pupillo, Guido

    2016-01-01

    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. PMID:27170160

  11. Interaction of epitaxial silicene with overlayers formed by exposure to Al atoms and O2 molecules

    International Nuclear Information System (INIS)

    As silicene is not chemically inert, the study and exploitation of its electronic properties outside of ultrahigh vacuum environments require the use of insulating capping layers. In order to understand if aluminum oxide might be a suitable encapsulation material, we used high-resolution synchrotron photoelectron spectroscopy to study the interactions of Al atoms and O2 molecules, as well as the combination of both, with epitaxial silicene on thin ZrB2(0001) films grown on Si(111). The deposition of Al atoms onto silicene, up to the coverage of about 0.4 Al per Si atoms, has little effect on the chemical state of the Si atoms. The silicene-terminated surface is also hardly affected by exposure to O2 gas, up to a dose of 4500 L. In contrast, when Al-covered silicene is exposed to the same dose, a large fraction of the Si atoms becomes oxidized. This is attributed to dissociative chemisorption of O2 molecules by Al atoms at the surface, producing reactive atomic oxygen species that cause the oxidation. It is concluded that aluminum oxide overlayers prepared in this fashion are not suitable for encapsulation since they do not prevent but actually enhance the degradation of silicene

  12. 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.

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

    Science.gov (United States)

    Litinskaya, Marina; Tignone, Edoardo; Pupillo, Guido

    2016-01-01

    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. PMID:27170160

  14. 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

  15. 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)

  16. 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.

  17. Interaction of Atomic and Molecular Hydrogen with Tholin Surfaces at Low Temperatures

    CERN Document Server

    Li, Ling; Vidali, Gianfranco; Frank, Yechiel; Lohmar, Ingo; Perets, Hagai B; Biham, Ofer; 10.1021/jp104944y

    2010-01-01

    We study the interaction of atomic and molecular hydrogen with a surface of tholin, a man-made polymer considered to be an analogue of aerosol particles present in Titan's atmosphere, using thermal programmed desorption at low temperatures below 30 K. The results are fitted and analyzed using a fine-grained rate equation model that describes the diffusion, reaction and desorption processes. We obtain the energy barriers for diffusion and desorption of atomic and molecular hydrogen. These barriers are found to be in the range of 30 to 60 meV, indicating that atom/molecule-surface interactions in this temperature range are dominated by weak adsorption forces. The implications of these results for the understanding of the atmospheric chemistry of Titan are discussed.

  18. Atomic Oxygen Interactions With Silicone Contamination on Spacecraft in Low Earth Orbit Studied

    Science.gov (United States)

    Banks, Bruce A.

    2001-01-01

    Silicones have been widely used on spacecraft as potting compounds, adhesives, seals, gaskets, hydrophobic surfaces, and atomic oxygen protective coatings. Contamination of optical and thermal control surfaces on spacecraft in low Earth orbit (LEO) has been an ever-present problem as a result of the interaction of atomic oxygen with volatile species from silicones and hydrocarbons onboard spacecraft. These interactions can deposit a contaminant that is a risk to spacecraft performance because it can form an optically absorbing film on the surfaces of Sun sensors, star trackers, or optical components or can increase the solar absorptance of thermal control surfaces. The transmittance, absorptance, and reflectance of such contaminant films seem to vary widely from very transparent SiOx films to much more absorbing SiOx-based films that contain hydrocarbons. At the NASA Glenn Research Center, silicone contamination that was oxidized by atomic oxygen has been examined from LEO spacecraft (including the Long Duration Exposure Facility and the Mir space station solar arrays) and from ground laboratory LEO simulations. The findings resulted in the development of predictive models that may help explain the underlying issues and effects. Atomic oxygen interactions with silicone volatiles and mixtures of silicone and hydrocarbon volatiles produce glassy SiOx-based contaminant coatings. The addition of hydrocarbon volatiles in the presence of silicone volatiles appears to cause much more absorbing (and consequently less transmitting) contaminant films than when no hydrocarbon volatiles are present. On the basis of the LDEF and Mir results, conditions of high atomic oxygen flux relative to low contaminant flux appear to result in more transparent contaminant films than do conditions of low atomic oxygen flux with high contaminant flux. Modeling predictions indicate that the deposition of contaminant films early in a LEO flight should depend much more on atomic oxygen flux than

  19. Long-range dispersion interactions. III: Method for two homonuclear atoms

    International Nuclear Information System (INIS)

    A procedure for systematically evaluating the long-range dispersion interaction between two homonuclear atoms in arbitrary LS coupled states is outlined. The method is then used to generate dispersion coefficients for a number of the low-lying states of the Na and Mg dimers

  20. Tunable self-assembled spin chains of strongly interacting cold atoms

    DEFF Research Database (Denmark)

    Loft, N. J. S.; Marchukov, O. V.; Petrosyan, D.; Zinner, N. T.

    2016-01-01

    We have developed an efficient computational method to treat long, one-dimensional systems of strongly-interacting atoms forming self-assembled spin chains. Such systems can be used to realize many spin chain model Hamiltonians tunable by the external confining potential. As a concrete...

  1. 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.

  2. Interaction potential and repulsive force between atoms whose internuclear separations are small

    International Nuclear Information System (INIS)

    The Thomas-Fermi equation is solved for the homonuclear diatomic molecule. The electronic density and electrostatic potential at each point are used to calculate energies and interaction potentials for very small internuclear separation distances. The repulsive force between atoms is derived by means of the virial theorem. (author)

  3. XSAMS: XML schema for atomic and molecular data and particle solid interactions. Summary report of an IAEA consultants' meeting

    International Nuclear Information System (INIS)

    Developments in computer technology offer exciting new opportunities for the reliable and convenient exchange of data. Therefore, in 2003 the Atomic and Molecular Data Unit initiated within the collaborative efforts of the A+M Data Centres Network a new standard for exchange of atomic, molecular and particle-solid interaction (AM/PSI) data based on the Extended Markup Language (XML). The standard is named XSAMS, which stands for XML Schema for Atoms, Molecules, and Solids. A working group composed of staff from the IAEA, NIST, ORNL, Observatoire Paris-Meudon and other institutions meets approximately biannually to discuss progress made on XSAMS, and to foresee new developments and actions to be taken to promote this standard for AM/PSI data exchange. Such a meeting was held 10-11 September 2009 at IAEA Headquarters, Vienna, and the discussions and results of the meeting are presented here. The principal concern of the meeting was the preparation of the first public release, version 0.1, of XSAMS. (author)

  4. 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.

  5. Interaction Network Estimation: Predicting Problem-Solving Diversity in Interactive Environments

    Science.gov (United States)

    Eagle, Michael; Hicks, Drew; Barnes, Tiffany

    2015-01-01

    Intelligent tutoring systems and computer aided learning environments aimed at developing problem solving produce large amounts of transactional data which make it a challenge for both researchers and educators to understand how students work within the environment. Researchers have modeled student-tutor interactions using complex networks in…

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

    Science.gov (United States)

    Safdari, Hadiseh; Zare Kamali, Milad; Shirazi, Amirhossein; Khalighi, Moein; Jafari, Gholamreza; Ausloos, Marcel

    2016-01-01

    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. PMID:27171424

  7. 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.

  8. Hierarchical interactions - network formation of organic molecules on graphene/Ru(0001)

    International Nuclear Information System (INIS)

    Bis(terpyridine)derivatives (BTP) form highly ordered hydrogen-bonded 2D networks on solid surfaces. The hydrogen bond configurations and therefore the resulting structures are steered via the positions of the nitrogen atoms within the BTP molecules. On smooth surfaces such as graphite or metal single crystals, the molecule-substrate interactions play a secondary role for the structure formation, mainly by determining the rotational orientations of the ordered networks. In this contribution, we demonstrate that more pronounced template effects arise for substrates where the molecule-substrate interaction varies laterally at the nanometer scale. As an example, we show the ordering behavior of BTP molecules on graphene monolayers grown on Ru(0001). Submolecularly resolved STM images show that the BTP molecules are confined to the valleys of the graphene. We compare the resulting supramolecular assemblies with the ordered 2D networks formed by the same molecules on smooth substrates, and discuss the effect of the template quantitatively by means of force field calculations and supporting thermal desorption experiments.

  9. miRTargetLink—miRNAs, Genes and Interaction Networks

    Science.gov (United States)

    Hamberg, Maarten; Backes, Christina; Fehlmann, Tobias; Hart, Martin; Meder, Benjamin; Meese, Eckart; Keller, Andreas

    2016-01-01

    Information on miRNA targeting genes is growing rapidly. For high-throughput experiments, but also for targeted analyses of few genes or miRNAs, easy analysis with concise representation of results facilitates the work of life scientists. We developed miRTargetLink, a tool for automating respective analysis procedures that are frequently applied. Input of the web-based solution is either a single gene or single miRNA, but also sets of genes or miRNAs, can be entered. Validated and predicted targets are extracted from databases and an interaction network is presented. Users can select whether predicted targets, experimentally validated targets with strong or weak evidence, or combinations of those are considered. Central genes or miRNAs are highlighted and users can navigate through the network interactively. To discover the most relevant biochemical processes influenced by the target network, gene set analysis and miRNA set analysis are integrated. As a showcase for miRTargetLink, we analyze targets of five cardiac miRNAs. miRTargetLink is freely available without restrictions at www.ccb.uni-saarland.de/mirtargetlink. PMID:27089332

  10. 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/

  11. 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

  12. Size and shape of grain boundary network components and their atomic structures in polycrystalline nanoscale materials

    International Nuclear Information System (INIS)

    Microstructure in polycrystalline materials is composed of grain boundary plane, triple junction line, and vertex point. They are the integral parts of the grain boundary network structure and the foundation for the structure-property relations. In polycrystalline, especially nanocrystalline, materials, it becomes increasingly difficult to probe the atomistic structure of the microstructure components directly in experiment due to the size limitation. Here, we present a numerical approach using pair correlation function from atomistic simulation to obtain the detailed information for atomic order and disorder in the grain boundary network in nanocrystalline materials. We show that the atomic structures in the different microstructural components are related closely to their geometric size and shape, leading to unique signatures for atomic structure in microstructural characterization at nanoscales. The dependence varies systematically with the characteristic dimension of the microstructural component: liquid-like disorder is found in vertex points, but a certain order persists in triple junctions and grain boundaries along the extended dimensions of these microstructure components

  13. 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.

  14. 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.

  15. 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.

  16. Anisotropic atom-surface interactions in the Casimir-Polder regime

    Science.gov (United States)

    Taillandier-Loize, T.; Baudon, J.; Dutier, G.; Perales, F.; Boustimi, M.; Ducloy, M.

    2014-05-01

    The distance dependence of the anisotropic atom-wall interaction is studied. The central result is the 1/z6 quadrupolar anisotropy decay in the retarded Casimir-Polder regime. Analysis of the transition region between nonretarded van der Waals regime (in 1/z3) and Casimir-Polder regime shows that the anisotropy crossover occurs at very short distances from the surface, on the order of 0.03λ, where λ is the atom characteristic wavelength. Possible experimental verifications of this distance dependence using surface-induced inelastic transitions are discussed.

  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. 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...

  19. 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...

  20. 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.

  1. 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.

  2. 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.

  3. Cognitive Vulnerability to Major Depression: View from the Intrinsic Network and Cross-network Interactions

    Science.gov (United States)

    Wang, Xiang; Öngür, Dost; Auerbach, Randy P.; Yao, Shuqiao

    2016-01-01

    Abstract Although it is generally accepted that cognitive factors contribute to the pathogenesis of major depressive disorder (MDD), there are missing links between behavioral and biological models of depression. Nevertheless, research employing neuroimaging technologies has elucidated some of the neurobiological mechanisms related to cognitive-vulnerability factors, especially from a whole-brain, dynamic perspective. In this review, we integrate well-established cognitive-vulnerability factors for MDD and corresponding neural mechanisms in intrinsic networks using a dual-process framework. We propose that the dynamic alteration and imbalance among the intrinsic networks, both in the resting-state and the rest-task transition stages, contribute to the development of cognitive vulnerability and MDD. Specifically, we propose that abnormally increased resting-state default mode network (DMN) activity and connectivity (mainly in anterior DMN regions) contribute to the development of cognitive vulnerability. Furthermore, when subjects confront negative stimuli in the period of rest-to-task transition, the following three kinds of aberrant network interactions have been identified as facilitators of vulnerability and dysphoric mood, each through a different cognitive mechanism: DMN dominance over the central executive network (CEN), an impaired salience network–mediated switching between the DMN and CEN, and ineffective CEN modulation of the DMN. This focus on interrelated networks and brain-activity changes between rest and task states provides a neural-system perspective for future research on cognitive vulnerability and resilience, and may potentially guide the development of new intervention strategies for MDD. PMID:27148911

  4. 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.

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

    Directory of Open Access Journals (Sweden)

    2005-12-01

    Full Text Available 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 are known, though comparatively few linear motifs have been discovered. Their short length (three to eight residues, and the fact that they often reside in disordered regions in proteins makes them difficult to detect through sequence comparison or experiment. Nevertheless, each new motif provides critical 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 on motif over-representation in non-homologous sequences, rediscovers known motifs and predicts dozens of others. Direct binding experiments reveal that two predicted motifs are indeed protein-binding modules: a DxxDxxxD protein phosphatase 1 binding motif with a KD of 22 microM and a VxxxRxYS motif 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.

  6. 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

  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. 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...

  9. Interacting loop-current model of superconducting networks

    International Nuclear Information System (INIS)

    The authors review their recent approximation scheme to calculate the normal-superconducting phase boundary, Tc(H), of a superconducting wire network in a magnetic field in terms of interacting loop currents. The theory is based on the London approximation of the linearized Ginzburg-Landau equation. An approximate general formula is derived for any two-dimensional space-filling lattice comprising tiles of two shapes. Many examples are provided illustrating the use of this method, with a particular emphasis on the fluxoid distribution. In addition to periodic lattices, quasiperiodic lattices and fractal Sierpinski gaskets are also discussed

  10. 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.

  11. Non-linear interactions of multi-level atoms with a near-resonant standing wave

    International Nuclear Information System (INIS)

    Using a semiclassical density matrix formalism we have calculated the behavior of multi-level atoms interacting with a standing wave field, and show how complex non-linear phenomena, including multi-photon effects, combine to produce saturation spectra as observed in experiments. We consider both 20-level sodium and 24-level rubidium models, contrasting these with a simple 2-level case. The influence of parameters such as atomic trajectory and the time the atom remains in the beam are shown to have a critical effect on the lineshape of these resonances and the emission/absorption processes. Stable oscillations in the excited state populations for both the two-level and multi-level cases are shown to be limit cycles. These limit cycles undergo period doubling as the system evolves into chaos. Finally, using a Monte Carlo treatment, these processes average to produce saturated absorption spectra complete with power and Doppler broadening effects consistent with experiment. (authors)

  12. Three-body interactions in the condensed phases of helium atom systems

    International Nuclear Information System (INIS)

    In this work we investigate how the description of several properties of helium atoms in the condensed phases are affected by the three-body terms of a very accurate inter-atomic potential. We introduce two phenomenological parameters in the three-body part of the inter-atomic potential in order to describe properly the equations of state of the solid and liquid phases. The calculations were performed using the multi-weight extension to the diffusion Monte Carlo method which allows accurate calculations of small energy differences in a significant way. The results show how the equations of state for both the liquid and solid phases and properties like the isothermal compressibility, the equilibrium, melting and freezing densities are affected by three-body interactions

  13. 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.

  14. 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

  15. Node-weighted interacting network measures improve the representation of real-world complex systems

    CERN Document Server

    Wiedermann, Marc; Heitzig, Jobst; Kurths, Jürgen

    2013-01-01

    Network theory provides a rich toolbox consisting of methods, measures, and models for studying the structure and dynamics of complex systems found in nature, society, or technology. Recently, it has been pointed out that many real-world complex systems are more adequately mapped by networks of interacting or interdependent networks, e.g., a power grid showing interdependency with a communication network. Additionally, in many real-world situations it is reasonable to include node weights into complex network statistics to reflect the varying size or importance of subsystems that are represented by nodes in the network of interest. E.g., nodes can represent vastly different surface area in climate networks, volume in brain networks or economic capacity in trade networks. In this letter, combining both ideas, we derive a novel class of statistical measures for analysing the structure of networks of interacting networks with heterogeneous node weights. Using a prototypical spatial network model, we show that th...

  16. C3 coefficients for the alkali atoms interacting with a graphene layer and carbon nanotube

    International Nuclear Information System (INIS)

    We evaluate separation dependent van der Waals dispersion (C3) coefficients for the interactions of the Li, Na, K and Rb atoms with a graphene layer and with a single walled carbon nanotube (CNT) using the hydrodynamic and Dirac models. The results from both the models are evaluated using accurate values of the dynamic polarizabilities of the above alkali atoms. Accountability of accurate dynamic polarizabilities of the alkali atoms to determine the C3 coefficients are accentuated by comparing the obtained coefficients using the precise values of the dynamic dipole polarizabilities against the values estimated from the single oscillator approximation that are generally used in the earlier calculations. For a practical description of the atom–surface interaction potentials, the C3 coefficients are given for a wide range of separation distances between the considered ground states of the atoms and the wall surfaces and also for different nanotube radii. The coefficients for the graphene layer are fitted to a logistic function of the separation distance. For CNT, we find a paraboloid kind of fit dependence both on the separation distances and radii of the CNT. (paper)

  17. 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

  18. 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.

  19. Powerful effective one-electron Hamiltonian for describing many-atom interacting systems

    International Nuclear Information System (INIS)

    In this paper, we present an alternative way to build the effective one-electron picture of a many-atom interacting system. By simplifying the many-body general problem we present two different options for the bond-pair model Hamiltonian. We have found that the successive approximations in order to achieve the effective description have a dramatic influence on the result. Thus, only the model that introduces the correct renormalization in the diagonal term due to the overlap is able to reproduce, even in a quantitative fashion, the main properties of simple homonuclear diatomic molecules. The success of the model resides in the accurate definitions (free of parametrization) of the Hamiltonian terms, which, therefore, could be used to describe more complex interacting systems such as polyatomic molecules, adsorbed species, or atoms scattered by a surface

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

    Energy Technology Data Exchange (ETDEWEB)

    Shantappa, Anil, E-mail: anilmalipatil@yahoo.co.in [Department of Physics, Veerappa Nisty Engineering College, Shorapur-585220, KARNATAKA (India); Hanagodimath, S. M., E-mail: smhmath@rediffmail.com [Department of Physics Gulbarga University, Gulbarga-585106, KARNATAKA (India)

    2015-08-28

    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., SiO{sub 2}-Na{sub 2}O, SiO{sub 2}-Na{sub 2}O-CaO and SiO{sub 2}-Na{sub 2}O-P{sub 2}O{sub 5} 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 (Z{sub PI,} {sub 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.

  1. 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.

  2. 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

  3. 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.

  4. 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...

  5. 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.

  6. 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.

  7. 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...

  8. Self-interaction in Green's-function theory of the hydrogen atom

    OpenAIRE

    Nelson, W.; Bokes, P.; Rinke, P.; Godby, R.

    2007-01-01

    Atomic hydrogen provides a unique test case for computational electronic structure methods, since its electronic excitation energies are known analytically. With only one electron, hydrogen contains no electronic correlation and is therefore particularly susceptible to spurious self-interaction errors introduced by certain computational methods. In this paper we focus on many-body perturbation theory (MBPT) in Hedin’s GW approximation. While the Hartree-Fock and the exact MBPT self-energy are...

  9. 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...

  10. Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions

    OpenAIRE

    Hur, Junguk; Özgür, Arzucan; Xiang, Zuoshuang; He, Yongqun

    2015-01-01

    Background Literature mining of gene-gene interactions has been enhanced by ontology-based name classifications. However, in biomedical literature mining, interaction keywords have not been carefully studied and used beyond a collection of keywords. Methods In this study, we report the development of a new Interaction Network Ontology (INO) that classifies >800 interaction keywords and incorporates interaction terms from the PSI Molecular Interactions (PSI-MI) and Gene Ontology (GO). Using IN...

  11. Atomes et lumière, interactions matière-rayonnement

    OpenAIRE

    Fabre, Claude

    2006-01-01

    I - Les outils de l'optique quantique 1 - Les approches phénoménologiques 2 - L'approche semi-classique 3 - Description quantique du champ électromagnétique libre 4 - Interaction entre atome et champ quantique II - Quelques phénomènes de l'optique quantique 5 - Emission spontanée 6 - Interactions quasi-résonnantes dans les systèmes à deux niveaux 7 - Systèmes à deux niveaux

  12. 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...

  13. Screened Coulomb interactions in metallic alloys. I. Universal screening in the atomic-sphere approximation

    DEFF Research Database (Denmark)

    Ruban, Andrei; Skriver, Hans Lomholt

    2002-01-01

    of the alloy composition, lattice spacing, and crystal structure. A formalism which allows a consistent treatment of the screened Coulomb interactions within the single-site mean-field approximation is outlined. We also derive the contribution of the screened Coulomb interactions to the S-(2) formalism...... the Madelung potential energy of a random alloy in the single-site, mean-field approximation. The Madelung potential makes density-functional calculations by the conventional single-site, coherent potential approximation practically identical to the more rigorous LSGF supercell results obtained with a single......-site local interaction zone. We demonstrate that the basic mechanism that governs the charge distribution is the screening of the net charges of the alloy components that makes the direct Coulomb interactions short ranged. In the atomic-sphere approximation, this screening appears to be almost independent...

  14. 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…

  15. 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

  16. Tight coevolution of proliferating cell nuclear antigen (PCNA)-partner interaction networks in fungi leads to interspecies network incompatibility.

    OpenAIRE

    Zamir, L.; Zaretsky, M.; Fridman, Y; Ner-Gaon, H.; Rubin, E; Aharoni, A.

    2012-01-01

    The structure and connectivity of protein-protein interaction (PPI) networks are maintained throughout evolution by coordinated changes (coevolution) of network proteins. Despite extensive research, relatively little is known regarding the molecular basis and functional implications of the coevolution of PPI networks. Here, we used proliferating cell nuclear antigen, a hub protein that mediates DNA replication and repair in eukaryotes, as a model system to study the coevolution of PPI network...

  17. 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.

  18. 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

  19. 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

  20. 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.

  1. Modeling attacker-defender interactions in information networks.

    Energy Technology Data Exchange (ETDEWEB)

    Collins, Michael Joseph

    2010-09-01

    The simplest conceptual model of cybersecurity implicitly views attackers and defenders as acting in isolation from one another: an attacker seeks to penetrate or disrupt a system that has been protected to a given level, while a defender attempts to thwart particular attacks. Such a model also views all non-malicious parties as having the same goal of preventing all attacks. But in fact, attackers and defenders are interacting parts of the same system, and different defenders have their own individual interests: defenders may be willing to accept some risk of successful attack if the cost of defense is too high. We have used game theory to develop models of how non-cooperative but non-malicious players in a network interact when there is a substantial cost associated with effective defensive measures. Although game theory has been applied in this area before, we have introduced some novel aspects of player behavior in our work, including: (1) A model of how players attempt to avoid the costs of defense and force others to assume these costs; (2) A model of how players interact when the cost of defending one node can be shared by other nodes; and (3) A model of the incentives for a defender to choose less expensive, but less effective, defensive actions.

  2. 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

  3. Casimir-Polder interaction between an atom and a cavity wall under the influence of real conditions

    International Nuclear Information System (INIS)

    The Casimir-Polder interaction between an atom and a metal wall is investigated under the influence of real conditions including the dynamic polarizability of the atom, finite conductivity of the wall metal, and nonzero temperature of the system. Both analytical and numerical results for the free energy and force are obtained over a wide range of atom-wall distances. Numerical computations are performed for an Au wall and metastable He*, Na, and Cs atoms. For the He* atom we demonstrate, as an illustration, that at short separations of about the Au plasma wavelength at room temperature the free energy deviates up to 35% and the force up to 57% from the classical Casimir-Polder result. Accordingly, such large deviations should be taken into account in precision experiments on atom-wall interactions. The combined account of different corrections to the Casimir-Polder interaction leads to the conclusion that at short separations the corrections due to the dynamic polarizability of an atom play a more important role than--and suppress--the corrections due to the nonideality of the metal wall. By comparison of the exact atomic polarizabilities with those in the framework of the single oscillator model, it is shown that the obtained asymptotic expressions enable calculation of the free energy and force for the atom-wall interaction under real conditions with a precision of 1%

  4. Investigating the topology of interacting networks - Theory and application to coupled climate subnetworks

    CERN Document Server

    Donges, Jonathan F; Marwan, Norbert; Zou, Yong; Kurths, Juergen

    2011-01-01

    Network theory provides various tools for investigating the structural or functional topology of many complex systems found in nature, technology and society. Nevertheless, it has recently been realised that a considerable number of systems of interest should be treated, more appropriately, as interacting networks or networks of networks. Here we introduce a novel graph-theoretical framework for studying the interaction structure between subnetworks embedded within a complex network of networks. This framework allows us to quantify the structural role of single vertices or whole subnetworks with respect to the interaction of a pair of subnetworks on local, mesoscopic and global topological scales. Climate networks have recently been shown to be a powerful tool for the analysis of climatological data. Applying the general framework for studying interacting networks, we introduce coupled climate subnetworks to represent and investigate the topology of statistical relationships between the fields of distinct cli...

  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. 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

  7. 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...

  8. Types of inter-atomic interactions at the MHC-peptide interface: Identifying commonality from accumulated data

    Directory of Open Access Journals (Sweden)

    Kangueane Pandjassarame

    2002-05-01

    Full Text Available Abstract Background Quantitative information on the types of inter-atomic interactions at the MHC-peptide interface will provide insights to backbone/sidechain atom preference during binding. Qualitative descriptions of such interactions in each complex have been documented by protein crystallographers. However, no comprehensive report is available to account for the common types of inter-atomic interactions in a set of MHC-peptide complexes characterized by variation in MHC allele and peptide sequence. The available x-ray crystallography data for these complexes in the Protein Databank (PDB provides an opportunity to identify the prevalent types of such interactions at the binding interface. Results We calculated the percentage distributions of four types of interactions at varying inter-atomic distances. The mean percentage distribution for these interactions and their standard deviation about the mean distribution is presented. The prevalence of SS and SB interactions at the MHC-peptide interface is shown in this study. SB is clearly dominant at an inter-atomic distance of 3Å. Conclusion The prevalently dominant SB interactions at the interface suggest the importance of peptide backbone conformation during MHC-peptide binding. Currently, available algorithms are developed for protein sidechain prediction upon fixed backbone template. This study shows the preference of backbone atoms in MHC-peptide binding and hence emphasizes the need for accurate peptide backbone prediction in quantitative MHC-peptide binding calculations.

  9. 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.

  10. 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...

  11. The exotic world of low-energy positron-atom interactions

    International Nuclear Information System (INIS)

    Full text: The interactions of low-energy positrons with atoms provides a host of problems for both experimentalists and theorists alike. For example, even one of the most fundamental questions in positron physics, whether a positron can form an electronically stable bound state with a neutral atom, was only in 1997 theoretically resolved as a 'yes'. I will discuss the application of the configuration-interaction (Cl) method to the study of various positronic atoms and ions, demonstrating the stability and structure of the bound states of PsH, e+Li, e+Be, e+Mg, e+Ca, e+Cu, CuPs, e+Zn, e+Sr and e+Cd. The Cl method has also been used in conjunction with the Kohn variational method to examine low-energy positron scattering and annihilation from H, He+ and Cu. The presence of localised electron-positron pairing means that these Cl calculations are extremely demanding. I will also mention the prospects for using positron scattering from metal vapours as a signature to detect their bound states. Copyright (2005) Australian Institute of Physics

  12. 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...

  13. Dynamic imaging of single DNA-protein interactions using atomic force microscopy

    International Nuclear Information System (INIS)

    Atomic force microscopy (AFM) imaging of static DNA-protein complexes, in air and in liquid, can be used to directly obtain quantitative and qualitative information on the structure of different complexes. For example, DNA length, the location of preferential binding sites for proteins and bending of DNA as a result of the complexation can all be measured. Recording consecutive AFM images of DNA and protein molecules under conditions that they are still able to move and interact, or dynamic AFM imaging, however, can reveal information on the dynamic aspects of the interactions between these molecules. Here, an overview is given of the technical challenges that need to be considered for successful dynamic AFM imaging studies of individual DNA-protein interactions. Necessary technical improvements to the AFM set-up and the development of new sample preparation methods are described in this paper

  14. Convergence of CI single center calculations of positron-atom interactions

    CERN Document Server

    Mitroy, J

    2006-01-01

    The Configuration Interaction (CI) method using orbitals centered on the nucleus has recently been applied to calculate the interactions of positrons interacting with atoms. Computational investigations of the convergence properties of binding energy, phase shift and annihilation rate with respect to the maximum angular momentum of the orbital basis for the e^+Cu and PsH bound states, and the e^+-H scattering system were completed. The annihilation rates converge very slowly with angular momentum, and moreover the convergence with radial basis dimension appears to be slower for high angular momentum. A number of methods of completing the partial wave sum are compared, an approach based on a Delta X_J = a/(J + 1/2)^n + b/(J + 1/2)^(n+1) form (with n = 4 for phase shift (or energy) and n = 2 for the annihilation rate) seems to be preferred on considerations of utility and underlying physical justification.

  15. 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

  16. Systematics of ground state multiplets of atomic nuclei in the delta-interaction approach

    International Nuclear Information System (INIS)

    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

  17. Systematics of ground state multiplets of atomic nuclei in the delta-interaction approach

    Science.gov (United States)

    Imasheva, L. T.; Ishkhanov, B. S.; Stepanov, M. E.; Tretyakova, T. Yu.

    2015-12-01

    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.

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

    DEFF Research Database (Denmark)

    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 functions. Games are designed to take advantage of the characteristics of the human players......, and by doing so they create in humans what in modern play theory is known as a “state of play”...

  20. Determine point-to-point networking interactions using regular expressions

    Directory of Open Access Journals (Sweden)

    Konstantin S. Deev

    2015-06-01

    Full Text Available As Internet growth and becoming more popular, the number of concurrent data flows start to increasing, which makes sense in bandwidth requested. Providers and corporate customers need ability to identify point-to-point interactions. The best is to use special software and hardware implementations that distribute the load in the internals of the complex, using the principles and approaches, in particular, described in this paper. This paper represent the principles of building system, which searches for a regular expression match using computing on graphics adapter in server station. A significant computing power and capability to parallel execution on modern graphic processor allows inspection of large amounts of data through sets of rules. Using the specified characteristics can lead to increased computing power in 30…40 times compared to the same setups on the central processing unit. The potential increase in bandwidth capacity could be used in systems that provide packet analysis, firewalls and network anomaly detectors.

  1. 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 are...... 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...... known, though comparatively few linear motifs have been discovered. Their short length (three to eight residues), and the fact that they often reside in disordered regions in proteins makes them difficult to detect through sequence comparison or experiment. Nevertheless, each new motif provides critical...

  2. 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%.

  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%. PMID:26941831

  4. 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...

  5. Dynamical behaviours of the nonlinear atom-field interaction in the presence of classical gravity: f-deformation approach

    International Nuclear Information System (INIS)

    In this paper, we investigate the effects of a classical gravitational field on the dynamical behaviour of the nonlinear atom-field interaction within the framework of the f-deformed Jaynes-Cummings model. For this purpose, we first introduce a set of new atomic operators obeying an f-deformed su(2) algebraic structure to derive an effective Hamiltonian for the system under consideration. Then by solving the Schroedinger equation in the interaction picture and considering certain initial quantum states for the atomic and radiation subsystems, we analyse the influence of gravity on the temporal evolution of the atomic population inversion, atomic dipole squeezing, atomic momentum diffusion, photon counting statistics and deformed quadrature squeezing of the radiation field.

  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. 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...

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. States interpolating between number and coherent states and their interaction with atomic systems

    International Nuclear Information System (INIS)

    Using the eigenvalue definition of binomial states we construct new intermediate number-coherent states which reduce to number and coherent states in two different limits. We reveal the connection of these intermediate states with photon-added coherent states and investigate their non-classical properties and quasiprobability distributions in detail. It is of interest to note that these new states, which interpolate between coherent states and number states, neither of which exhibit squeezing, are nevertheless squeezed states. A scheme to produce these states is proposed. We also study the interaction of these states with atomic systems in the framework of the two-photon Jaynes-Cummings model, and describe the response of the atomic system as it varies between the pure Rabi oscillation and the collapse-revival mode and investigate field observables such as photon number distribution, entropy and the Q-function. (author)

  13. 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.

  14. 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…

  15. 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…

  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. Summary of the first meeting of ASEAN Network of Regulatory Bodies on Atomic Energy (ASEANTOM)

    International Nuclear Information System (INIS)

    The 1st Meeting of ASEAN Network of Regulatory Bodies on Atomic Energy (ASEANTOM) was organized in Phuket, Thailand on 3 - 4 September, 2013. The meeting was held on annually basis following the Meeting to Finalize the Term of Reference (TOR) in Bangkok, Thailand on 29 August, 2012. The objective of the meeting is to review and finalize TOR, and to set up the action plan of ASEANTOM. The action plan is an expected outcome of the meeting. The Meeting consisted of 41 participants from IAEA and ASEAN Member States (AMS), namely, Cambodia, Laos, Singapore, Indonesia, Malaysia, Myanmar, Philippines, Vietnam and Thailand. Only Brunei Darussalam could not attend the Meeting. Participant's organizations were regulatory body or relevant authorities, and Ministry of Foreign Affairs.

  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. 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.

  20. 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...