WorldWideScience

Sample records for atomic interaction networks

  1. Atomic & Molecular Interactions

    Energy Technology Data Exchange (ETDEWEB)

    None

    2002-07-12

    The Gordon Research Conference (GRC) on Atomic & 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 Emphasis was placed on current unpublished research and discussion of the future target areas in this field.

  2. 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.

  3. Self-organized atomic switch networks

    Science.gov (United States)

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

    2014-01-01

    The spontaneous emergence of complex behavior in dynamical systems occurs through the collective interaction of nonlinear elements toward a highly correlated, non-equilibrium critical state. Criticality has been proposed as a model for understanding complexity in systems whose behavior can be approximated as a state lying somewhere between order and chaos. Here we present unique, purpose-built devices, known as atomic switch networks (ASN), specifically designed to generate the class of emergent properties which underlie critical dynamics in complex systems. The network is an open, dissipative system comprised of highly interconnected (˜109/cm2) atomic switch interfaces wired through the spontaneous electroless deposition of metallic silver fractal architectures. The functional topology of ASN architectures self-organizes to produce persistent critical dynamics without fine-tuning, indicating a capacity for memory and learning via persistent critical states toward potential utility in real-time, neuromorphic computation.

  4. 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

    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 simulation...

  5. 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.

  6. Entanglement Swapping: Entangling Atoms That Never Interacted

    CERN Document Server

    Guerra, E S

    2005-01-01

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

  7. Resonant interaction modified by the atomic environment

    Energy Technology Data Exchange (ETDEWEB)

    Sainz, I; Klimov, A B; Chumakov, S M [Departamento de Fisica, Universidad de Guadalajara, Revolucion 1500, 44410, Guadalajara, Jal. (Mexico)

    2003-04-01

    The dynamics of a resonant atom interacting with a quantum cavity field in the presence of many off-resonant atoms is studied. In the framework of the effective Hamiltonian approach we show that the results of elimination of non-resonant transitions are (a) a dynamical Stark shift of the field frequency, dependent on the populations of non-resonant atoms, (b) dependence of the coupling constant between the resonant atom and the field on the populations of non-resonant atoms, and (c) an effective dipole-dipole interaction between non-resonant atoms. Two effects (the coherent influence and dephasing) of the off-resonant environment on the dynamics of the resonant atom are discussed.

  8. 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...

  9. Nagaoka's atomic model and hyperfine interactions.

    Science.gov (United States)

    Inamura, Takashi T

    2016-01-01

    The prevailing view of Nagaoka's "Saturnian" atom is so misleading that today many people have an erroneous picture of Nagaoka's vision. They believe it to be a system involving a 'giant core' with electrons circulating just outside. Actually, though, in view of the Coulomb potential related to the atomic nucleus, Nagaoka's model is exactly the same as Rutherford's. This is true of the Bohr atom, too. To give proper credit, Nagaoka should be remembered together with Rutherford and Bohr in the history of the atomic model. It is also pointed out that Nagaoka was a pioneer of understanding hyperfine interactions in order to study nuclear structure.

  10. Atoms of multistationarity in chemical reaction networks

    CERN Document Server

    Joshi, Badal

    2011-01-01

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

  11. Social Interaction in Learning Networks

    NARCIS (Netherlands)

    Sloep, Peter

    2009-01-01

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

  12. Strong interaction physics from hadronic atoms

    Science.gov (United States)

    Batty, C. J.; Friedman, E.; Gal, A.

    1997-08-01

    Hadronic atoms provide a unique laboratory for studying strong interactions and nuclear medium effects at zero kinetic energy. Previous results from analyses of strong-interaction data consisting of level shifts, widths and yields in π-, K -, p¯ and ∑ - atoms are reviewed. Recent results from fits to comprehensive sets of data in terms of density-dependent optical potentials that respect the low-density limit, where the interaction tends to the free hadron nucleon value, are discussed. The importance of using realistic nuclear density distributions is highlighted. The introduction of density dependence in most cases significantly improves the fit to the data and leads to some novel results. For K - atoms, a substantial attraction of order 200 MeV in nuclear matter is suggested, with interesting repercussions for K¯ condensation and the evolution of strangeness in high-density stars. For p¯ atoms it is found that a reasonable p-wave strength can be accommodated in the fitted optical potential, in agreement with the energy dependence observed for some low-energy p¯N reactions. For ∑ - atoms, the fitted potential becomes repulsive inside the nucleus, implying that Σ hyperons generally do not bind in nuclei in agreement with recent measurements. This repulsion significantly affects calculated masses of neutron stars.

  13. Atom-Light Interactions in Photonic Crystals

    CERN Document Server

    Goban, A; Yu, S -P; Hood, J D; Muniz, J A; Lee, J H; Martin, M J; McClung, A C; Choi, K S; Chang, D E; Painter, O; Kimble, H J

    2013-01-01

    The integration of nanophotonics and atomic physics has been a long-sought goal that would open new frontiers for optical physics. Here, we report the development of the first integrated optical circuit with a photonic crystal capable of both localizing and interfacing atoms with guided photons in the device. By aligning the optical bands of a photonic crystal waveguide (PCW) with selected atomic transitions, our platform provides new opportunities for novel quantum transport and many-body phenomena by way of photon-mediated atomic interactions along the PCW. From reflection spectra measured with average atom number N = 1.1$\\pm$0.4, we infer that atoms are localized within the PCW by Casimir-Polder and optical dipole forces. The fraction of single-atom radiative decay into the PCW is $\\Gamma_{\\rm 1D}/\\Gamma'$ = 0.32$\\pm$0.08, where $\\Gamma_{1D}$ is the rate of emission into the guided mode and $\\Gamma'$ is the decay rate into all other channels. $\\Gamma_{\\rm 1D}/\\Gamma'$ is quoted without enhancement due to a...

  14. Long-range interactions between Rydberg atoms

    Science.gov (United States)

    Deiglmayr, Johannes

    2016-10-01

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

  15. Anisotropic Interactions between Cold Rydberg Atoms

    Science.gov (United States)

    2015-09-28

    AFRL-AFOSR-CL-TR-2015-0002 Anisotropic interactions between cold Rydberg atoms Luis Marcassa INSTITUTO DE FISICA DE SAO CARLOS Final Report 09/28...problem with the report +551633739806 Organization / Institution name Instituto de Fisica de Sao Carlos Grant/Contract Title The full title of the

  16. Atomic hydrogen interaction with Ru(1010).

    Science.gov (United States)

    Vesselli, E; Comelli, G; Rosei, R

    2004-05-01

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

  17. Network Physiology: Mapping Interactions Between Networks of Physiologic Networks

    Science.gov (United States)

    Ivanov, Plamen Ch.; Bartsch, Ronny P.

    The human organism is an integrated network of interconnected and interacting organ systems, each representing a separate regulatory network. The behavior of one physiological system (network) may affect the dynamics of all other systems in the network of physiologic networks. Due to these interactions, failure of one system can trigger a cascade of failures throughout the entire network. We introduce a systematic method to identify a network of interactions between diverse physiologic organ systems, to quantify the hierarchical structure and dynamics of this network, and to track its evolution under different physiologic states. We find a robust relation between network structure and physiologic states: every state is characterized by specific network topology, node connectivity and links strength. Further, we find that transitions from one physiologic state to another trigger a markedly fast reorganization in the network of physiologic interactions on time scales of just a few minutes, indicating high network flexibility in response to perturbations. This reorganization in network topology occurs simultaneously and globally in the entire network as well as at the level of individual physiological systems, while preserving a hierarchical order in the strength of network links. Our findings highlight the need of an integrated network approach to understand physiologic function, since the framework we develop provides new information which can not be obtained by studying individual systems. The proposed system-wide integrative approach may facilitate the development of a new field, Network Physiology.

  18. 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.

  19. Atoms and Molecules Interacting with Light

    Science.gov (United States)

    van der Straten, Peter; Metcalf, Harold

    2016-02-01

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

  20. 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.

  1. 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 `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 Netherlands. Networking appears to be mediated by policy and regulatory imperatives....

  2. Controllability in protein interaction networks.

    Science.gov (United States)

    Wuchty, Stefan

    2014-05-13

    Recently, the focus of network research shifted to network controllability, prompting us to determine proteins that are important for the control of the underlying interaction webs. In particular, we determined minimum dominating sets of proteins (MDSets) in human and yeast protein interaction networks. Such groups of proteins were defined as optimized subsets where each non-MDSet protein can be reached by an interaction from an MDSet protein. Notably, we found that MDSet proteins were enriched with essential, cancer-related, and virus-targeted genes. Their central position allowed MDSet proteins to connect protein complexes and to have a higher impact on network resilience than hub proteins. As for their involvement in regulatory functions, MDSet proteins were enriched with transcription factors and protein kinases and were significantly involved in bottleneck interactions, regulatory links, phosphorylation events, and genetic interactions.

  3. 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 ...

  4. 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...

  5. Nanoarchitectonic atomic switch networks for unconventional computing

    Science.gov (United States)

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

    2016-11-01

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

  6. Nanoindentation: Toward the sensing of atomic interactions

    Science.gov (United States)

    Fraxedas, J.; Garcia-Manyes, S.; Gorostiza, P.; Sanz, F.

    2002-04-01

    The mechanical properties of surfaces of layered materials (highly oriented pyrolytic graphite, InSe, and GaSe) and single-crystal ionic materials (NaCl, KBr, and KCl) have been investigated at the nanometer scale by using nanoindentations produced with an atomic force microscope with ultrasharp tips. Special attention has been devoted to the elastic response of the materials before the onset of plastic yield. A new model based on an equivalent spring constant that takes into account the changes in in-plane interactions on nanoindentation is proposed. The results of this model are well correlated with those obtained by using the Debye model of solid vibrations.

  7. 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.

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

    Science.gov (United States)

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

    2016-09-20

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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Interacting Atomic Interferometry for Rotation Sensing Approaching the Heisenberg Limit

    Science.gov (United States)

    Ragole, Stephen; Taylor, Jacob M.

    2016-11-01

    Atom interferometers provide exquisite measurements of the properties of noninertial frames. While atomic interactions are typically detrimental to good sensing, efforts to harness entanglement to improve sensitivity remain tantalizing. Here we explore the role of interactions in an analogy between atomic gyroscopes and SQUIDs, motivated by recent experiments realizing ring-shaped traps for ultracold atoms. We explore the one-dimensional limit of these ring systems with a moving weak barrier, such as that provided by a blue-detuned laser beam. In this limit, we employ Luttinger liquid theory and find an analogy with the superconducting phase-slip qubit, in which the topological charge associated with persistent currents can be put into superposition. In particular, we find that strongly interacting atoms in such a system could be used for precision rotation sensing. We compare the performance of this new sensor to an equivalent noninteracting atom interferometer, and find improvements in sensitivity and bandwidth beyond the atomic shot-noise limit.

  14. Spin-sensitive atom mirror via spin-orbit interaction

    Science.gov (United States)

    Zhou, Lu; Zheng, Ren-Fei; Zhang, Weiping

    2016-11-01

    Based on the spin-orbit coupling recently implemented in a neutral cold-atom gas, we propose a scheme to realize spin-dependent scattering of cold atoms. In particular we consider a matter wave packet of cold-atom gas impinging upon a step potential created by the optical light field, inside of which the atoms are subject to spin-orbit interaction. We show that the proposed system can act as a spin polarizer or spin-selective atom mirror for the incident atomic beam. The principle and the operating parameter regime of the system are carefully discussed.

  15. Some studies of the interaction between N-two level atoms and three level atom

    Directory of Open Access Journals (Sweden)

    D.A.M. Abo-Kahla

    2016-07-01

    Full Text Available In this paper, we present the analytical solution for the model that describes the interaction between a three level atom and two systems of N-two level atoms. The effect of the quantum numbers on the atomic inversion and the purity, for some special cases of the initial states, are investigated. We observe that the atomic inversion and the purity change remarkably by the change of the quantum numbers.

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

    CERN Document Server

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

    2015-01-01

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

  17. Enhanced Quantum Reflection of Ultracold Atoms with Strong Interatomic Interaction

    Institute of Scientific and Technical Information of China (English)

    LIU Min; ZHAN Ming-Sheng

    2008-01-01

    We calculate the reflection probability for ultracold alkali atoms incident on a solid surface. By considering the interatomic interaction and using the WKB method, it is shown that the repulsive interaction between atoms has the effect of increasing the reflection probability. The increasing amplitude is related with the interatomic interaction and the depth of atom-surface potential. In addition, we also perform a numerical calculation to testify the effect of the interatomic interaction, and the analytic result is proven by the numerical result.

  18. Interaction-Free Effects Between Distant Atoms

    CERN Document Server

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

    2016-01-01

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

  19. 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.

  20. 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.

  1. Protein interaction networks from literature mining

    Science.gov (United States)

    Ihara, Sigeo

    2005-03-01

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

  2. An Elementary Quantum Network of Single Atoms in Optical Cavities

    CERN Document Server

    Ritter, Stephan; Hahn, Carolin; Reiserer, Andreas; Neuzner, Andreas; Uphoff, Manuel; Mücke, Martin; Figueroa, Eden; Bochmann, Jörg; Rempe, Gerhard

    2012-01-01

    Quantum networks are distributed quantum many-body systems with tailored topology and controlled information exchange. They are the backbone of distributed quantum computing architectures and quantum communication. Here we present a prototype of such a quantum network based on single atoms embedded in optical cavities. We show that atom-cavity systems form universal nodes capable of sending, receiving, storing and releasing photonic quantum information. Quantum connectivity between nodes is achieved in the conceptually most fundamental way: by the coherent exchange of a single photon. We demonstrate the faithful transfer of an atomic quantum state and the creation of entanglement between two identical nodes in independent laboratories. The created nonlocal state is manipulated by local qubit rotation. This efficient cavity-based approach to quantum networking is particularly promising as it offers a clear perspective for scalability, thus paving the way towards large-scale quantum networks and their applicati...

  3. “Hard probes” of strongly-interacting atomic gases

    Energy Technology Data Exchange (ETDEWEB)

    Nishida, Yusuke [Los Alamos National Laboratory

    2012-06-18

    We investigate properties of an energetic atom propagating through strongly interacting atomic gases. The operator product expansion is used to systematically compute a quasiparticle energy and its scattering rate both in a spin-1/2 Fermi gas and in a spinless Bose gas. Reasonable agreement with recent quantum Monte Carlo simulations even at a relatively small momentum k/kF > 1.5 indicates that our large-momentum expansions are valid in a wide range of momentum. We also study a differential scattering rate when a probe atom is shot into atomic gases. Because the number density and current density of the target atomic gas contribute to the forward scattering only, its contact density (measure of short-range pair correlation) gives the leading contribution to the backward scattering. Therefore, such an experiment can be used to measure the contact density and thus provides a new local probe of strongly interacting atomic gases.

  4. Rydberg atom interactions from 300 K to 300 K

    Science.gov (United States)

    Pillet, P.; Gallagher, T. F.

    2016-09-01

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

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

    Science.gov (United States)

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

    2016-09-01

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

  6. Reactive Collisions and Interactions of Ultracold Dipolar Atoms

    Science.gov (United States)

    2014-10-29

    rotate and vibrate and where the atomic Zeeman states are coupled by the anisotropic interactions. The calculations were performed with the symmetrized...calculation for Dy atoms can be found in [10] and for Er in [11]. A first-principle coupled-channel model allowed us to calculate anisotropy- induced mag- netic... vibrational levels due to the presence of the third atom . In addition, we studied the dynamic polarizability of the N = 0 and N = 1 rotational levels of the

  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.; 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

  8. 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...

  9. 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)

  10. Processus d'interaction entre photons et atomes

    CERN Document Server

    Fellot, Dominique

    1996-01-01

    This work expounds the basic force interactions between photons and atoms, as well as an analysis of more complex processes. Various theoretical methods are introduced and illustrated with simple systems that help broach that subject.

  11. Discovering functional interaction patterns in protein-protein interaction networks

    Directory of Open Access Journals (Sweden)

    Can Tolga

    2008-06-01

    Full Text Available Abstract Background In recent years, a considerable amount of research effort has been directed to the analysis of biological networks with the availability of genome-scale networks of genes and/or proteins of an increasing number of organisms. A protein-protein interaction (PPI network is a particular biological network which represents physical interactions between pairs of proteins of an organism. Major research on PPI networks has focused on understanding the topological organization of PPI networks, evolution of PPI networks and identification of conserved subnetworks across different species, discovery of modules of interaction, use of PPI networks for functional annotation of uncharacterized proteins, and improvement of the accuracy of currently available networks. Results In this article, we map known functional annotations of proteins onto a PPI network in order to identify frequently occurring interaction patterns in the functional space. We propose a new frequent pattern identification technique, PPISpan, adapted specifically for PPI networks from a well-known frequent subgraph identification method, gSpan. Existing module discovery techniques either look for specific clique-like highly interacting protein clusters or linear paths of interaction. However, our goal is different; instead of single clusters or pathways, we look for recurring functional interaction patterns in arbitrary topologies. We have applied PPISpan on PPI networks of Saccharomyces cerevisiae and identified a number of frequently occurring functional interaction patterns. Conclusion With the help of PPISpan, recurring functional interaction patterns in an organism's PPI network can be identified. Such an analysis offers a new perspective on the modular organization of PPI networks. The complete list of identified functional interaction patterns is available at http://bioserver.ceng.metu.edu.tr/PPISpan/.

  12. 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

  13. 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.

  14. Identification of Topological Network Modules in Perturbed Protein Interaction Networks

    Science.gov (United States)

    Sardiu, Mihaela E.; Gilmore, Joshua M.; Groppe, Brad; Florens, Laurence; Washburn, Michael P.

    2017-01-01

    Biological networks consist of functional modules, however detecting and characterizing such modules in networks remains challenging. Perturbing networks is one strategy for identifying modules. Here we used an advanced mathematical approach named topological data analysis (TDA) to interrogate two perturbed networks. In one, we disrupted the S. cerevisiae INO80 protein interaction network by isolating complexes after protein complex components were deleted from the genome. In the second, we reanalyzed previously published data demonstrating the disruption of the human Sin3 network with a histone deacetylase inhibitor. Here we show that disrupted networks contained topological network modules (TNMs) with shared properties that mapped onto distinct locations in networks. We define TMNs as proteins that occupy close network positions depending on their coordinates in a topological space. TNMs provide new insight into networks by capturing proteins from different categories including proteins within a complex, proteins with shared biological functions, and proteins disrupted across networks. PMID:28272416

  15. 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.

  16. 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...

  17. Photon-mediated interactions between distant artificial atoms.

    Science.gov (United States)

    van Loo, Arjan F; Fedorov, Arkady; Lalumière, Kevin; Sanders, Barry C; Blais, Alexandre; Wallraff, Andreas

    2013-12-20

    Photon-mediated interactions between atoms are of fundamental importance in quantum optics, quantum simulations, and quantum information processing. The exchange of real and virtual photons between atoms gives rise to nontrivial interactions, the strength of which decreases rapidly with distance in three dimensions. Here, we use two superconducting qubits in an open one-dimensional transmission line to study much stronger photon-mediated interactions. Making use of the possibility to tune these qubits by more than a quarter of their transition frequency, we observe both coherent exchange interactions at an effective separation of 3λ/4 and the creation of super- and subradiant states at a separation of one photon wavelength λ. In this system, collective atom-photon interactions and applications in quantum communication may be explored.

  18. Interaction of dopant atoms with stacking faults in silicon

    Science.gov (United States)

    Ohno, Yutaka; Tokumoto, Yuki; Taneichi, Hiroto; Yonenaga, Ichiro; Togase, Kensuke; Nishitani, Sigeto R.

    2012-08-01

    The width of a stacking fault ribbon bound by a pair of partial dislocations in silicon crystals was unchanged when boron and gallium atoms of p-type dopant were agglomerated nearby the ribbon by annealing, even though the width increased when n-type dopant atoms were agglomerated as previously reported [Y. Ohno, Y. Tokumoto, I. Yonenaga, Thin Solid Films, accepted for publication]. The origin of the width-increase in n-type crystals was proposed as the reduction of the stacking fault energy, from 58±5 down to 46±5 mJ/m2, due to an electronic interaction between the ribbon and the n-type dopant atoms, and the interaction energy was estimated to be 0.15±0.05 eV. On the other hand, the interaction of p-type dopant atoms with stacking faults was not detected.

  19. Interaction-induced decoherence of atomic BLOCH oscillations.

    Science.gov (United States)

    Buchleitner, Andreas; Kolovsky, Andrey R

    2003-12-19

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

  20. Network Physiology: How Organ Systems Dynamically Interact.

    Directory of Open Access Journals (Sweden)

    Ronny P Bartsch

    Full Text Available We systematically study how diverse physiologic systems in the human organism dynamically interact and collectively behave to produce distinct physiologic states and functions. This is a fundamental question in the new interdisciplinary field of Network Physiology, and has not been previously explored. Introducing the novel concept of Time Delay Stability (TDS, we develop a computational approach to identify and quantify networks of physiologic interactions from long-term continuous, multi-channel physiological recordings. We also develop a physiologically-motivated visualization framework to map networks of dynamical organ interactions to graphical objects encoded with information about the coupling strength of network links quantified using the TDS measure. Applying a system-wide integrative approach, we identify distinct patterns in the network structure of organ interactions, as well as the frequency bands through which these interactions are mediated. We establish first maps representing physiologic organ network interactions and discover basic rules underlying the complex hierarchical reorganization in physiologic networks with transitions across physiologic states. Our findings demonstrate a direct association between network topology and physiologic function, and provide new insights into understanding how health and distinct physiologic states emerge from networked interactions among nonlinear multi-component complex systems. The presented here investigations are initial steps in building a first atlas of dynamic interactions among organ systems.

  1. Network Physiology: How Organ Systems Dynamically Interact.

    Science.gov (United States)

    Bartsch, Ronny P; Liu, Kang K L; Bashan, Amir; Ivanov, Plamen Ch

    2015-01-01

    We systematically study how diverse physiologic systems in the human organism dynamically interact and collectively behave to produce distinct physiologic states and functions. This is a fundamental question in the new interdisciplinary field of Network Physiology, and has not been previously explored. Introducing the novel concept of Time Delay Stability (TDS), we develop a computational approach to identify and quantify networks of physiologic interactions from long-term continuous, multi-channel physiological recordings. We also develop a physiologically-motivated visualization framework to map networks of dynamical organ interactions to graphical objects encoded with information about the coupling strength of network links quantified using the TDS measure. Applying a system-wide integrative approach, we identify distinct patterns in the network structure of organ interactions, as well as the frequency bands through which these interactions are mediated. We establish first maps representing physiologic organ network interactions and discover basic rules underlying the complex hierarchical reorganization in physiologic networks with transitions across physiologic states. Our findings demonstrate a direct association between network topology and physiologic function, and provide new insights into understanding how health and distinct physiologic states emerge from networked interactions among nonlinear multi-component complex systems. The presented here investigations are initial steps in building a first atlas of dynamic interactions among organ systems.

  2. Influence of dissipation on two-atom dispersion interactions

    Science.gov (United States)

    Barcellona, Pablo; Buhmann, Stefan Yoshi

    2015-03-01

    We consider the dispersion interaction between two neutral, ground-state atoms at zero and finite temperature by means of a dynamical approach. Our result differs from the previous ones obtained with time-independent perturbation theory because it correctly accounts for the influence of dissipation via the atomic decay rates. Modern measurements of Casimir force seem to suggest a suppressed influence of dissipation. Our new result shows similar features and can hence help resolve the Drude-plasma debate. We also consider the interaction between a ground-state atom and an excited atom. There are discordant results in the literature for the retarded potential: one oscillating and one monotonous. Our dynamical result uniquely leads to the oscillating result when taking into account the decay rates. This work was supported by the DFG (Grant BU 1803/3-1).

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

    Institute of Scientific and Technical Information of China (English)

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

    2009-01-01

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

  4. Explorers of the Universe: Interactive Electronic Network

    Science.gov (United States)

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

    2000-01-01

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

  5. Nanoscale light-matter interactions in atomic cladding waveguides.

    Science.gov (United States)

    Stern, Liron; Desiatov, Boris; Goykhman, Ilya; Levy, Uriel

    2013-01-01

    Alkali vapours, such as rubidium, are being used extensively in several important fields of research such as slow and stored light nonlinear optics quantum computation, atomic clocks and magnetometers. Recently, there is a growing effort towards miniaturizing traditional centimetre-size vapour cells. Owing to the significant reduction in device dimensions, light-matter interactions are greatly enhanced, enabling new functionalities due to the low power threshold needed for nonlinear interactions. Here, taking advantage of the mature platform of silicon photonics, we construct an efficient and flexible platform for tailored light-vapour interactions on a chip. Specifically, we demonstrate light-matter interactions in an atomic cladding waveguide, consisting of a silicon nitride nano-waveguide core with a rubidium vapour cladding. We observe the efficient interaction of the electromagnetic guided mode with the rubidium cladding and show that due to the high confinement of the optical mode, the rubidium absorption saturates at powers in the nanowatt regime.

  6. 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...

  7. Scalar-pseudoscalar interaction in the francium atom

    Science.gov (United States)

    Skripnikov, L. V.; Maison, D. E.; Mosyagin, N. S.

    2017-02-01

    Fr atom can be successively used to search for the atomic permanent electric dipole moment (EDM) [Hyperfine Interact. 236, 53 (2015), 10.1007/s10751-015-1193-1; J. Phys.: Conference Series 691, 012017 (2016), 10.1088/1742-6596/691/1/012017]. It can be induced by the permanent electron EDM predicted by modern extensions of the standard model to be nonzero at the level accessible by the new generation of EDM experiments. We consider another mechanism of the atomic EDM generation in Fr. This is caused by the scalar-pseudoscalar nucleus-electron neutral current interaction with the dimensionless strength constant kT ,P. Similar to the electron EDM this interaction violates both spatial parity and time-reversal symmetries and can also induce permanent atomic EDM. It was shown in [Phys. Rev. D 89, 056006 (2014), 10.1103/PhysRevD.89.056006] that the scalar-pseudoscalar contribution to the atomic EDM can dominate over the direct contribution from the electron EDM within the standard model. We report high-accuracy combined all-electron and two-step relativistic coupled cluster treatment of the effect from the scalar-pseudoscalar interaction in the Fr atom. Up to the quadruple cluster amplitudes within the coupled cluster method with single, double, triple, and noniterative quadruple amplitudes, CCSDT(Q), were included in correlation treatment. This calculation is required for the interpretation of the experimental data in terms of kT ,P. The resulted EDM of the Fr atom expressed in terms of kT ,P is dFr=kT ,P4.50 ×10-18e cm , where e is the (negative) charge of the electron. The value of the ionization potential of the 2S1 /2 ground state of Fr calculated within the same methods is in very good agreement with the experimental datum.

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

    Institute of Scientific and Technical Information of China (English)

    DongChuan-Hua

    2003-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    董传华

    2003-01-01

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

  10. 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...

  11. Theory of noncontact friction for atom-surface interactions

    Science.gov (United States)

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

    2016-08-01

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

  12. Evanescent light-matter Interactions in Atomic Cladding Wave Guides

    CERN Document Server

    Stern, Liron; Goykhman, Ilya; Levy, Uriel

    2012-01-01

    Alkali vapors, and in particular rubidium, are being used extensively in several important fields of research such as slow and stored light non-linear optics3 and quantum computation. Additionally, the technology of alkali vapors plays a major role in realizing myriad industrial applications including for example atomic clocks magentometers8 and optical frequency stabilization. Lately, there is a growing effort towards miniaturizing traditional centimeter-size alkali vapor cells. Owing to the significant reduction in device dimensions, light matter interactions are greatly enhanced, enabling new functionalities due to the low power threshold needed for non-linear interactions. Here, taking advantage of the mature Complimentary Metal-Oxide-Semiconductor (CMOS) compatible platform of silicon photonics, we construct an efficient and flexible platform for tailored light vapor interactions on a chip. Specifically, we demonstrate light matter interactions in an atomic cladding wave guide (ACWG), consisting of CMOS ...

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

    Institute of Scientific and Technical Information of China (English)

    LIU Yong-Jun; LIU Ying

    2006-01-01

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

  14. Time-domain Ramsey interferometry with interacting Rydberg atoms

    Science.gov (United States)

    Sommer, Christian; Pupillo, Guido; Takei, Nobuyuki; Takeda, Shuntaro; Tanaka, Akira; Ohmori, Kenji; Genes, Claudiu

    2016-11-01

    We theoretically investigate the dynamics of a gas of strongly interacting Rydberg atoms subject to a time-domain Ramsey interferometry protocol. The many-body dynamics is governed by an Ising-type Hamiltonian with long-range interactions of tunable strength. We analyze and model the contrast degradation and phase accumulation of the Ramsey signal and identify scaling laws for varying interrogation times, ensemble densities, and ensemble dimensionalities.

  15. 2004 Atomic and Molecular Interactions Gordon Research Conference

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Paul J. Dagdigian

    2004-10-25

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

  16. Atomic Force Microscopy of dynamic protein DNA interactions

    NARCIS (Netherlands)

    Noort, van Simon Johannes Theodorus

    1999-01-01

    In this thesis a dedicated Atomic Force Microscopy (AFM) setup is used for imaging biochemical reactions with molecular resolution. The basis for the high resolution of AFM is the combination of a small probe, close proximity to the sample and a short-range interaction between the probe and the samp

  17. Measurement of strong interaction effects in antiprotonic helium atoms

    Energy Technology Data Exchange (ETDEWEB)

    Davies, J.D.; Gorringe, T.P.; Lowe, J.; Nelson, J.M.; Playfer, S.M.; Pyle, G.J.; Squier, G.T.A. (Birmingham Univ. (UK). Dept. of Physics); Baker, C.A.; Batty, C.J.; Clark, S.A.

    1984-09-27

    The strong interaction shift and width for the 2 p level and the width for the 3d level have been measured for antiprotonic helium atoms. The results are compared with optical model calculations. The possible existence of strongly bound antiproton states in nuclei is discussed.

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

    CERN Document Server

    Torres, J M; Seligman, T H

    2009-01-01

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

  19. 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...

  20. Interactivity vs. fairness in networked linux systems

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Wenji; Crawford, Matt; /Fermilab

    2007-01-01

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

  1. Retardation effects in induced atomic dipole-dipole interactions

    CERN Document Server

    Graham, S D

    2016-01-01

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

  2. Interaction of laser-cooled 87Rb atoms with higher order modes of an optical nanofibre

    Science.gov (United States)

    Kumar, Ravi; Gokhroo, Vandna; Deasy, Kieran; Maimaiti, Aili; Frawley, Mary C.; Phelan, Ciarán; Chormaic, Síle Nic

    2015-01-01

    Optical nanofibres are used to confine light to sub-wavelength regions and are very promising tools for the development of optical fibre-based quantum networks using cold, neutral atoms. To date, experimental studies on atoms near nanofibres have focussed on fundamental fibre mode interactions. In this work, we demonstrate the integration of a few-mode optical nanofibre into a magneto-optical trap for 87Rb atoms. The nanofibre, with a waist diameter of ∼700 nm, supports both the fundamental and first group of higher order modes (HOMs) and is used for atomic fluorescence and absorption studies. In general, light propagating in higher order fibre modes has a greater evanescent field extension around the waist in comparison with the fundamental mode. By exploiting this behaviour, we demonstrate that the detected signal of fluorescent photons emitted from a cloud of cold atoms centred at the nanofibre waist is larger if HOMs are also included. In particular, the signal from HOMs appears to be about six times larger than that obtained for the fundamental mode. Absorption of on-resonance, HOM probe light by the laser-cooled atoms is also observed. These advances should facilitate the realization of atom trapping schemes based on HOM interference.

  3. 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.

  4. 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.

  5. 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.

  6. A Waveguide Platform for Collective Light-Atom Interaction

    DEFF Research Database (Denmark)

    Sørensen, Heidi Lundgaard

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

  7. String order via Floquet interactions in atomic systems

    Science.gov (United States)

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

    2016-08-01

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

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

    CERN Document Server

    Wang, Zhaoying; Wu, Yunhan

    2016-01-01

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

  9. D-state Rydberg electrons interacting with ultracold atoms

    Energy Technology Data Exchange (ETDEWEB)

    Krupp, Alexander Thorsten

    2014-10-02

    This thesis was established in the field of ultracold atoms where the interaction of highly excited D-state electrons with rubidium atoms was examined. This work is divided into two main parts: In the first part we study D-state Rydberg molecules resulting from the binding of a D-state Rydberg electron to a ground state rubidium atom. We show that we can address specific rovibrational molecular states by changing our laser detuning and thus create perfectly aligned axial or antialigned toroidal molecules, in good agreement with our theoretical calculations. Furthermore the influence of the electric field on the Rydberg molecules was investigated, creating novel states which show a different angular dependence and alignment. In the second part of this thesis we excite single D-state Rydberg electrons in a Bose-Einstein condensate. We study the lifetime of these Rydberg electrons, the change of the shape of our condensate and the atom losses in the condensate due to this process. Moreover, we observe quadrupolar shape oscillations of the whole condensate created by the consecutive excitation of Rydberg atoms and compare all results to previous S-state measurements. In the outlook we propose a wide range of further experiments including the proposal of imaging a single electron wavefunction by the imprint of its orbit into the Bose-Einstein condensate.

  10. Synchronization in networks with multiple interaction layers

    CERN Document Server

    del Genio, Charo I; Bonamassa, Ivan; Boccaletti, Stefano

    2016-01-01

    The structure of many real-world systems is best captured by networks consisting of several interaction layers. Understanding how a multi-layered structure of connections affects the synchronization properties of dynamical systems evolving on top of it is a highly relevant endeavour in mathematics and physics, and has potential applications to several societally relevant topics, such as power grids engineering and neural dynamics. We propose a general framework to assess stability of the synchronized state in networks with multiple interaction layers, deriving a necessary condition that generalizes the Master Stability Function approach. We validate our method applying it to a network of R\\"ossler oscillators with a double layer of interactions, and show that highly rich phenomenology emerges. This includes cases where the stability of synchronization can be induced even if both layers would have individually induced unstable synchrony, an effect genuinely due to the true multi-layer structure of the interact...

  11. Super-Coulombic atom–atom interactions in hyperbolic media

    Science.gov (United States)

    Cortes, Cristian L.; Jacob, Zubin

    2017-01-01

    Dipole–dipole interactions, which govern phenomena such as cooperative Lamb shifts, superradiant decay rates, Van der Waals forces and 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 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 confirming the giant long-range enhancement. We also propose multiple experimental platforms to verify our predicted effect with phonon–polaritonic hexagonal boron nitride, plasmonic super-lattices and hyperbolic meta-surfaces as well. Our work paves the way for the control of cold atoms above hyperbolic meta-surfaces and the study of many-body physics with hyperbolic media. PMID:28120826

  12. Thermoelectricity in a junction between interacting cold atomic Fermi gases

    Science.gov (United States)

    Sekera, Tibor; Bruder, Christoph; Belzig, Wolfgang

    2016-09-01

    A gas of interacting ultracold fermions can be tuned into a strongly interacting regime using a Feshbach resonance. Here, we theoretically study quasiparticle transport in a system of two reservoirs of interacting ultracold fermions on the BCS side of the BCS-BEC crossover coupled weakly via a tunnel junction. Using the generalized BCS theory, we calculate the time evolution of the system that is assumed to be initially prepared in a nonequilibrium state characterized by a particle number imbalance or a temperature imbalance. A number of characteristic features like sharp peaks in quasiparticle currents or transitions between the normal and superconducting states are found. We discuss signatures of the Seebeck and the Peltier effects and the resulting temperature difference of the two reservoirs as a function of the interaction parameter (kFa ) -1. The Peltier effect may lead to an additional cooling mechanism for ultracold fermionic atoms.

  13. 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.

  14. A conserved mammalian protein interaction network.

    Directory of Open Access Journals (Sweden)

    Åsa Pérez-Bercoff

    Full Text Available Physical interactions between proteins mediate a variety of biological functions, including signal transduction, physical structuring of the cell and regulation. While extensive catalogs of such interactions are known from model organisms, their evolutionary histories are difficult to study given the lack of interaction data from phylogenetic outgroups. Using phylogenomic approaches, we infer a upper bound on the time of origin for a large set of human protein-protein interactions, showing that most such interactions appear relatively ancient, dating no later than the radiation of placental mammals. By analyzing paired alignments of orthologous and putatively interacting protein-coding genes from eight mammals, we find evidence for weak but significant co-evolution, as measured by relative selective constraint, between pairs of genes with interacting proteins. However, we find no strong evidence for shared instances of directional selection within an interacting pair. Finally, we use a network approach to show that the distribution of selective constraint across the protein interaction network is non-random, with a clear tendency for interacting proteins to share similar selective constraints. Collectively, the results suggest that, on the whole, protein interactions in mammals are under selective constraint, presumably due to their functional roles.

  15. Theory of noncontact friction for atom-surface interactions

    CERN Document Server

    Jentschura, U D; DeKieviet, M

    2016-01-01

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

  16. 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.

  17. Interaction of atomic oxygen with a graphite surface

    Science.gov (United States)

    Mateljevic, Natasa

    This project was a part of the Multi University Research Initiative (MURI) Center for Materials Chemistry in the Space Environment which seeks to develop a quantitative and predictive understanding of how materials degrade or become passivated in the space environment. This is a critical research area for the Department of Defense (DoD) and National Aeronautics and Space Administration (NASA) given the large and increasing dependence on satellites and manned spacecrafts that reside in, or pass through, the low-Earth orbit (LEO) space environment. In this work, we completed three separate projects. First, we carried out ab initio electronic structure studies of the interaction of oxygen atoms with graphite surfaces. The (O3 P) ground state of oxygen interacts weakly with the graphite surface while the excited (O1D) state interacts more strongly with a binding energy sufficient for a high coverage of oxygen to be maintained on the surface. Thus, it requires a transition from O(3P) to O(1D) in order for oxygen to strongly bind. Since graphite is a semi-metal, it requires a vanishingly small energy to remove an electron of up spin from just below the Fermi level, and replace it with a down spin electron just above the Fermi level; spin-orbit interaction is not required to switch the state of the oxygen atom. We have examined this complexity for the first time and developed guidelines for properly describing chemical reactivity on graphite surfaces. The second project is a kinetic Monte Carlo study of the erosion of graphite by energetic oxygen atoms in LEO and in the laboratory. These simulations, in conjunction with experiments by our MURI collaborators, reveal new insights about reaction pathways. Finally, we have developed a new model for accommodation of energy and momentum in collisions of gases with highly corrugated surfaces. This model promises to be valuable in simulating frictional heating and drag of objects moving through the atmosphere.

  18. Excitation of hydrogen atoms in collisions with helium atoms: the role of electron–electron interaction

    Science.gov (United States)

    Frémont, F.; Belyaev, A. K.

    2017-02-01

    Cross sections for producing H(nl) excited state atoms in H(1s) + He(1s2) collisions are calculated using the CTMC method, at impact energies ranging from 20 eV to 100 keV. The role of the electron correlation is studied. In the first step, the interactions between each pair of the three electrons are neglected. This leads to disagreement of the calculated total cross section for producing H(2l) atoms with previous experimental and theoretical results. In a second step, the electron–electron interaction is taken into account in a rigorous way, that is, in the form of the pure Coulomb potential. To make sure that the He target is stable before the collision, phenomenological potentials for the electron–helium-nucleus interactions that simulate the Heisenberg principle are included in addition to the Coulomb potential. The excitation cross section calculated in the frame of this model is in remarkable agreement with previous data in the range between 200 eV and 5 keV. At other energies, discrepancies are revealed, but only by a factor of less than 2 at high energies. The present results show the decisive role of the electron–electron interaction during collisions. In addition, they demonstrate the ability of classical mechanics to take into account the effects of the electron correlation.

  19. Atoms and Ions Interacting with Particles and Fields: Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Robicheaux, Francis [Auburn Univ., AL (United States)

    2014-09-18

    This grant supported research in basic atomic, molecular and optical physics related to the interactions of atoms with particles and fields. The duration of the grant was the 10 year period from 8/2003 to 8/2013. All of the support from the grant was used to pay salaries of the PI, postdocs, graduate students, and undergraduates and travel to conferences and meetings. The results were in the form of publications in peer reviewed journals. There were 65 peer reviewed publications over these 10 years with 8 of the publications in Physical Review Letters; all of the other articles were in respected peer reviewed journals (Physical Review A, New Journal of Physics, Journal of Physics B, ...). I will disuss the results for the periods of time relevant for each grant period.

  20. 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.

  1. 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.

  2. Artificial abelian gauge potentials induced by dipole-dipole interactions between Rydberg atoms

    CERN Document Server

    Cesa, A

    2013-01-01

    We analyze the influence of dipole-dipole interactions between Rydberg atoms on the generation of abelian artificial gauge potentials and fields. When two Rydberg atoms are driven by a uniform laser field, we show that the combined atom-atom and atom-field interactions give rise to new, non-uniform, artificial gauge potentials. We identify the mechanism responsible for the emergence of these gauge potentials. Analytical expressions for the latter indicate that the strongest artificial magnetic fields are reached in the regime intermediate between the dipole blockade regime and the regime in which the atoms are sufficiently far apart such that atom-light interaction dominates over atom-atom interactions. We discuss the differences and similarities of artificial gauge fields originating from resonant dipole-dipole and van der Waals interactions. We also give an estimation of experimentally attainable artificial magnetic fields resulting from this mechanism.

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

    Indian Academy of Sciences (India)

    P Anantha Lakshmi; Ashoka Vudayagiri; Shaik Ahmed

    2014-08-01

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

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

    CERN Document Server

    Guerin, W; Kaiser, R

    2016-01-01

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

  5. Excitation dynamics of interacting Rydberg atoms in small lattices

    Energy Technology Data Exchange (ETDEWEB)

    Wu, G., E-mail: gwu@physnet.uni-hamburg.de [Zentrum für Optische Quantentechnologien, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg (Germany); Physikalisches Institut, Universität Heidelberg, Im Neuenheimer Feld 226, 69120 Heidelberg (Germany); Kurz, M.; Liebchen, B. [Zentrum für Optische Quantentechnologien, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg (Germany); Schmelcher, P. [Zentrum für Optische Quantentechnologien, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg (Germany); The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg (Germany)

    2015-01-23

    We study the Rydberg excitation dynamics of laser-driven atoms confined in a one-dimensional three-site lattice with open boundary conditions. Different regular excitation patterns are obtained within various parameter regimes. In the case of a weak Rydberg–Rydberg interaction, the excitation probability possesses a nodal structure which is characterized by an envelope with a period inversely proportional to the interaction. For strong Rydberg interaction we observe dipole blockade and antiblockade effects and an appropriate detuning leads to an overall oscillatory behavior of the Rydberg probability density which is modulated only by small oscillations. Besides an exact diagonalization procedure we study the system by performing first and second order perturbation theory as well as a spectral analysis. - Highlights: • We study Rydberg excitation in small 1-d lattices. • For weak Rydberg interaction, the excitation probability possesses an envelope structure. • For strong Rydberg interaction, we observe dipole blockade and antiblockade effects. • A specific detuning leads to degeneracy and regular oscillatory behavior of the Rydberg density.

  6. 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.

  7. 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.

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

    Directory of Open Access Journals (Sweden)

    Loic Royer

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

  9. The electron-atom interaction in partially ionized dense plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Omarbakiyeva, Yu A; Ramazanov, T S; Roepke, G [IETP, Al Farabi Kazakh National University, Tole Bi 96a, Almaty 050012 (Kazakhstan)], E-mail: yultuz@physics.kz

    2009-05-29

    The electron-atom interaction is considered in dense partially ionized plasmas. The separable potential is constructed from scattering data using effective radius theory. Parameters of the interaction potential were obtained from phase shifts, scattering length and effective radius. The binding energy of the electron in the H{sup -} ion is determined for the singlet channel on the basis of the reconstructed separable potential. In dense plasmas, the influence of the Pauli exclusion principle on the phase shifts and the binding energy is considered. Due to the Pauli blocking, the binding energy vanishes at the Mott density. At that density the behavior of the phase shifts is drastically changed. This leads to modifications of macroscopic properties such as composition and transport coefficients.

  10. 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...

  11. All-atom Molecular Dynamics Simulationsand NMR Spectroscopy Study on Interactions and Structures in N-Glycylglycine Aqueous Solution

    Institute of Scientific and Technical Information of China (English)

    Rong Zhang; Wen-juan Wu; Jing-man Huang; Xin Meng

    2011-01-01

    All-atom molecular dynamics (MD) simulation and the NMR spectra are used to investigate the interactions in N-glycylglycine aqueous solution.Different types of atoms exhibit different capability in forming hydrogen bonds by the radial distribution function analysis.Some typical dominant aggregates are found in different types of hydrogen bonds by the statistical hydrogen-bonding network.Moreover,temperature-dependent NMR are used to compare with the results of the MD simulations.The chemical shifts of the three hydrogen atoms all decrease with the temperature increasing which reveals that the hydrogen bonds are dominant in the glycylglycine aqueous solution.And the NMR results show agreement with the MD simulations.All-atom MD simulations and NMR spectra are successful in revealing the structures and interactions in the N-glycylglycine-water mixtures.

  12. Atom-light interactions in quasi-one-dimensional nanostructures: A Green's-function perspective

    Science.gov (United States)

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

    2017-03-01

    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, identifying signatures of dispersive and dissipative interactions between atoms. We also demonstrate the applicability of our analysis to problems involving three-level atoms, such as electromagnetically induced transparency. Finally we examine recent experiments, and anticipate future observations of atom-atom interactions in photonic band gaps.

  13. Interaction of Photon Vortex Beams with Atomic Matter

    Science.gov (United States)

    Solyanik, Maria; Afanasev, Andrei; Carlson, Carl E.

    2017-01-01

    In our work we consider helical Bessel beams' (BB's) propagation and interaction with isotropic matter. Dynamical properties of the beams with non-zero orbital angular momentum (OAM), which are determined by spatial degrees of freedom and polarization, modify the fundamental processes in light-matter interactions. Circular dichroism of BBs propagating in hydrogen gas was considered within the frame of studying the vortex beams' attenuation due to photoabsorption in hydrogen gas. In this case, the phenomenon is due to the topology of the wave front, contrary to the zero OAM case, when the change in polarization state is due to matter inhomogeneity. The effect of circular dichroism has been predicted by calculating the beam ellipticity evolution when traversing an isotropic target. According to our results, the BBs' transverse ellipticity profile has a structure of concentric circular maxima which correspond to minima of the intensity. The characteristic polarization singularity arises on the beam axis as the result of interaction with matter. It is shown, that even for the case of the paraxial approximation the effect of circular dichroism takes place. These signatures can be used for theoretical and experimental analysis of the interactions of optical vortices with atomic matter.

  14. 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.

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

    CERN Document Server

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

    2013-01-01

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

  16. 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

  17. 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

  18. 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.

  19. Atom interaction propensities of oxygenated chemical functions in crystal packings

    Directory of Open Access Journals (Sweden)

    Christian Jelsch

    2017-03-01

    Full Text Available The crystal contacts of several families of hydrocarbon compounds substituted with one or several types of oxygenated chemical groups were analyzed statistically using the Hirshfeld surface methodology. The propensity of contacts to occur between two chemical types is described with the contact enrichment descriptor. The systematic large enrichment ratios of some interactions like the O—H...O hydrogen bonds suggests that these contacts are a driving force in the crystal packing formation. The same statement holds for the weaker C—H...O hydrogen bonds in ethers, esters and ketones, in the absence of polar H atoms. The over-represented contacts in crystals of oxygenated hydrocarbons are generally of two types: electrostatic attractions (hydrogen bonds and hydrophobic interactions. While Cl...O interactions are generally avoided, in a minority of chloro-oxygenated hydrocarbons, significant halogen bonding does occur. General tendencies can often be derived for many contact types, but outlier compounds are instructive as they display peculiar or rare features. The methodology also allows the detection of outliers which can be structures with errors. For instance, a significant number of hydroxylated molecules displaying over-represented non-favorable oxygen–oxygen contacts turned out to have wrongly oriented hydroxyl groups. Beyond crystal packings with a single molecule in the asymmetric unit, the behavior of water in monohydrate compounds and of crystals with Z′ = 2 (dimers are also investigated. It was found in several cases that, in the presence of several oxygenated chemical groups, cross-interactions between different chemical groups (e.g. water/alcohols; alcohols/phenols are often favored in the crystal packings. While some trends in accordance with common chemical principles are retrieved, some unexpected results can however appear. For example, in crystals of alcohol–phenol compounds, the strong O—H...O hydrogen bonds between

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

    CERN Document Server

    Zhou, Wenting; Rizzuto, Lucia

    2016-01-01

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

  1. Structural properties and interaction energies affecting drug design. An approach combining molecular simulations, statistics, interaction energies and neural networks.

    Science.gov (United States)

    Ioannidis, Dimitris; Papadopoulos, Georgios E; Anastassopoulos, Georgios; Kortsaris, Alexandros; Anagnostopoulos, Konstantinos

    2015-06-01

    In order to elucidate some basic principles for protein-ligand interactions, a subset of 87 structures of human proteins with their ligands was obtained from the PDB databank. After a short molecular dynamics simulation (to ensure structure stability), a variety of interaction energies and structural parameters were extracted. Linear regression was performed to determine which of these parameters have a potentially significant contribution to the protein-ligand interaction. The parameters exhibiting relatively high correlation coefficients were selected. Important factors seem to be the number of ligand atoms, the ratio of N, O and S atoms to total ligand atoms, the hydrophobic/polar aminoacid ratio and the ratio of cavity size to the sum of ligand plus water atoms in the cavity. An important factor also seems to be the immobile water molecules in the cavity. Nine of these parameters were used as known inputs to train a neural network in the prediction of seven other. Eight structures were left out of the training to test the quality of the predictions. After optimization of the neural network, the predictions were fairly accurate given the relatively small number of structures, especially in the prediction of the number of nitrogen and sulfur atoms of the ligand.

  2. 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.

  3. Interactively Evolving Compositional Sound Synthesis Networks

    DEFF Research Database (Denmark)

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

    2015-01-01

    While the success of electronic music often relies on the uniqueness and quality of selected timbres, many musicians struggle with complicated and expensive equipment and techniques to create their desired sounds. Instead, this paper presents a technique for producing novel timbres that are evolved...... by the musician through interactive evolutionary computation. Each timbre is produced by an oscillator, which is represented by a special type of artificial neural network (ANN) called a compositional pattern producing network (CPPN). While traditional ANNs compute only sigmoid functions at their hidden nodes......, CPPNs can theoretically compute any function and can build on those present in traditional synthesizers (e.g. square, sawtooth, triangle, and sine waves functions) to produce completely novel timbres. Evolved with NeuroEvolution of Augmenting Topologies (NEAT), the aim of this paper is to explore...

  4. Atomic interaction mechanism for designing the interface of W/Zr-based bulk metallic glass composites

    OpenAIRE

    Li, Z K; Fu, H. M.; Sha, P. F.; Zhu, Z. W.; A. M. Wang; Li, H.; Zhang, H. W.; Zhang, H. F.; Hu, Z. Q.

    2015-01-01

    The interaction between active element Zr and W damages the W fibers and the interface and decreases the mechanical properties, especially the tensile strength of the W fibers reinforced Zr-based bulk metallic glass composites (BMGCs). From the viewpoint of atomic interaction, the W-Zr interaction can be restrained by adding minor elements that have stronger interaction with W into the alloy. The calculation about atomic interaction energy indicates that Ta and Nb preferred to segregate on th...

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

    CERN Document Server

    Kikkawa, Ayumi

    2016-01-01

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

  6. 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.

  7. 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.

  8. 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 $\\beta$...

  9. 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 ...

  10. 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.

  11. 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.

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

    Institute of Scientific and Technical Information of China (English)

    CHEN Jingbiao; WANG Fengzhi; YANG Donghai; WANG YiQiu

    2001-01-01

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

  13. 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...

  14. Fidelity of quantum state for interacting system of light field and atomic Bose-Einstein condensate

    Institute of Scientific and Technical Information of China (English)

    Chunjia Huang; Ming Zhou; Fanzhi Kong; Jiayuan Fang; Kewei Mo

    2005-01-01

    @@ The evolution characteristics of quantum state fidelity in an interacting system of single-mode light field and atomic Bose-Einstein condensate have been studied and the influence of the initial light field intensity and the interaction among atoms of Bose-Einstein condensate on the quantum state fidelity respectively have been discussed.

  15. 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.

  16. 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.

  17. 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.

  18. Non-integer Quantum Transition, a True Non-perturbation Effect in Laser-Atom Interaction

    Institute of Scientific and Technical Information of China (English)

    ZHANG Qi-Ren

    2007-01-01

    We show that in the quantum transition of an atom interacting with an intense laser of circular frequencyω, the energy difference between the initial and the final states of the atom is not necessarily an integer multiple of the quantum energy (h)ω. This kind of non-integer transition is a true non-perturbation effect in laser-atom interaction.

  19. 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.

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

    Directory of Open Access Journals (Sweden)

    MacLellan W Robb

    2008-07-01

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

  2. Graphene as a flexible template for controlling magnetic interactions between metal atoms

    Science.gov (United States)

    Lee, Sungwoo; Kim, Dongwook; Robertson, Alex W.; Yoon, Euijoon; Hong, Suklyun; Ihm, Jisoon; Yu, Jaejun; Warner, Jamie H.; Lee, Gun-Do

    2017-03-01

    Metal-doped graphene produces magnetic moments that have potential application in spintronics. Here we use density function theory computational methods to show how the magnetic interaction between metal atoms doped in graphene can be controlled by the degree of flexure in a graphene membrane. Bending graphene by flexing causes the distance between two substitutional Fe atoms covalently bonded in graphene to gradually increase and these results in the magnetic moment disappearing at a critical strain value. At the critical strain, a carbon atom can enter between the two Fe atoms and blocks the interaction between relevant orbitals of Fe atoms to quench the magnetic moment. The control of interactions between doped atoms by exploiting the mechanical flexibility of graphene is a unique approach to manipulating the magnetic properties and opens up new opportunities for mechanical-magnetic 2D device systems.

  3. 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

    2016-05-13

    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.

  4. The remote implementation of all possible generalized quantum measurements on a single atomic qubit in a quantum network

    Institute of Scientific and Technical Information of China (English)

    Han Yang; Wu Chun-Wang; Wu Wei; Chen Ping-Xing; Li Cheng-Zu

    2009-01-01

    To implement generalized quantum measurement (GQM) one has to extend the original Hilbert space.Generally speaking,the additional dimensions of the ancilla space increase as the number of the operators of the CQM n increases.This paper presents a scheme for deterministically implementing all possible n-operator GQMs on a single atomic qubit by using only one 2-dimensional ancillary atomic qubit repeatedly,which remarkably reduces the complexity of the realistic physical system.Here the qubit is encoded in the internal states of an atom trapped in an optical cavity and single-photon pulses are employed to provide the interaction between qublts.It shows that the scheme can be performed remotely,and thus it is suitable for implementing GQM in a quantum network.What is more,the number of the total ancilla dimensions in our scheme achieves the theoretic low bound.

  5. 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

  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. 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.

  8. Multiple Tipping Points and Optimal Repairing in Interacting Networks

    CERN Document Server

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

    2015-01-01

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

  9. 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.

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

    Science.gov (United States)

    Blum, Torsten; Kohlbacher, Oliver

    2008-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Gaurav Pandey

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

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

    Science.gov (United States)

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

    2016-07-01

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

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

    Science.gov (United States)

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

    2016-07-22

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

  14. Mining minimal motif pair sets maximally covering interactions in a protein-protein interaction network

    NARCIS (Netherlands)

    Boyen, P.; Neven, F.; Valentim, F.L.; Dijk, van A.D.J.

    2013-01-01

    Correlated motif covering (CMC) is the problem of finding a set of motif pairs, i.e., pairs of patterns, in the sequences of proteins from a protein-protein interaction network (PPI-network) that describe the interactions in the network as concisely as possible. In other words, a perfect solution fo

  15. Quantum Discord Dynamics of Two Atoms Interacting with Two Quantized Field Modes through a Raman Interaction with Phase Decoherence

    Institute of Scientific and Technical Information of China (English)

    QIAN Yi; XU Jing-Bo

    2011-01-01

    We investigate the quantum discord dynamics of two effective two-level atoms independently interacting with two quantized field modes through a Raman interaction in the presence of phase decoherence.The influence of the phase decoherence and detuning on the evolution of the quantum discord and entanglement between two atoms is discussed.It is found that the quantum discord is more robust than the entanglement under the phase decoherence,and the amount of discord and entanglement between two atoms can be increased by adjusting the detuning.

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

    Science.gov (United States)

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

    2016-10-01

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

  17. 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.

  18. Modelization of nanospace interaction involving a ferromagnetic atom: a spin polarization effect study by thermogravimetric analysis.

    Science.gov (United States)

    Santhanam, K S V; Chen, Xu; Gupta, S

    2014-04-01

    Ab initio studies of ferromagnetic atom interacting with carbon nanotubes have been reported in the literature that predict when the interaction is strong, a higher hybridization with confinement effect will result in spin polarization in the ferromagnetic atom. The spin polarization effect on the thermal oxidation to form its oxide is modeled here for the ferromagnetic atom and its alloy, as the above studies predict the 4s electrons are polarized in the atom. The four models developed here provide a pathway for distinguishing the type of interaction that exists in the real system. The extent of spin polarization in the ferromagnetic atom has been examined by varying the amount of carbon nanotubes in the composites in the thermogravimetric experiments. In this study we report the experimental results on the CoNi alloy which appears to show selective spin polarization. The products of the thermal oxidation has been analyzed by Fourier Transform Infrared Spectroscopy.

  19. Van der Waals and Casimir interactions between atoms and carbon nanotubes

    OpenAIRE

    Klimchitskaya, G. L.(Central Astronomical Observatory at Pulkovo of the Russian Academy of Sciences, 196140, St. Petersburg, Russia); Blagov, E. V.; Mostepanenko, V. M.

    2008-01-01

    The van der Waals and Casimir interactions of a hydrogen atom (molecule) with a single-walled and a multiwalled carbon nanotubes are compared. It is shown that the macroscopic concept of graphite dielectric permittivity is already applicable for nanotubes with only two or three walls. The absorption of hydrogen atoms by a nanotube at separations below one nanometer is considered. The lateral force due to exchange repulsion moves the atom to a position above the cell center, where it is absorb...

  20. Interference of Atomic Bose-Einstein Condensate Interacting with Laser Field

    Institute of Scientific and Technical Information of China (English)

    YU Zhao-Xian; JIAO Zhi-Yong; SUN Jin-Zuo

    2004-01-01

    Interference of an atomic Bose-Einstein condensate interacting with a laser field in a double-well potential with dissipation is investigated. If properly selecting the laser field and the initial states of the atoms in the two wells,we find that the intensity exhibits revivals and collapses. The fidelity of interference is affected by the total number of atoms in the two wells and dissipation.

  1. Entanglement and coherence of a three-level atom in Λ configuration interacting with two fields

    Institute of Scientific and Technical Information of China (English)

    Zhang Jian-Song; Xu Jing-Bo

    2009-01-01

    We investigate the entanglement of a three-level atom in A configuration interacting with two quantized field modes by using logarithmic negativity. Then, we study the relationship of the atomic coherence and the entanglement between two fields which are initially prepared in vacuum or thermal states. We find that if the two fields are prepared in thermal states, the atomic coherence can induce the entanglement between two thermal fields. However, there is no coherence-induced entanglement between two vacuum fields.

  2. 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.``

  3. Atomic forces between noble gas atoms, alkali ions, and halogen ions for surface interactions

    Science.gov (United States)

    Wilson, J. W.; Outlaw, R. A.; Heinbockel, J. H.

    1988-01-01

    The components of the physical forces between noble gas atoms, alkali ions, and halogen ions are analyzed and a data base developed from analysis of the two-body potential data, the alkali-halide molecular data, and the noble gas crystal and salt crystal data. A satisfactory global fit to this molecular and crystal data is then reproduced by the model to within several percent. Surface potentials are evaluated for noble gas atoms on noble gas surfaces and salt crystal surfaces with surface tension neglected. Within this context, the noble gas surface potentials on noble gas and salt crystals are considered to be accurate to within several percent.

  4. Squeezing in the interaction of radiation with two-level atoms

    OpenAIRE

    Bandyopadhyay, Abir; Rai, Jagdish

    1995-01-01

    We propose a simple experimental procedure to produce squeezing and other non-classical properties like photon antibunching of radiation, and amplification without population inversion. The method also decreases the uncertainties of the angular-momentum quadratures representing the two-level atomic system in the interaction of the two-level atoms with quantized radiation.

  5. 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…

  6. Influence of degree correlations on network structure and stability in protein-protein interaction networks

    Directory of Open Access Journals (Sweden)

    Zimmer Ralf

    2007-08-01

    Full Text Available Abstract Background The existence of negative correlations between degrees of interacting proteins is being discussed since such negative degree correlations were found for the large-scale yeast protein-protein interaction (PPI network of Ito et al. More recent studies observed no such negative correlations for high-confidence interaction sets. In this article, we analyzed a range of experimentally derived interaction networks to understand the role and prevalence of degree correlations in PPI networks. We investigated how degree correlations influence the structure of networks and their tolerance against perturbations such as the targeted deletion of hubs. Results For each PPI network, we simulated uncorrelated, positively and negatively correlated reference networks. Here, a simple model was developed which can create different types of degree correlations in a network without changing the degree distribution. Differences in static properties associated with degree correlations were compared by analyzing the network characteristics of the original PPI and reference networks. Dynamics were compared by simulating the effect of a selective deletion of hubs in all networks. Conclusion Considerable differences between the network types were found for the number of components in the original networks. Negatively correlated networks are fragmented into significantly less components than observed for positively correlated networks. On the other hand, the selective deletion of hubs showed an increased structural tolerance to these deletions for the positively correlated networks. This results in a lower rate of interaction loss in these networks compared to the negatively correlated networks and a decreased disintegration rate. Interestingly, real PPI networks are most similar to the randomly correlated references with respect to all properties analyzed. Thus, although structural properties of networks can be modified considerably by degree

  7. Graph spectral analysis of protein interaction network evolution

    OpenAIRE

    Thorne, Thomas; Stumpf, Michael P. H.

    2012-01-01

    We present an analysis of protein interaction network data via the comparison of models of network evolution to the observed data. We take a Bayesian approach and perform posterior density estimation using an approximate Bayesian computation with sequential Monte Carlo method. Our approach allows us to perform model selection over a selection of potential network growth models. The methodology we apply uses a distance defined in terms of graph spectra which captures the network data more natu...

  8. Atomic interaction mechanism for designing the interface of W/Zr-based bulk metallic glass composites

    Science.gov (United States)

    Li, Z. K.; Fu, H. M.; Sha, P. F.; Zhu, Z. W.; Wang, A. M.; Li, H.; Zhang, H. W.; Zhang, H. F.; Hu, Z. Q.

    2015-03-01

    The interaction between active element Zr and W damages the W fibers and the interface and decreases the mechanical properties, especially the tensile strength of the W fibers reinforced Zr-based bulk metallic glass composites (BMGCs). From the viewpoint of atomic interaction, the W-Zr interaction can be restrained by adding minor elements that have stronger interaction with W into the alloy. The calculation about atomic interaction energy indicates that Ta and Nb preferred to segregate on the W substrate surface. Sessile drop experiment proves the prediction and corresponding in-situ coating appears at the interface. Besides, the atomic interaction mechanism was proven to be effective in many other systems by the sessile drop technique. Considering the interfacial morphology, Nb was added into the alloy to fabricate W/Zr-based BMGCs. As expected, the Nb addition effectively suppressed the W-Zr reaction and damage to W fibers. Both the compressive and tensile properties are improved obviously.

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

    Science.gov (United States)

    Ganmor, Elad; Segev, Ronen; Schneidman, Elad

    2011-02-23

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

  10. The computational power of interactive recurrent neural networks.

    Science.gov (United States)

    Cabessa, Jérémie; Siegelmann, Hava T

    2012-04-01

    In classical computation, rational- and real-weighted recurrent neural networks were shown to be respectively equivalent to and strictly more powerful than the standard Turing machine model. Here, we study the computational power of recurrent neural networks in a more biologically oriented computational framework, capturing the aspects of sequential interactivity and persistence of memory. In this context, we prove that so-called interactive rational- and real-weighted neural networks show the same computational powers as interactive Turing machines and interactive Turing machines with advice, respectively. A mathematical characterization of each of these computational powers is also provided. It follows from these results that interactive real-weighted neural networks can perform uncountably many more translations of information than interactive Turing machines, making them capable of super-Turing capabilities.

  11. 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.

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

    Science.gov (United States)

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

    2016-11-01

    We demonstrate experimentally that a dense 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 dense cloud. It implies that a large phase shift is imprinted on the continuous laser beam. Our system may thus be useful for applications to quantum technologies, such as variable delay line for individual photons or phase imprint between two beams at the single-photon level.

  13. Different patterns of collagen-proteoglycan interaction: a scanning electron microscopyand atomic force microscopy study

    Directory of Open Access Journals (Sweden)

    A Ruggeri

    2009-12-01

    Full Text Available The extracellular matrix of unfixed, unstained rat corneal stroma, visualized with high-resolution scanning electron microscopy and atomic force microscopy after minimal preliminary treatment, appears composed of straight, parallel, uniform collagen fibrils regularly spaced by a three-dimensional, irregular network of thin, delicate proteoglycan filaments. Rat tail tendon, observed under identical conditions, appears instead made of heterogeneous, closely packed fibrils interwoven with orthogonal proteoglycan filaments. Pre-treatment with cupromeronic blue just thickens the filaments without affecting their spatial layout. Digestion with chondroitinase ABC rids the tendon matrix of all its interconnecting filaments while the corneal stroma architecture remains virtually unaffected, its fibrils always being separated by an evident interfibrillar spacing which is never observed in tendon. Our observations indicate that matrix proteoglycans are responsible for both the highly regular interfibrillar spacing which is distinctive of corneal stroma, and the strong interfibrillar binding observed in tendon. These opposite interaction patterns appear to be distinctive of different proteo- glycan species. The molecular details of proteoglycan interactions are still incompletely understood and are the subject of ongoing research.

  14. 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.

  15. Interactive Naive Bayesian network: A new approach of constructing gene-gene interaction network for cancer classification.

    Science.gov (United States)

    Tian, Xue W; Lim, Joon S

    2015-01-01

    Naive Bayesian (NB) network classifier is a simple and well-known type of classifier, which can be easily induced from a DNA microarray data set. However, a strong conditional independence assumption of NB network sometimes can lead to weak classification performance. In this paper, we propose a new approach of interactive naive Bayesian (INB) network to weaken the conditional independence of NB network and classify cancers using DNA microarray data set. We selected the differently expressed genes (DEGs) to reduce the dimension of the microarray data set. Then, an interactive parent which has the biggest influence among all DEGs is searched for each DEG. And then we calculate a weight to represent the interactive relationship between a DEG and its parent. Finally, the gene-gene interaction network is constructed. We experimentally test the INB network in terms of classification accuracy using leukemia and colon DNA microarray data sets, then we compare it with the NB network. The INB network can get higher classification accuracies than NB network. And INB network can show the gene-gene interactions visually.

  16. 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.

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

    Science.gov (United States)

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

    2016-07-08

    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.

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

    DEFF Research Database (Denmark)

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

    2015-01-01

    We consider a one-dimensional gas of cold atoms with strong contact interactions and construct an effective spin-chain Hamiltonian for a two-component system. The resulting Heisenberg spin model can be engineered by manipulating the shape of the external confining potential of the atomic gas. We...... 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...

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

    CERN Document Server

    Moroz, A

    2004-01-01

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

  20. Atom-scale molecular interactions in lipid raft mixtures

    DEFF Research Database (Denmark)

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

    2009-01-01

    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...

  1. 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.

  2. Semiclassical electrodynamics of alien atoms in interacting media II. Two-level systems

    Science.gov (United States)

    Elçi, Ahmet

    1985-03-01

    The previously developed self-consistent mean field theory of atoms entering an interacting medium is specialized to two-level alien atoms. It is shown that the medium may invert or split the original two levels, and that there is an intimate connection between the dressed atom spectrum and the statistical nature of the ensemble of alien atoms in the self-consistent mean field approximation. The optical susceptibility of alien atoms while inside the medium is calculated, and the lineshape and position of the optical resonance are shown to depend on the intensity of the optical field applied. There may be more than one phase possible for the atomic ensemble as a result of optical excitation.

  3. 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.

  4. Multimode Kapitza-Dirac interferometer on Bose-Einstein condensates with atomic interactions

    Science.gov (United States)

    He, Tianchen; Niu, Pengbin

    2017-03-01

    The dynamics of multimode interferometers for Bose Einstein condensation (BEC) with atomic interactions confined to a harmonic trap is investigated. At the initial time t = 0, several spatially addressable wave packets (modes) with different momenta are created by the first Kapitza-Dirac pulse. These modes are coherently recombined by the harmonic potential with atomic interactions. The second Kapitza-Dirac pulse splits the evolved modes a second time and separates them along different paths for a second time. The signal to noise ratio is numerically calculated by the Fisher information and the Cramér-Rao lower bound. We find that the small atomic interactions decrease the measurement accuracy for current atom interferometers when measuring the gravitational acceleration. Its impact on measurement precision can be reduced by improving the Kapitza-Dirac strength.

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

    Science.gov (United States)

    Parrish, Robert M; Sherrill, C David

    2014-07-28

    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

  6. 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.

  7. 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].

  8. 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].

  9. 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.

  10. Metal-graphene interaction studied via atomic resolution scanning transmission electron microscopy.

    Science.gov (United States)

    Zan, Recep; Bangert, Ursel; Ramasse, Quentin; Novoselov, Konstantin S

    2011-03-09

    Distributions and atomic sites of transition metals and gold on suspended graphene were investigated via high-resolution scanning transmission electron microscopy, especially using atomic resolution high angle dark field imaging. All metals, albeit as singular atoms or atom aggregates, reside in the omni-present hydrocarbon surface contamination; they do not form continuous films, but clusters or nanocrystals. No interaction was found between Au atoms and clean single-layer graphene surfaces, i.e., no Au atoms are retained on such surfaces. Au and also Fe atoms do, however, bond to clean few-layer graphene surfaces, where they assume T and B sites, respectively. Cr atoms were found to interact more strongly with clean monolayer graphene, they are possibly incorporated at graphene lattice imperfections and have been observed to catalyze dissociation of C-C bonds. This behavior might explain the observed high frequency of Cr-cluster nucleation, and the usefulness as wetting layer, for depositing electrical contacts on graphene.

  11. Functional characterization and topological modularity of molecular interaction networks

    Directory of Open Access Journals (Sweden)

    Koyutürk Mehmet

    2010-01-01

    Full Text Available Abstract Background Analyzing interaction networks for functional characterization poses significant challenges arising from the noisy, incomplete, and generic nature of both the interaction data as well as functional annotation of molecules. Network-based methods focus on interacting molecules (pairs or sets occurring in close proximity to infer functional associations. Results In this paper we perform a formal comparative investigation of the relationship between functional coherence and topological proximity in networks. We investigate the problem of assessing the coherence of sets of biomolecules (or segments thereof taking into account functional specificity as well as the distribution of functional attributes across entity groups. We also propose novel measures of topological proximity that are more robust to noisy and incomplete interaction data. Conclusion We derive the following results in this paper: (i there exists strong correlation between functional similarity and topological proximity in various network abstractions, with domain interaction networks (DDIs demonstrating higher correlation than protein interaction networks (PPIs; (ii measures that quantify coherence among entire sets of proteins are superior to aggregates of known pair-wise measures; and (iii random-walk based measures of topological proximity are better suited to existing interaction data. We validate our methods on diverse data, including experimentally and computationally derived PPIs and DDIs, as well as on sets of known biologically related groups of molecules.

  12. The Multiphoton Interaction of Lambda Model Atom and Two-Mode Fields

    Science.gov (United States)

    Liu, Tang-Kun

    1996-01-01

    The system of two-mode fields interacting with atom by means of multiphotons is addressed, and the non-classical statistic quality of two-mode fields with interaction is discussed. Through mathematical calculation, some new rules of non-classical effects of two-mode fields which evolue with time, are established.

  13. Molecular mechanics on bonding and non-bonding interactions in (atom@C60)

    Institute of Scientific and Technical Information of China (English)

    朱传宝; 徐志谨; 严继民

    1997-01-01

    The interactions between the embedded atom X (X=Li,Na,K,Rb,Cs; F,Cl,Br,I) and C60cage in the endohedral-form complexes (X@C60) are calculated and discussed according to molecular mechanics from the point of view of the bonding and non-bonding.It is found from the computational results that for atoms with radii larger than Li’s,their locations with the minimum interaction in (X@C60) are at the cage center,while atom Li has an off-center location with the minimum interaction deviation of-0.05 nm,and the cage-environment in C60 can be regarded as sphero-symmetry in the region with radius r of ~0.2 nm.It is shown that the interaction between X and C60 cage is of non-bonding characteristic,and this non-bonding interaction is not purely electrostatic.The repulsion and dispersion in non-bonding interactions should not be neglected,which make important contribution to the location with minimum interaction of X,at center or off center.Some rules about the variations of interactions with atomic radii have been ob

  14. 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.

  15. 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.

  16. The networks as a new forms of international interaction

    OpenAIRE

    Dorosh, Lesya

    2013-01-01

    This article is devoted to the problem of modern treatments of the system of international relations, attention is paid to its network measurement. It’s analyzed the types of international networks and shown tendencies of transformation of the international interactions from the international anarchy with the priority of the state sovereignty to the horizontal cooperation on the branch self-government. It’s identified that the network of the international relations causes the changes of th...

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

    Directory of Open Access Journals (Sweden)

    Yang Zhihao

    2011-10-01

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

  18. Guidelines to foster interaction in online communities for Learning Networks

    NARCIS (Netherlands)

    Berlanga, Adriana; Rusman, Ellen; Bitter-Rijpkema, Marlies; Sloep, Peter

    2009-01-01

    The original publication is available from www.springerlink.com. Berlanga, A., Rusman, E., Bitter-Rijpkema, M., & Sloep, P. B. (2009). Guidelines to foster interaction in online communities for Learning Networks. In R. Koper (Ed.), Learning Network Services for Professional Development (pp. 27-42).

  19. 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),…

  20. Interacting Social Processes on Interconnected Networks

    Science.gov (United States)

    Alvarez-Zuzek, Lucila G.; La Rocca, Cristian E.; Vazquez, Federico; Braunstein, Lidia A.

    2016-01-01

    We propose and study a model for the interplay between two different dynamical processes –one for opinion formation and the other for decision making– on two interconnected networks A and B. The opinion dynamics on network A corresponds to that of the M-model, where the state of each agent can take one of four possible values (S = −2,−1, 1, 2), describing its level of agreement on a given issue. The likelihood to become an extremist (S = ±2) or a moderate (S = ±1) is controlled by a reinforcement parameter r ≥ 0. The decision making dynamics on network B is akin to that of the Abrams-Strogatz model, where agents can be either in favor (S = +1) or against (S = −1) the issue. The probability that an agent changes its state is proportional to the fraction of neighbors that hold the opposite state raised to a power β. Starting from a polarized case scenario in which all agents of network A hold positive orientations while all agents of network B have a negative orientation, we explore the conditions under which one of the dynamics prevails over the other, imposing its initial orientation. We find that, for a given value of β, the two-network system reaches a consensus in the positive state (initial state of network A) when the reinforcement overcomes a crossover value r*(β), while a negative consensus happens for r βc. We develop an analytical mean-field approach that gives an insight into these regimes and shows that both dynamics are equivalent along the crossover line (r*, β*). PMID:27689698

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

    Science.gov (United States)

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

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

  2. 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...

  3. 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.

  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. 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.

  6. Rydberg blockade with multivalent atoms: effect of Rydberg series perturbation on van der Waals interactions

    CERN Document Server

    Topcu, Turker

    2015-01-01

    We investigate the effect of series perturbation on the second order dipole-dipole interactions between strontium atoms in $5sns({^1}S_0)$ and $5snp({^1}P_1)$ Rydberg states as a means of engineering long-range interactions between atoms in a way that gives an exceptional level of control over the strength and the sign of the interaction by changing $n$. We utilize experimentally available data to estimate the importance of perturber states at low $n$, and find that van der Waals interaction between two strontium atoms in the $5snp({^1}P_1)$ states shows strong peaks outside the usual hydrogenic $n^{11}$ scaling. We identify this to be the result of the perturbation of $5snd({^1}D_2)$ intermediate states by the $4d^2({^1}D_2)$ and $4dn's({^1}D_2)$ states in the $n<20$ range. This demonstrates that divalent atoms in general present a unique advantage for creating substantially stronger or weaker interaction strengths than those can be achieved using alkali metal atoms due to their highly perturbed spectra t...

  7. 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.

  8. Description of Atom-Field Interaction via Quantized Caldirola-Kanai Hamiltonian

    Science.gov (United States)

    Daneshmand, Roohollah; Tavassoly, Mohammad Kazem

    2017-01-01

    In this paper we outline an approach to the study of atom-field interacting systems, where the Hamiltonian of the field is simply inspired from the quantized Caldirola-Kanai Hamiltonian. As a simple physical realization of the model, the interaction between a two-level atom with such a single-mode field is studied. The explicit form of the atom-field entangled state associated with the considered system is analytically deduced and the dynamics of a few of its physical properties is numerically evaluated. To achieve the latter purposes, the temporal behavior of the degree of entanglement, atomic population inversion as well as sub-Poissonian statistics and quadrature squeezing of the field are evaluated. Moreover, the effects of the intensity of initial field and the damping parameter within the Caldirola-Kanai Hamiltonian on the above-mentioned criteria are investigated. As is shown, by adjusting the latter evolved parameters one can appropriately tune the discussed physical quantities.

  9. 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.

  10. Chaos and flights in the atom-photon interaction in cavity QED.

    Science.gov (United States)

    Prants, S V; Edelman, M; Zaslavsky, G M

    2002-10-01

    We study dynamics of the atom-photon interaction in cavity quantum electrodynamics, considering a cold two-level atom in a single-mode high-finesse standing-wave cavity as a nonlinear Hamiltonian system with three coupled degrees of freedom: translational, internal atomic, and the field. The system proves to have different types of motion including Lévy flights and chaotic walkings of an atom in a cavity. The corresponding equations of motion for expectation values of the atom and field variables have two characteristic time scales: fast Rabi oscillations of the internal atomic and field quantities and slow translational oscillations of the center of the atom mass. It is shown that the translational motion, related to the atom recoils, is governed by an equation of a parametric nonlinear pendulum with a frequency modulated by the Rabi oscillations. This type of dynamics is chaotic with some width of the stochastic layer that is estimated analytically. The width is fairly small for realistic values of the control parameters, the normalized detuning delta and atomic recoil frequency alpha. We consider the Poincaré sections of the dynamics, compute the Lyapunov exponents, and find a range of the detuning, |delta| less, similar 3, where chaos is prominent. It is demonstrated how the atom-photon dynamics with a given value of alpha depends on the values of delta and initial conditions. Two types of Lévy flights, one corresponding to the ballistic motion of the atom and the other corresponding to small oscillations in a potential well, are found. These flights influence statistical properties of the atom-photon interaction such as distribution of Poincaré recurrences and moments of the atom position x. The simulation shows different regimes of motion, from slightly abnormal diffusion with approximately tau(1.13) at delta=1.2 to a superdiffusion with approximately tau(2.2) at delta=1.92 that corresponds to a superballistic motion of the atom with an acceleration. The

  11. Modelling laser-atom interactions in the strong field regime

    CERN Document Server

    Galstyan, A; Mota-Furtado, F; O'Mahony, P F; Janssens, N; Jenkins, S D; Chuluunbaatar, O; Piraux, B

    2016-01-01

    We consider the ionisation of atomic hydrogen by a strong infrared field. We extend and study in more depth an existing semi-analytical model. Starting from the time-dependent Schroedinger equation in momentum space and in the velocity gauge we substitute the kernel of the non-local Coulomb potential by a sum of N separable potentials, each of them supporting one hydrogen bound state. This leads to a set of N coupled one-dimensional linear Volterra integral equations to solve. We analyze the gauge problem for the model, the different ways of generating the separable potentials and establish a clear link with the strong field approximation which turns out to be a limiting case of the present model. We calculate electron energy spectra as well as the time evolution of electron wave packets in momentum space. We compare and discuss the results obtained with the model and with the strong field approximation and examine in this context, the role of excited states.

  12. Information Entropy Squeezing of a Two-Level Atom Interacting with Two-Mode Coherent Fields

    Institute of Scientific and Technical Information of China (English)

    LIU Xiao-Juan; FANG Mao-Fa

    2004-01-01

    From a quantum information point of view we investigate the entropy squeezing properties for a two-level atom interacting with the two-mode coherent fields via the two-photon transition. We discuss the influences of the initial state of the system on the atomic information entropy squeezing. Our results show that the squeezed component number,squeezed direction, and time of the information entropy squeezing can be controlled by choosing atomic distribution angle,the relative phase between the atom and the two-mode field, and the difference of the average photon number of the two field modes, respectively. Quantum information entropy is a remarkable precision measure for the atomic squeezing.

  13. On the interaction between radiation-induced defects and foreign interstitial atoms in {alpha}-iron

    Energy Technology Data Exchange (ETDEWEB)

    Nikolaev, Alexander L., E-mail: nikolaev@imp.uran.ru [Institute of Metal Physics, Russian Academy of Sciences Ural Branch 18, S. Kovalevskaya St., Ekaterinburg 620990 (Russian Federation); Kurennykh, Tatiana E. [Institute of Metal Physics, Russian Academy of Sciences Ural Branch 18, S. Kovalevskaya St., Ekaterinburg 620990 (Russian Federation)

    2011-07-31

    Interaction between Frenkel pair (FP) defects and nitrogen atoms in {alpha}-iron has been investigated by means of resistivity recovery method. Both FP defects are attracted to nitrogen atoms. Dissociation of self-interstitial atoms from nitrogen atoms is observed at 165 K while that of vacancies at 250 K. The binding energies of FP defects with nitrogen are both about 0.1-0.15 eV. A weak RR stage is observed at 340 K assigned to the presence of carbon in concentration of about 1 appm. Analysis of its features leads to a conclusion on a dissociation (binding) energy of vacancy-carbon atom pairs of about 0.9 (0.35) eV.

  14. Networks of ProteinProtein Interactions: From Uncertainty to Molecular Details.

    Science.gov (United States)

    Garcia-Garcia, Javier; Bonet, Jaume; Guney, Emre; Fornes, Oriol; Planas, Joan; Oliva, Baldo

    2012-05-01

    Proteins are the bricks and mortar of cells. The work of proteins is structural and functional, as they are the principal element of the organization of the cell architecture, but they also play a relevant role in its metabolism and regulation. To perform all these functions, proteins need to interact with each other and with other bio-molecules, either to form complexes or to recognize precise targets of their action. For instance, a particular transcription factor may activate one gene or another depending on its interactions with other proteins and not only with DNA. Hence, the ability of a protein to interact with other bio-molecules, and the partners they have at each particular time and location can be crucial to characterize the role of a protein. Proteins rarely act alone; they rather constitute a mingled network of physical interactions or other types of relationships (such as metabolic and regulatory) or signaling cascades. In this context, understanding the function of a protein implies to recognize the members of its neighborhood and to grasp how they associate, both at the systemic and atomic level. The network of physical interactions between the proteins of a system, cell or organism, is defined as the interactome. The purpose of this review is to deepen the description of interactomes at different levels of detail: from the molecular structure of complexes to the global topology of the network of interactions. The approaches and techniques applied experimentally and computationally to attain each level are depicted. The limits of each technique and its integration into a model network, the challenges and actual problems of completeness of an interactome, and the reliability of the interactions are reviewed and summarized. Finally, the application of the current knowledge of protein-protein interactions on modern network medicine and protein function annotation is also explored.

  15. 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.

  16. 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

    2014-07-30

    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.

  17. 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.

  18. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, Christopher David [Los Alamos National Laboratory

    2008-01-01

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

  20. Interaction Enhanced Imaging of Rydberg P states. Preparation and detection of Rydberg atoms for engineering long-range interactions

    Science.gov (United States)

    Gavryusev, Vladislav; Ferreira-Cao, Miguel; Kekić, Armin; Zürn, Gerhard; Signoles, Adrien

    2016-12-01

    The Interaction Enhanced Imaging technique allows to detect the spatial distribution of strongly interacting impurities embedded within a gas of background atoms used as a contrast medium [1]. Here we present a detailed study of this technique, applied to detect Rydberg P states. We experimentally realize fast and efficient three-photon excitation of P states, optimized according to the results of a theoretical effective two-level model. Few Rydberg P-state atoms, prepared in a small cloud with dimensions comparable to the blockade radius, are detected with a good sensitivity by averaging over 50 shots. The main aspects of the technique are described with a hard-sphere model, finding good agreement with experimental data. This work paves the way to a non-destructive optical detection of single Rydberg atoms with high spatial and temporal resolution.

  1. 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.

  2. 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.

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

    Institute of Scientific and Technical Information of China (English)

    Shao Xiao-Qiang; Chen Li; Zhang Shou

    2009-01-01

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

  4. 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

    2014-10-01

    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), alerting and orienting cues were independently manipulated, thus allowing examination of interactions between these 2 networks, as well as between them and the executive attention network. In Experiment 2 (N = 159), additional changes were made to the task in order to foster exogenous orienting cues. Results from both studies consistently revealed separate developmental trajectories for each attention network. Children younger than 7 years exhibited stronger benefits from having an alerting auditory signal prior to the target presentation. Developmental changes in orienting were mostly observed on response accuracy between middle and late childhood, whereas executive attention showed increases in efficiency between 7 years and older ages, and further improvements in late childhood. Of importance, across both experiments, significant interactions between alerting and orienting, as well as between each of these and the executive attention network, were observed. Alerting cues led to speeding shifts of attention and enhancing orienting processes. Also, both alerting and orienting cues modulated the magnitude of the flanker interference effect. These findings inform current theoretical models of human attention and its development, characterizing for the first time, the age-related course of attention networks interactions that, present in adults, stem from further refinements over childhood.

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

    Science.gov (United States)

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

    2009-06-26

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

  6. Atoms and Forces of Interaction Between Elementary Particles in the Expanding Universe

    CERN Document Server

    Gorbatenko, M V

    2011-01-01

    The earlier developed algorithm for constructing a self-conjugate Hamiltonian in the representation for Dirac particles interacting with a general gravitational field is extended to the case of electromagnetic fields. This Hamiltonian is applied to the case when the gravitational field describes the spatially flat Friedmann model, and the electromagnetic field is the Coulomb potential extended to the case of this model. The analysis of atomic systems and electromagnetic forces of interaction under the conditions of spatially flat expansion of the universe has demonstrated that the system of atomic levels does not change with cosmological time. Spectral lines of atoms in the spatially flat Friedmann model are identical at different points of cosmological time. In this case the redshift is stipulated entirely by the growth of wavelength of photons at movement in the expending universe. At the same time force of interaction between elementary particles can change with expansion of the universe.

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

    Science.gov (United States)

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

    2016-10-01

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

  8. Evolutionary pressure on the topology of protein interface interaction networks.

    Science.gov (United States)

    Johnson, Margaret E; Hummer, Gerhard

    2013-10-24

    The densely connected structure of protein-protein interaction (PPI) networks reflects the functional need of proteins to cooperate in cellular processes. However, PPI networks do not adequately capture the competition in protein binding. By contrast, the interface interaction network (IIN) studied here resolves the modular character of protein-protein binding and distinguishes between simultaneous and exclusive interactions that underlie both cooperation and competition. We show that the topology of the IIN is under evolutionary pressure, and we connect topological features of the IIN to specific biological functions. To reveal the forces shaping the network topology, we use a sequence-based computational model of interface binding along with network analysis. We find that the more fragmented structure of IINs, in contrast to the dense PPI networks, arises in large part from the competition between specific and nonspecific binding. The need to minimize nonspecific binding favors specific network motifs, including a minimal number of cliques (i.e., fully connected subgraphs) and many disconnected fragments. Validating the model, we find that these network characteristics are closely mirrored in the IIN of clathrin-mediated endocytosis. Features unexpected on the basis of our motif analysis are found to indicate either exceptional binding selectivity or important regulatory functions.

  9. 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

  10. 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".

  11. The balance of weak and strong interactions in genetic networks.

    Directory of Open Access Journals (Sweden)

    Juan F Poyatos

    Full Text Available Genetic interactions are being quantitatively characterized in a comprehensive way in several model organisms. These data are then globally represented in terms of genetic networks. How are interaction strengths distributed in these networks? And what type of functional organization of the underlying genomic systems is revealed by such distribution patterns? Here, I found that weak interactions are important for the structure of genetic buffering between signaling pathways in Caenorhabditis elegans, and that the strength of the association between two genes correlates with the number of common interactors they exhibit. I also determined that this network includes genetic cascades balancing weak and strong links, and that its hubs act as particularly strong genetic modifiers; both patterns also identified in Saccharomyces cerevisae networks. In yeast, I further showed a relation, although weak, between interaction strengths and some phenotypic/evolutionary features of the corresponding target genes. Overall, this work demonstrates a non-random organization of interaction strengths in genetic networks, a feature common to other complex networks, and that could reflect in this context how genetic variation is eventually influencing the phenotype.

  12. 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.

  13. 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).

  14. Interactions of satellite-speed helium atoms with satellite-surfaces. 1. Spatial distributions of reflected helium atoms

    Energy Technology Data Exchange (ETDEWEB)

    Liu, S.M.; Rodgers, W.E.; Knuth, E.L.

    1975-06-01

    Interactions of satellite-speed helium atoms with practical satellite surfaces were investigated experimentally, and spatial distributions of satellite-speed helium beams scattered from four different engineering surfaces were measured. The 7000-m/s helium beams were produced using an arc-heated supersonic molecular beam source. The test surfaces included cleaned 6061-T6 aluminum plate, anodized aluminum foil, white paint, and quartz surfaces. Both in-plane (in the plane containing the incident beam and the surface normal) and out-of-plane spatial distributions of reflected helium atoms were measured for six different incidence angles (0, 15, 30, 45, 60, and 75 deg from the surface normal). It was found that a large fraction of the incident helium atoms were scattered back in the vicinity of the incoming beam, particularly in the case of glancing incidence angles. This unexpected scattering feature results perhaps from the gross roughness of these test surfaces. This prominent backscattering could yield drag coefficients which are higher than for surfaces with either forward-lobed or diffusive (cosine) scattering patterns. (auth)

  15. Engineering exciton interactions with Zeeman excitations of highly magnetic atoms on an optical lattice

    CERN Document Server

    Hernandez, R A Vargas

    2015-01-01

    We show that Zeeman excitations in an ensemble of highly magnetic atoms trapped in an optical lattice lead to interacting Frenkel excitons described by a tunable $t$-$V$ model. The dispersion of the excitons and the interactions between excitons can be tuned in a wide range by transferring atoms to different Zeeman states. We show that these parameters are insensitive to an external magnetic field, which leads to an interesting possibility of engineering lattice models with significant particle-non-conserving terms. We consider the coupling of the Zeeman excitations to the translational motion of atoms in the lattice and show that the resulting Hamiltonian is equivalent to a polaron Hamiltonian, where the mathematical form of the particle - phonon interaction can be tuned by transferring atoms to different Zeeman states. We calculate the model parameters for the specific system of Dy atoms on an optical lattice with the lattice site separation 266 nm and show that the exciton interaction parameters can be tun...

  16. 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…

  17. 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.

  18. 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.

  19. Approximate Toffoli Gate Originated from a Single Resonant Interaction of Cavity Dissipation and Atomic Spontaneous Emission

    Institute of Scientific and Technical Information of China (English)

    GU Xiao-Yan; CHEN Chang-Yong; SUN Jian-Qiang

    2008-01-01

    We propose a potentially practical scheme to implement an approximate three-qubit Toffoli gate by a single resonant interaction in dissipative cavity QED in which the cavity mode decay and atomic spontaneous emission are considered. The scheme does not require two-qubit controlled-NOT gates but uses a three-qubit phase gate and two Hadamard gates, where the approximate phase gate can be implemented by only a single dissipative resonant interaction of atoms with the cavity mode. Discussions are made for the advantages and the experimental feasibility of our scheme.

  20. 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.

  1. 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.

  2. 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.

  3. Revealing physical interaction networks from statistics of collective dynamics

    Science.gov (United States)

    Nitzan, Mor; Casadiego, Jose; Timme, Marc

    2017-01-01

    Revealing physical interactions in complex systems from observed collective dynamics constitutes a fundamental inverse problem in science. Current reconstruction methods require access to a system’s model or dynamical data at a level of detail often not available. We exploit changes in invariant measures, in particular distributions of sampled states of the system in response to driving signals, and use compressed sensing to reveal physical interaction networks. Dynamical observations following driving suffice to infer physical connectivity even if they are temporally disordered, are acquired at large sampling intervals, and stem from different experiments. Testing various nonlinear dynamic processes emerging on artificial and real network topologies indicates high reconstruction quality for existence as well as type of interactions. These results advance our ability to reveal physical interaction networks in complex synthetic and natural systems. PMID:28246630

  4. 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.

  5. A Study of Feature Interactions in Intelligent Networks

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

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

  6. Quantum field entropy of the system with interaction between moving Bell-state atoms and coherent light field

    Institute of Scientific and Technical Information of China (English)

    ZHANG Cai-hua; Sachuerfu; Gerile

    2011-01-01

    The field entropy of the system with two moving atoms interacting with the coherent state is investigated by means of the full quantum theory.Under the different initial states with two atoms,the influences of the light field intensity and the atomic motion on the field entropy are discussed.The results indicate that the motion of the atoms leads to strict periodicity in the field entropy evolution.When the two atoms are in the Bell state initially,the system is in a completely disentangled state.For the atoms initially at other Bell states,the field periodically entangles with the atoms.

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

    Science.gov (United States)

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

    2015-03-19

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

  8. 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...

  9. 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...

  10. 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

  11. Predicting genetic interactions with random walks on biological networks

    Directory of Open Access Journals (Sweden)

    Singh Ambuj K

    2009-01-01

    Full Text Available Abstract Background Several studies have demonstrated that synthetic lethal genetic interactions between gene mutations provide an indication of functional redundancy between molecular complexes and pathways. These observations help explain the finding that organisms are able to tolerate single gene deletions for a large majority of genes. For example, system-wide gene knockout/knockdown studies in S. cerevisiae and C. elegans revealed non-viable phenotypes for a mere 18% and 10% of the genome, respectively. It has been postulated that the low percentage of essential genes reflects the extensive amount of genetic buffering that occurs within genomes. Consistent with this hypothesis, systematic double-knockout screens in S. cerevisiae and C. elegans show that, on average, 0.5% of tested gene pairs are synthetic sick or synthetic lethal. While knowledge of synthetic lethal interactions provides valuable insight into molecular functionality, testing all combinations of gene pairs represents a daunting task for molecular biologists, as the combinatorial nature of these relationships imposes a large experimental burden. Still, the task of mapping pairwise interactions between genes is essential to discovering functional relationships between molecular complexes and pathways, as they form the basis of genetic robustness. Towards the goal of alleviating the experimental workload, computational techniques that accurately predict genetic interactions can potentially aid in targeting the most likely candidate interactions. Building on previous studies that analyzed properties of network topology to predict genetic interactions, we apply random walks on biological networks to accurately predict pairwise genetic interactions. Furthermore, we incorporate all published non-interactions into our algorithm for measuring the topological relatedness between two genes. We apply our method to S. cerevisiae and C. elegans datasets and, using a decision tree

  12. Competition between finite-size effects and dipole-dipole interactions in few-atom systems

    Science.gov (United States)

    Damanet, François; Martin, John

    2016-11-01

    In this paper, we study the competition between finite-size effects (i.e. discernibility of particles) and dipole-dipole interactions in few-atom systems coupled to the electromagnetic field in vacuum. We consider two hallmarks of cooperative effects, superradiance and subradiance, and compute for each the rate of energy radiated by the atoms and the coherence of the atomic state during the time evolution. We adopt a statistical approach in order to extract the typical behaviour of the atomic dynamics and average over random atomic distributions in spherical containers with prescribed {k}0R with k 0 the radiation wavenumber and R the average interatomic distance. Our approach allows us to highlight the tradeoff between finite-size effects and dipole-dipole interactions in superradiance/subradiance. In particular, we show the existence of an optimal value of {k}0R for which the superradiant intensity and coherence pulses are the less affected by dephasing effects induced by dipole-dipole interactions and finite-size effects.

  13. Study of the scalar-pseudoscalar interaction in the francium atom

    CERN Document Server

    Skripnikov, L V; Mosyagin, N S

    2016-01-01

    Fr atom can be successively used to search for the atomic permanent electric dipole moment (EDM) [Hyperfine Interactions 236, 53 (2015); Journal of Physics: Conference Series 691, 012017 (2016)]. It can be induced by the permanent electron EDM predicted by modern extensions of the standard model to be nonzero at the level accessible by the new generation of EDM experiments. We consider another mechanism of the atomic EDM generation in Fr. This is caused by the scalar-pseudoscalar nucleus-electron neutral current interaction with the dimensionless strength constant, $k_{T,P}$. Similar to the electron EDM this interaction violates both spatial parity and time-reversal symmetries and can also induce permanent atomic EDM. It was shown in [Phys. Rev. D 89, 056006 (2014)] that the scalar-pseudoscalar contribution to the atomic EDM can dominate over the direct contribution from the electron EDM within the standard model. We report high-accuracy combined all-electron and two-step relativistic coupled cluster treatmen...

  14. 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.

  15. 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.

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

    CERN Multimedia

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

  17. 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.

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

    Science.gov (United States)

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

    2014-11-01

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

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

    Science.gov (United States)

    Jones, Ryan; Saint, Reece; Olmos, Beatriz

    2017-01-01

    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 comparable to 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 (linear) driving limit, we make progress in understanding the signatures of collective behavior in these many-body systems. Furthermore, we shed light on the role of disorder and averaging 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.

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

    Directory of Open Access Journals (Sweden)

    Gozde Kar

    2009-12-01

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

  2. 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...

  3. Influence of atomic force microscope tip-sample interaction on the study of scaling behavior

    NARCIS (Netherlands)

    Aue, J.; de Hosson, J.T.M.

    1997-01-01

    Images acquired with atomic force microscopy are based on tip-sample interaction. It is shown that using scanning probe techniques for determining scaling parameters of a surface leads to an underestimate of the actual scaling dimension, due to the dilation of tip and surface. How much we underestim

  4. Fundamental symmetries and interactions studied with radioactive isotopes in atom traps

    NARCIS (Netherlands)

    Wilschut, H.W.E.M.; Gacsi, Z; Dombradi, Z; Krasznahorkay, A

    2005-01-01

    The structure of certain nuclei and atoms allow one to study fundamental symmetries and interactions. In this review we consider the search for Time-Reversal invariance Violation (TRV). We consider two options: TRV in beta decay or the search for the forbidden Electric Dipole Moment (EDM). In both c

  5. Structural and chemical evolution of single-wall carbon nanotubes under atomic and molecular deuterium interaction

    NARCIS (Netherlands)

    Lisowski, W.; Keim, E.G.; Berg, van den A.H.J.; Smithers, M.A.

    2005-01-01

    The interaction of atomic (D) and molecular (D2) deuterium, as present in a (D + D2) gas mixture, with single-wall carbon nanotubes (SWNTs) has been studied by means of a combination of scanning electron microscopy, transmission electron microscopy and X-ray photoelectron spectroscopy. The SWNT samp

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

    Science.gov (United States)

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

    2013-04-01

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

  7. 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.

  8. Quantum Statistical Properties of Binomial Field Interacting with Two Entangled Atoms

    Institute of Scientific and Technical Information of China (English)

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

    2008-01-01

    Quantum statistical properties of the binomial field interacting with the two entangled atoms are investi-gated for the different initial conditions. It is found that the sub-Poissonian distribution and the antibunching effect can be presented for the certain ranges of the involved parameters.

  9. An experimental investigation of the interaction law of Kr atoms through small-angle neutron scattering

    Energy Technology Data Exchange (ETDEWEB)

    Benmore, C.J.; Egelstaff, P.A. [Guelph Univ., ON (Canada). Dept. of Physics; Formisano, F.; Barocchi, F. [Dipartimento di Fisica, Universita di Firenze, largo E.Fermi 2, 50125 Firenze (Italy)]|[Istituto Nazionale di Fisica della Materia, Unita di ricerca di Firenze, largo E.Fermi 2, 50125 Firenze (Italy); Magli, R. [Istituto Nazionale di Fisica della Materia, Unita di ricerca di Firenze, largo E.Fermi 2, 50125 Firenze (Italy)]|[Dipartimento di Energetica ``S.Stecco``, Universita di Firenze, via di S.Marta 3, 50139 Firenze (Italy); Bafile, U. [Istituto di Elettronica Quantistica, Consiglio Nazionale delle Ricerche, via Panciatichi 56/30, Firenze 50127 (Italy); Robinson, R.A. [Los Alamos National Laboratory, LANSCE, Los Alamos, NM 87545 (United States); Verkerk, P. [Interfacultair Reactor Instituut, Technische Universiteit Delft, Mekelweg 15, 2629 JB Delft (Netherlands)

    1997-06-01

    The first direct determination of the London dispersive contribution to the long-range interaction energy of pairs of krypton atoms is discussed. The result, obtained using a SANS technique, is in good agreement with previous estimates present in literature. (orig.).

  10. The interaction of intrinsic dynamics and network topology in determining network burst synchrony.

    Science.gov (United States)

    Gaiteri, Chris; Rubin, Jonathan E

    2011-01-01

    The pre-Bötzinger complex (pre-BötC), within the mammalian respiratory brainstem, represents an ideal system for investigating the synchronization properties of complex neuronal circuits via the interaction of cell-type heterogeneity and network connectivity. In isolation, individual respiratory neurons from the pre-BötC may be tonically active, rhythmically bursting, or quiescent. Despite this intrinsic heterogeneity, coupled networks of pre-BötC neurons en bloc engage in synchronized bursting that can drive inspiratory motor neuron activation. The region's connection topology has been recently characterized and features dense clusters of cells with occasional connections between clusters. We investigate how the dynamics of individual neurons (quiescent/bursting/tonic) and the betweenness centrality of neurons' positions within the network connectivity graph interact to govern network burst synchrony, by simulating heterogeneous networks of computational model pre-BötC neurons. Furthermore, we compare the prevalence and synchrony of bursting across networks constructed with a variety of connection topologies, analyzing the same collection of heterogeneous neurons in small-world, scale-free, random, and regularly structured networks. We find that several measures of network burst synchronization are determined by interactions of network topology with the intrinsic dynamics of neurons at central network positions and by the strengths of synaptic connections between neurons. Surprisingly, despite the functional role of synchronized bursting within the pre-BötC, we find that synchronized network bursting is generally weakest when we use its specific connection topology, which leads to synchrony within clusters but poor coordination across clusters. Overall, our results highlight the relevance of interactions between topology and intrinsic dynamics in shaping the activity of networks and the concerted effects of connectivity patterns and dynamic heterogeneities.

  11. Point Process Modeling for Directed Interaction Networks

    Science.gov (United States)

    2011-10-01

    Enron corporation between 1998 and 2002. These e-mail interaction data give rise to the following questions: Homophily To what extent are traits shared...methods Our example analysis uses publicly available data from the Enron e-mail corpus (Cohen, 2009), a large subset of the e-mail messages sent within...the Enron corporation between 1998 and 2002, and made public as the result of a subpoena by the U.S. Federal Energy Regulatory Commission during an

  12. Probing the Extent of Randomness in Protein Interaction Networks

    Science.gov (United States)

    2008-07-11

    elegans [16], Plasmodium falciparum [17], Campylobacter jejuni [18], and Homo sapiens [7]. A number of efforts to compile and, in some cases, curate the...Weighted Connectivity in Two PPI Networks. (A) Helicobacter pylori and (B) Campylobacter jejuni . For k1k2.10, probabilities of interaction P(k1,k2) were...Four PPI Networks and their DCDW Equivalents. (A) Drosophila melanogaster, (B) Campylobacter jejuni , (C) Escherichia coli (HT2), and (D) Escherichia

  13. Characterizing interactions in online social networks during exceptional events

    CERN Document Server

    Omodei, Elisa; Arenas, Alex

    2015-01-01

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

  14. 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.

  15. 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.

  16. The polarity sub-network in the yeast network of protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Luca Paris

    2011-12-01

    Full Text Available Rare, but highly connected, hub proteins subdivide hierarchically global networks of interacting proteins into modular clusters. Most biological research, however, focuses on functionally defined sub-networks. Thus, it is important to know whether the sub-networks retain the same topology of the global networks, from which they derive. To address this issue, we have analyzed the protein-protein interaction sub-network that participates in the polarized growth of the budding yeast Saccharomyces cerevisiae and that is derived from the global network of this model organism. We have observed that, in contrast to global networks, the distribution of connectivity k (i.e., the number of interactions per protein does not follow a power law, but decays exponentially, which reflects the local absence of hub proteins. Nonetheless, far from being randomly organized, the polarity sub-network can be subdivided into functional modules. In addition, most non-hub connector proteins, besides ensuring communications among modules, are linked mutually and contribute to the formation of the polarisome, a structure that coordinates actin assembly with polarized growth. These findings imply that identifying critical proteins within sub-networks (e.g., for the aim of targeted therapy requires searching not only for hubs but also for key non-hub connectors, which might remain otherwise unnoticed due to their relatively low connectivity.

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

    Science.gov (United States)

    van Doorn, Gerrit Sander; Taborsky, Michael

    2012-03-01

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

  18. Interface-resolved network of protein-protein interactions.

    Directory of Open Access Journals (Sweden)

    Margaret E Johnson

    Full Text Available We define an interface-interaction network (IIN to capture the specificity and competition between protein-protein interactions (PPI. This new type of network represents interactions between individual interfaces used in functional protein binding and thereby contains the detail necessary to describe the competition and cooperation between any pair of binding partners. Here we establish a general framework for the construction of IINs that merges computational structure-based interface assignment with careful curation of available literature. To complement limited structural data, the inclusion of biochemical data is critical for achieving the accuracy and completeness necessary to analyze the specificity and competition between the protein interactions. Firstly, this procedure provides a means to clarify the information content of existing data on purported protein interactions and to remove indirect and spurious interactions. Secondly, the IIN we have constructed here for proteins involved in clathrin-mediated endocytosis (CME exhibits distinctive topological properties. In contrast to PPI networks with their global and relatively dense connectivity, the fragmentation of the IIN into distinctive network modules suggests that different functional pressures act on the evolution of its topology. Large modules in the IIN are formed by interfaces sharing specificity for certain domain types, such as SH3 domains distributed across different proteins. The shared and distinct specificity of an interface is necessary for effective negative and positive design of highly selective binding targets. Lastly, the organization of detailed structural data in a network format allows one to identify pathways of specific binding interactions and thereby predict effects of mutations at specific surfaces on a protein and of specific binding inhibitors, as we explore in several examples. Overall, the endocytosis IIN is remarkably complex and rich in features masked

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

    Science.gov (United States)

    Gill, Joel C.; Malamud, Bruce D.

    2016-08-01

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

  20. 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.

  1. TP53 mutations, expression and interaction networks in human cancers.

    Science.gov (United States)

    Wang, Xiaosheng; Sun, Qingrong

    2017-01-03

    Although the associations of p53 dysfunction, p53 interaction networks and oncogenesis have been widely explored, a systematic analysis of TP53 mutations and its related interaction networks in various types of human cancers is lacking. Our study explored the associations of TP53 mutations, gene expression, clinical outcomes, and TP53 interaction networks across 33 cancer types using data from The Cancer Genome Atlas (TCGA). We show that TP53 is the most frequently mutated gene in a number of cancers, and its mutations appear to be early events in cancer initiation. We identified genes potentially repressed by p53, and genes whose expression correlates significantly with TP53 expression. These gene products may be especially important nodes in p53 interaction networks in human cancers. This study shows that while TP53-truncating mutations often result in decreased TP53 expression, other non-truncating TP53 mutations result in increased TP53 expression in some cancers. Survival analyses in a number of cancers show that patients with TP53 mutations are more likely to have worse prognoses than TP53-wildtype patients, and that elevated TP53 expression often leads to poor clinical outcomes. We identified a set of candidate synthetic lethal (SL) genes for TP53, and validated some of these SL interactions using data from the Cancer Cell Line Project. These predicted SL genes are promising candidates for experimental validation and the development of personalized therapeutics for patients with TP53-mutated cancers.

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

    Science.gov (United States)

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

    2015-12-01

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

  3. Manipulating the tunneling of ultracold atoms through a mazer cavity via vacuum-multiparticle interactions

    Science.gov (United States)

    Badshah, Fazal; Basit, Abdul; Ali, Hamad; Ge, Guo-Qin

    2017-02-01

    We study the tunneling and traversal time of ultracold two-level atoms through a high quality microwave cavity containing N  -  1 ground state atoms. The phase time of tunneling may be considered as a measure of the time required to traverse the cavity which exhibits both super and subclassical traversal behaviors. Here we examine that superclassical phase time behavior suppresses with the increase in the number of motionless ground state atoms inside the cavity. It happens due to the multipartite influence in the interaction that traps the incident atom into its upper state such that it does not observe any induced potential. Accordingly, for larger atomic samples, the incident atoms in the initial excited states get perfect transmission and tunnel through the cavity nearly with the same speed as they would have moved through a free space. This is true for any width of potential and the particle’s speed provided that the center-of-mass energy of the incident particle lies in the classically forbidden range.

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

    CERN Document Server

    Cotrufo, Michele; Verhagen, Ewold

    2016-01-01

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

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

    Science.gov (United States)

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

    2015-04-01

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

  6. 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.

  7. 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)

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

    CERN Document Server

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

    2016-01-01

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

  9. Network Physiology: Mapping interactions between complex physiological systems

    OpenAIRE

    Ivanov, Plamen Ch.

    2016-01-01

    The human organism is an integrated network where multi-component organ systems, each with its own regulatory mechanisms, continuously interact to optimize and coordinate their function. Organ-to-organ interactions occur at multiple levels and spatiotemporal time scales to produce distinct physiologic states: wake and sleep; light and deep sleep; consciousness and unconsciousness. Disrupting organ communications can lead to dysfunction of individual systems or to collapse of the entire organ...

  10. Stabilization of perturbed Boolean network attractors through compensatory interactions

    Science.gov (United States)

    2014-01-01

    Background Understanding and ameliorating the effects of network damage are of significant interest, due in part to the variety of applications in which network damage is relevant. For example, the effects of genetic mutations can cascade through within-cell signaling and regulatory networks and alter the behavior of cells, possibly leading to a wide variety of diseases. The typical approach to mitigating network perturbations is to consider the compensatory activation or deactivation of system components. Here, we propose a complementary approach wherein interactions are instead modified to alter key regulatory functions and prevent the network damage from triggering a deregulatory cascade. Results We implement this approach in a Boolean dynamic framework, which has been shown to effectively model the behavior of biological regulatory and signaling networks. We show that the method can stabilize any single state (e.g., fixed point attractors or time-averaged representations of multi-state attractors) to be an attractor of the repaired network. We show that the approach is minimalistic in that few modifications are required to provide stability to a chosen attractor and specific in that interventions do not have undesired effects on the attractor. We apply the approach to random Boolean networks, and further show that the method can in some cases successfully repair synchronous limit cycles. We also apply the methodology to case studies from drought-induced signaling in plants and T-LGL leukemia and find that it is successful in both stabilizing desired behavior and in eliminating undesired outcomes. Code is made freely available through the software package BooleanNet. Conclusions The methodology introduced in this report offers a complementary way to manipulating node expression levels. A comprehensive approach to evaluating network manipulation should take an "all of the above" perspective; we anticipate that theoretical studies of interaction modification

  11. 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.

  12. 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

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

    Directory of Open Access Journals (Sweden)

    Preecha Patumcharoenpol

    2016-03-01

    Full Text Available 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

  14. Stability as a natural selection mechanism on interacting networks

    Directory of Open Access Journals (Sweden)

    Francisco A. Tamarit

    2010-02-01

    Full Text Available Biological networks of interacting agents exhibit similar topological properties for a wide range of scales, from cellular to ecological levels, suggesting the existence of a common evolutionary origin. A general evolutionary mechanism based on global stability has been proposed recently  [J I Perotti, et al., Phys. Rev. Lett. 103, 108701 (2009]. This mechanism was incorporated into a  model of a growing network of interacting agents in which each new agent's membership in the network is determined by the agent's effect on the network's global stability. In this work, we analyze different quantities that characterize the topology of the emerging networks, such as global connectivity, clustering and average nearest neighbors degree, showing that they reproduce scaling behaviors frequently observed in several biological systems. The influence of the stability selection  mechanism on the dynamics associated to the resulting network, as well as  the interplay  between some topological and functional features are also analyzed.Received: 17 July 2010; Accepted: 27 September 2010; Edited by: D. H. Zanette; Reviewed by: V. M. Eguiluz, Inst. Fisica Interdisciplinar y Sist. Complejos, Palma de Mallorca, Spain; DOI: 10.4279/PIP.020005

  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).

  16. 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.

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

    Science.gov (United States)

    Acencio, Marcio Luis; Bovolenta, Luiz Augusto; Camilo, Esther; Lemke, Ney

    2013-01-01

    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 in cancer research

  18. 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

  19. Quantum mechanical study of atomic hydrogen interaction with a fluorinated boron-substituted coronene radical.

    Science.gov (United States)

    Zhang, Hong; Smith, Sean C; Nanbu, Shinkoh; Nakamura, Hiroki

    2009-04-08

    In this work we study the transmission of atomic hydrogen across a fluorinated boron-substituted coronene radical (C(19)H(12)BF(6)) as a model for partially fluorinated and boron-doped nanotubes or fullerenes. Complete active space self-consistent field (CASSCF) and multi-reference configuration interaction (MRCI) methods are employed to calculate the potential energy surfaces for both ground and excited electronic states, and one-dimensional R-matrix propagation is utilized to investigate the transmission/reflection dynamics of atomic hydrogen, through the central six-member ring of the fluorinated boron-substituted coronene radical. The quantum scattering includes resonance effects as well as non-adiabatic transitions between the ground and excited electronic states. Within the sudden approximation, both centre and off-centre approach trajectories have been investigated. Implications for atomic hydrogen encapsulation by carbon nanotube and fullerene are discussed.

  20. Few-body Cs Rydberg Atom Interactions in a 1064 nm Dipole Trap

    Science.gov (United States)

    Booth, Donald; Tallant, Jonathan; Marangoni, Bruno; Marcassa, Luis; Shaffer, James

    2011-05-01

    In studying few-body physics, the number density of atoms is an important parameter in achieving a good signal to noise ratio. We have recently improved our apparatus by implementing a crossed 1064 nm far off-resonance trap (FORT), which enables us to trap atoms at three orders of magnitude greater density than our MOT. Future directions for the apparatus, which include the study of anisotropic interactions among Rydberg atoms in the dipole trap, three-body recombination, ``trilobite-like'' molecules, and the detection of ultra-long range Rydberg macrodimers in Cs, will be described. Our presentation will focus on data on three-body recombination and long-range Rydberg ``trilobite-like'' molecules. We acknowledge funding from ARO (W911NF-08-1-0257), NSF (PHY-0855324) and NSF (OISE-0756321).

  1. 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.

  2. 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 ...

  3. The impact of lone pair-π interactions on photochromic properties in 1-D naphthalene diimide coordination networks.

    Science.gov (United States)

    Liu, Jian-Jun; Guan, Ying-Fang; Chen, Yong; Lin, Mei-Jin; Huang, Chang-Cang; Dai, Wen-Xin

    2015-10-21

    Lone pair-π interaction is an important but less studied binding force. Generally, it is too weak to influence the physical properties of supramolecular systems. Herein we reported the first example exhibiting the impact of lone pair-π interactions on photochromic properties of naphthalene diimide based coordination networks. In three isostructural 1-D networks, [(DPNDI)ZnX2] (DPNDI = N,N-di(4-pyridyl)-1,4,5,8-naphthalene diimide, X = Cl for 1, X = Br for 2 and X = I for 3), they exhibit different electron-transfer photochromic behaviors due to different lone pair-π interactions between the capped halogen atoms and electron-deficient DPNDI moieties. Specifically, 1 and 2 but not 3 are photochromic, which is attributed to a stronger lone pair-π interaction in 3 than those in 1 and 2. This study anticipates breaking a new path for designing novel photochromic materials through such unnoticeable supramolecular interactions.

  4. Dynamic modularity in protein interaction networks predicts breast cancer outcome

    DEFF Research Database (Denmark)

    Taylor, Ian W; Linding, Rune; Warde-Farley, David

    2009-01-01

    Changes in the biochemical wiring of oncogenic cells drives phenotypic transformations that directly affect disease outcome. Here we examine the dynamic structure of the human protein interaction network (interactome) to determine whether changes in the organization of the interactome can be used...... to predict patient outcome. An analysis of hub proteins identified intermodular hub proteins that are co-expressed with their interacting partners in a tissue-restricted manner and intramodular hub proteins that are co-expressed with their interacting partners in all or most tissues. Substantial differences...

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. Comparison of protein interaction networks reveals species conservation and divergence

    Directory of Open Access Journals (Sweden)

    Teng Maikun

    2006-10-01

    Full Text Available Abstract Background Recent progresses in high-throughput proteomics have provided us with a first chance to characterize protein interaction networks (PINs, but also raised new challenges in interpreting the accumulating data. Results Motivated by the need of analyzing and interpreting the fast-growing data in the field of proteomics, we propose a comparative strategy to carry out global analysis of PINs. We compare two PINs by combining interaction topology and sequence similarity to identify conserved network substructures (CoNSs. Using this approach we perform twenty-one pairwise comparisons among the seven recently available PINs of E.coli, H.pylori, S.cerevisiae, C.elegans, D.melanogaster, M.musculus and H.sapiens. In spite of the incompleteness of data, PIN comparison discloses species conservation at the network level and the identified CoNSs are also functionally conserved and involve in basic cellular functions. We investigate the yeast CoNSs and find that many of them correspond to known complexes. We also find that different species harbor many conserved interaction regions that are topologically identical and these regions can constitute larger interaction regions that are topologically different but similar in framework. Based on the species-to-species difference in CoNSs, we infer potential species divergence. It seems that different species organize orthologs in similar but not necessarily the same topology to achieve similar or the same function. This attributes much to duplication and divergence of genes and their associated interactions. Finally, as the application of CoNSs, we predict 101 protein-protein interactions (PPIs, annotate 339 new protein functions and deduce 170 pairs of orthologs. Conclusion Our result demonstrates that the cross-species comparison strategy we adopt is powerful for the exploration of biological problems from the perspective of networks.

  10. Demonstration of strong Rydberg blockade in three-atom systems with anisotropic interactions

    CERN Document Server

    Barredo, Daniel; Labuhn, Henning; Béguin, Lucas; Vernier, Aline; Nogrette, Florence; Lahaye, Thierry; Browaeys, Antoine

    2014-01-01

    We study the Rydberg blockade in a system of three atoms arranged in different 2D geometries (linear and triangular configurations). In the strong blockade regime, we observe high-contrast, coherent collective oscillations of the single excitation probability, and an almost perfect van der Waals blockade. Our data is consistent with a total population in doubly and triply excited states below 2%. In the partial blockade regime, we directly observe the anisotropy of the van der Waals interactions between $|nD\\rangle$ Rydberg states in the triangular configuration. A simple model, that only uses independently measured two-body van der Waals interactions, fully reproduces the dynamics of the system without any adjustable parameter. These results are extremely promising for scalable quantum information processing and quantum simulation with neutral atoms.

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

    CERN Document Server

    Tscherbul, Timur V; Buchachenko, Alexei A

    2015-01-01

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

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

    Science.gov (United States)

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

    2015-04-01

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

  13. Long-Range Atom--Wall Interactions and Mixing Terms: Metastable Hydrogen

    CERN Document Server

    Jentschura, U D

    2015-01-01

    We investigate the interaction of metastable 2S hydrogen atoms with a perfectly conducting wall, including parity-breaking S-P mixing terms (with full account of retardation). The neighboring 2P_1/2 and 2P_3/2 levels are found to have a profound effect on the transition from the short-range, nonrelativistic regime, to the retarded form of the Casimir-Polder interaction. The corresponding P state admixtures to the metastable 2S state are calculated. We find the long-range asymptotics of the retarded Casimir-Polder potentials and mixing amplitudes, for general excited states, including a fully quantum electrodynamic treatment of the dipole-quadrupole mixing term. The decay width of the metastable 2S state is roughly doubled even at a comparatively large distance of 918 atomic units (Bohr radii) from the perfect conductor. The magnitude of the calculated effects is compared to the unexplained Sokolov effect.

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

    Directory of Open Access Journals (Sweden)

    Tejbir Singh

    2013-08-01

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

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

    Science.gov (United States)

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

    2010-05-01

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

  16. 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.

  17. Interaction-based nonlinear quantum metrology with a cold atomic ensemble

    OpenAIRE

    2014-01-01

    In this manuscript we present an experimental and theoretical investigation of quantum-noise-limited measurement by nonlinear interferometry, or from another perspective, quantum-noise-limited interaction-based measurement. The experimental work is performed using a polarization-based quantum interface between propagating light pulses and cold rubidium-87 atoms trapped in an optical dipole trap. We first review the theory of quantum metrology and estimation theory, and we describe theor...

  18. 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.

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

    Directory of Open Access Journals (Sweden)

    Kimberly Glass

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

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

    Science.gov (United States)

    Glass, Kimberly; Huttenhower, Curtis; Quackenbush, John; Yuan, Guo-Cheng

    2013-01-01

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

  1. 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.

  2. Effective atomic numbers, electron densities and kinetic energy released in matter of vitamins for photon interaction

    Science.gov (United States)

    Shantappa, A.; Hanagodimath, S. M.

    2014-01-01

    Effective atomic numbers, electron densities of some vitamins (Retinol, Riboflavin, Niacin, Biotin, Folic acid, Cobalamin, Phylloquinone and Flavonoids) composed of C, H, O, N, Co, P and S have been calculated for total and partial photon interactions by the direct method for energy range 1 keV-100 GeV by using WinXCOM and kinetic energy released in matter (Kerma) relative to air is calculated in energy range of 1 keV-20 MeV. Change in effective atomic number and electron density with energy is calculated for all photon interactions. Variation of photon mass attenuation coefficients with energy are shown graphically only for total photon interaction. It is observed that change in mass attenuation coefficient with composition of different chemicals is very large below 100 keV and moderate between 100 keV and 10 MeV and negligible above 10 MeV. Behaviour of vitamins is almost indistinguishable except biotin and cobalamin because of large range of atomic numbers from 1(H) to 16 (S) and 1(H) to 27(Co) respectively. K a value shows a peak due to the photoelectric effect around K-absorption edge of high- Z constituent of compound for biotin and cobalamin.

  3. 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...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-06-15

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

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

    CERN Document Server

    Flambaum, V V

    2016-01-01

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

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

    DEFF Research Database (Denmark)

    Bruun, Georg Morten; Pethick, C. J.

    2011-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2008-01-01

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

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

    Science.gov (United States)

    Saffman, M.

    2016-10-01

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

  9. Cold Atom Physics Using Ultra-Thin Optical Fibers: Light-Induced Dipole Forces and Surface Interactions

    CERN Document Server

    Sagu'e, G; Meschede, D; Rauschenbeutel, A; Vetsch, E

    2007-01-01

    The strong evanescent field around ultra-thin unclad optical fibers bears a high potential for detecting, trapping, and manipulating cold atoms. Introducing such a fiber into a cold atom cloud, we investigate the interaction of a small number of cold Caesium atoms with the guided fiber mode and with the fiber surface. Using high resolution spectroscopy, we observe and analyze light-induced dipole forces, van der Waals interaction, and a significant enhancement of the spontaneous emission rate of the atoms. The latter can be assigned to the modification of the vacuum modes by the fiber.

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

    Institute of Scientific and Technical Information of China (English)

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

    2008-01-01

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

  11. 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.

  12. Atomic Force Microscopy Study of the Interactions of Indolicidin with Model Membranes and DNA.

    Science.gov (United States)

    Fojan, Peter; Gurevich, Leonid

    2017-01-01

    The cell membrane is the first barrier and quite often the primary target that antimicrobial peptides (AMPs) have to destroy or penetrate to fulfill their mission. Upon penetrating through the membrane, the peptides can further attack intracellular targets, in particular DNA. Studying the interaction of an antimicrobial peptide with a cell membrane and DNA holds keys to understanding its killing mechanisms. Commonly, these interactions are studied by using optical or scanning electron microscopy and appropriately labeled peptides. However, labeling can significantly affect the hydrophobicity, conformation, and size of the peptide, hence altering the interaction significantly. Here, we describe the use of atomic force microscopy (AFM) for a label-free study of the interactions of peptides with model membranes under physiological conditions and DNA as a possible intracellular target.

  13. Identifying dysregulated pathways in cancers from pathway interaction networks

    Directory of Open Access Journals (Sweden)

    Liu Ke-Qin

    2012-06-01

    Full Text Available Abstract Background Cancers, a group of multifactorial complex diseases, are generally caused by mutation of multiple genes or dysregulation of pathways. Identifying biomarkers that can characterize cancers would help to understand and diagnose cancers. Traditional computational methods that detect genes differentially expressed between cancer and normal samples fail to work due to small sample size and independent assumption among genes. On the other hand, genes work in concert to perform their functions. Therefore, it is expected that dysregulated pathways will serve as better biomarkers compared with single genes. Results In this paper, we propose a novel approach to identify dysregulated pathways in cancer based on a pathway interaction network. Our contribution is three-fold. Firstly, we present a new method to construct pathway interaction network based on gene expression, protein-protein interactions and cellular pathways. Secondly, the identification of dysregulated pathways in cancer is treated as a feature selection problem, which is biologically reasonable and easy to interpret. Thirdly, the dysregulated pathways are identified as subnetworks from the pathway interaction networks, where the subnetworks characterize very well the functional dependency or crosstalk between pathways. The benchmarking results on several distinct cancer datasets demonstrate that our method can obtain more reliable and accurate results compared with existing state of the art methods. Further functional analysis and independent literature evidence also confirm that our identified potential pathogenic pathways are biologically reasonable, indicating the effectiveness of our method. Conclusions Dysregulated pathways can serve as better biomarkers compared with single genes. In this work, by utilizing pathway interaction networks and gene expression data, we propose a novel approach that effectively identifies dysregulated pathways, which can not only be used

  14. Note: Artificial neural networks for the automated analysis of force map data in atomic force microscopy

    Science.gov (United States)

    Braunsmann, Christoph; Schäffer, Tilman E.

    2014-05-01

    Force curves recorded with the atomic force microscope on structured samples often show an irregular force versus indentation behavior. An analysis of such curves using standard contact models (e.g., the Sneddon model) would generate inaccurate Young's moduli. A critical inspection of the force curve shape is therefore necessary for estimating the reliability of the generated Young's modulus. We used a trained artificial neural network to automatically recognize curves of "good" and of "bad" quality. This is especially useful for improving the analysis of force maps that consist of a large number of force curves.

  15. Comparison and evaluation of network clustering algorithms applied to genetic interaction networks.

    Science.gov (United States)

    Hou, Lin; Wang, Lin; Berg, Arthur; Qian, Minping; Zhu, Yunping; Li, Fangting; Deng, Minghua

    2012-01-01

    The goal of network clustering algorithms detect dense clusters in a network, and provide a first step towards the understanding of large scale biological networks. With numerous recent advances in biotechnologies, large-scale genetic interactions are widely available, but there is a limited understanding of which clustering algorithms may be most effective. In order to address this problem, we conducted a systematic study to compare and evaluate six clustering algorithms in analyzing genetic interaction networks, and investigated influencing factors in choosing algorithms. The algorithms considered in this comparison include hierarchical clustering, topological overlap matrix, bi-clustering, Markov clustering, Bayesian discriminant analysis based community detection, and variational Bayes approach to modularity. Both experimentally identified and synthetically constructed networks were used in this comparison. The accuracy of the algorithms is measured by the Jaccard index in comparing predicted gene modules with benchmark gene sets. The results suggest that the choice differs according to the network topology and evaluation criteria. Hierarchical clustering showed to be best at predicting protein complexes; Bayesian discriminant analysis based community detection proved best under epistatic miniarray profile (EMAP) datasets; the variational Bayes approach to modularity was noticeably better than the other algorithms in the genome-scale networks.

  16. Self-Trapping State and Atomic Tunnelling Current of an Atomic Bose-Einstein Condensate Interacting with a Laser Field in a Double-Well Potential

    Institute of Scientific and Technical Information of China (English)

    YU Zhao-Xian; JIAO Zhi-Yong

    2002-01-01

    We present a theoretical treatment of dynamics of an atomic Bose-Einstein condensation interacting witha single-mode quantized travelling-wave laser field in a double-well potential. When the atom-field system is initiallyin a coherent state, expressions for the energy exchange between atoms and photons are derived. It is revealed thatatoms in the two wells can be in a self-trapping state when the tunnelling frequency satisfies two specific conditions,in which the resonant and far off-resonant cases are included. It is found that there is an alternating current with twodifferent sinusoidal oscillations between the two wells, but no dc characteristic of the atomic tunnelling current occurs.It should be emphasized that when without the laser field, both the population difference and the atomic tunnellingcurrent are only a single oscillation. But they will respectively become a superposition of two oscillations with differentoscillatory frequencies in the presence of the laser field. For the two oscillations of the population difference, one alwayshas an increment in the oscillatory frequency, the other can have an increment or a decrease under different cases. Theseconclusions are also suitable to those of the atomic tunnelling current. As a possible application, by measurement of theatomic tunnelling current between the two wells, the number of Bose-condensed atoms can be evaluated. lBy properlyselecting the laser field, the expected atomic tunnelling current can be obtained too.

  17. [The interaction between nerve cells and carbon nanotube networks made by CVD process investigation].

    Science.gov (United States)

    Bobrinetskiĭ, I I; Seleznev, A S; Gaĭduchenko, I A; Fedorov, G E; Domantovskiĭ, A G; Presniakov, M Iu; Podcherniaeva, R Ia; Mikhaĭlova, G R; Suetina, I A

    2013-01-01

    In this research we investigate neuroblastoma cells cultivated on single-walled carbon nanotubes networks made by CVD method on silicon substrates. The complex analysis of grown cells made by atomic force, electron microscopy and Raman spectroscopy was carried out and the effect of nanotube growth process on proliferation factor was investigated. It is shown that despite of a weak decrease in proliferation, cell morphology remains unchanged and no physical or chemical interaction between carbon nanotubes and cells is observed. The results of the research can be used to investigate the interaction between conductive nanomaterials and cells for the development of neural replacement implants. Also they can be useful in bio-electronic interface investigation of signal propagation in neurons.

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

    DEFF Research Database (Denmark)

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

    2005-01-01

    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...... (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...... hundreds of linear motifs yet to be discovered that will give molecular insight into protein networks and greatly illuminate cellular processes....

  19. Topology-free querying of protein interaction networks.

    Science.gov (United States)

    Bruckner, Sharon; Hüffner, Falk; Karp, Richard M; Shamir, Ron; Sharan, Roded

    2010-03-01

    In the network querying problem, one is given a protein complex or pathway of species A and a protein-protein interaction network of species B; the goal is to identify subnetworks of B that are similar to the query in terms of sequence, topology, or both. Existing approaches mostly depend on knowledge of the interaction topology of the query in the network of species A; however, in practice, this topology is often not known. To address this problem, we develop a topology-free querying algorithm, which we call Torque. Given a query, represented as a set of proteins, Torque seeks a matching set of proteins that are sequence-similar to the query proteins and span a connected region of the network, while allowing both insertions and deletions. The algorithm uses alternatively dynamic programming and integer linear programming for the search task. We test Torque with queries from yeast, fly, and human, where we compare it to the QNet topology-based approach, and with queries from less studied species, where only topology-free algorithms apply. Torque detects many more matches than QNet, while giving results that are highly functionally coherent.

  20. Reconstituting Protein Interaction Networks Using Parameter-Dependent Domain-Domain Interactions

    Science.gov (United States)

    2013-05-07

    that approximately 80% of eukaryotic proteins and 67% of prokaryotic proteins have multiple domains [13,14]. Most annotation databases characterize...domain annotations, Domain-domain interactions, Protein-protein interaction networks Background The living cell is a dynamic, interconnected system...detailed in Methods. Here, we illustrate its application on a well- annotated single- cell organism. We created a merged set of protein-domain annotations

  1. 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......, and by doing so they create in humans what in modern play theory is known as a “state of play”...

  2. Weighted protein interaction network analysis of frontotemporal dementia\\ud

    OpenAIRE

    Ferrari, Raffaele; Lovering, Ruth C.; Hardy, John; Lewis, Patrick A.; Manzoni, Claudia

    2016-01-01

    The genetic analysis of complex disorders has undoubtedly led to the identification of a wealth of associations between genes and specific traits. However, moving from genetics to biochemistry one gene at a time has, to date, rather proved inefficient and under-powered to comprehensively explain the molecular basis of phenotypes. Here we present a novel approach, weighted protein−protein\\ud interaction network analysis (W-PPI-NA), to highlight key functional players within relevant biological...

  3. 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.

  4. Interactions between synaptic vesicle fusion proteins explored by atomic force microscopy.

    Science.gov (United States)

    Yersin, A; Hirling, H; Steiner, P; Magnin, S; Regazzi, R; Hüni, B; Huguenot, P; De los Rios, P; Dietler, G; Catsicas, S; Kasas, S

    2003-07-22

    Measuring the biophysical properties of macromolecular complexes at work is a major challenge of modern biology. The protein complex composed of vesicle-associated membrane protein 2, synaptosomal-associated protein of 25 kDa, and syntaxin 1 [soluble N-ethyl-maleimide-sensitive factor attachment protein receptor (SNARE) complex] is essential for docking and fusion of neurotransmitter-filled synaptic vesicles with the presynaptic membrane. To better understand the fusion mechanisms, we reconstituted the synaptic SNARE complex in the imaging chamber of an atomic force microscope and measured the interaction forces between its components. Each protein was tested against the two others, taken either individually or as binary complexes. This approach allowed us to determine specific interaction forces and dissociation kinetics of the SNAREs and led us to propose a sequence of interactions. A theoretical model based on our measurements suggests that a minimum of four complexes is probably necessary for fusion to occur. We also showed that the regulatory protein neuronal Sec1 injected into the atomic force microscope chamber prevented the complex formation. Finally, we measured the effect of tetanus toxin protease on the SNARE complex and its activity by on-line registration during tetanus toxin injection. These experiments provide a basis for the functional study of protein microdomains and also suggest opportunities for sensitive screening of drugs that can modulate protein-protein interactions.

  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. Accessing electronic and vibronic quanta and their coherent interactions in atomically precise nanostructures

    Science.gov (United States)

    Zeltzer, Gabriel

    In condensed matter systems the spatial limit is given by the fundamental atomic and molecular interactions. Controlling matter at these length scales hold promise in both fundamental scientific research as well as applications in nanotechnology and related fields such as electronics, biochemistry and medicine. Atomic and molecular manipulation on surfaces has opened a new realm of possibilities where materials can be engineered at the spatial limit and artificial structures can be constructed with a bottom-up approach, one building block at a time. This thesis describes nanostructures assembled from CO molecules on Cu(111) using a custom-built low-temperature ultra-high vacuum (UHV) scanning tunneling microscope (STM). The design and performance of the atom-manipulation apparatus that has enabled these experiments is presented. The control of electronic and vibronic states is demonstrated in several coherent quantum geometries and interactions between these two degrees of freedom are investigated. This work has revealed a virtual vibron process where non-local vibrons are synthesized and focused using a two-dimensional electron gas as a propagation medium and molecular oscillators as a source. Analysis of higher order harmonic modes of quartz tuning fork sensors is presented in the context of high frequency optical homodyne interferometric detection of subnanometer oscillatory motion. Further developments which could expand upon the work presented herein, in which STM may be combined with quantum force sensing through the use of quartz tuning forks, are suggested.

  7. 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...

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

    Science.gov (United States)

    Taber, Keith S.

    2013-08-01

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

  9. 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

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

    NARCIS (Netherlands)

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

    2009-01-01

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

  11. 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.

  12. Probing the interactions between lignin and inorganic oxides using atomic force microscopy

    Science.gov (United States)

    Wang, Jingyu; Qian, Yong; Deng, Yonghong; Liu, Di; Li, Hao; Qiu, Xueqing

    2016-12-01

    Understanding the interactions between lignin and inorganic oxides has both fundamental and practical importance in industrial and energy fields. In this work, the specific interactions between alkali lignin (AL) and three inorganic oxide substrates in aqueous environment are quantitatively measured using atomic force microscopy (AFM). The results show that the average adhesion force between AL and metal oxide such as Al2O3 or MgO is nearly two times bigger than that between AL and nonmetal oxide such as SiO2 due to the electrostatic difference and cation-π interaction. When 83% hydroxyl groups of AL is blocked by acetylation, the adhesion forces between AL and Al2O3, MgO and SiO2 decrease 43, 35 and 75% respectively, which indicate hydrogen bonds play an important role between AL and inorganic oxides, especially in AL-silica system.

  13. 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.

  14. Laser-material interaction during atom probe tomography of oxides with embedded metal nanoparticles

    Science.gov (United States)

    Shinde, D.; Arnoldi, L.; Devaraj, A.; Vella, A.

    2016-10-01

    Oxide-supported metal nano-particles are of great interest in catalysis but also in the development of new large-spectrum-absorption materials. The design of such nano materials requires three-dimensional characterization with a high spatial resolution and elemental selectivity. The laser assisted Atom Probe Tomography (La-APT) presents both these capacities if an accurate understanding of laser-material interaction is developed. In this paper, we focus on the fundamental physics of field evaporation as a function of sample geometry, laser power, and DC electric field for Au nanoparticles embedded in MgO. By understanding the laser-material interaction through experiments and a theoretical model of heat diffusion inside the sample after the interaction with laser pulse, we point out the physical origin of the noise and determine the conditions to reduce it by more than one order of magnitude, improving the sensitivity of the La-APT for metal-dielectric composites.

  15. 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.

  16. 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.

  17. Probing spin-orbit-interaction-induced electron dynamics in the carbon atom by multiphoton ionization

    Science.gov (United States)

    Rey, H. F.; van der Hart, H. W.

    2014-09-01

    We use R-matrix theory with time dependence (RMT) to investigate multiphoton ionization of ground-state atomic carbon with initial orbital magnetic quantum number ML=0 and ML=1 at a laser wavelength of 390 nm and peak intensity of 1014W/cm2. Significant differences in ionization yield and ejected-electron momentum distribution are observed between the two values for ML. 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 ML=0, the dynamics with respect to time delay of an ionizing probe pulse modeled by using RMT theory is found to be in good agreement with available experimental data.

  18. Three-body bound states in dipole-dipole interacting Rydberg atoms

    CERN Document Server

    Kiffner, Martin; Jaksch, Dieter

    2013-01-01

    We show that the dipole-dipole interaction between three identical Rydberg atoms can give rise to bound trimer states. The microscopic origin of these states is fundamentally different from Efimov physics. Two stable trimer configurations exist where the atoms form the vertices of an equilateral triangle in a plane perpendicular to a static electric field. The triangle edge length typically exceeds $R\\approx 2\\,\\mu\\text{m}$, and each configuration is two-fold degenerate due to Kramers' degeneracy. The depth of the potential wells and the triangle edge length can be controlled by external parameters. We establish the Borromean nature of the trimer states, analyze the quantum dynamics in the potential wells and describe methods for their production and detection.

  19. Probing the short range spin dependent interactions by polarized {sup 3}He atom beams

    Energy Technology Data Exchange (ETDEWEB)

    Yan, H. [China Academy of Engineering Physics, Institute of Nuclear Physics and Chemistry, Mianyang, Sichuan (China); Indiana University, Center for Exploration of Energy and Matter, Bloomington, IN (United States); Sun, G.A.; Gong, J.; Pang, B.B.; Wang, Y.; Yang, Y.W.; Zhang, J.; Zhang, Y. [China Academy of Engineering Physics, Institute of Nuclear Physics and Chemistry, Mianyang, Sichuan (China)

    2014-10-15

    Experiments using polarized {sup 3}He atom beams to search for short range spin dependent forces are proposed. High intensity, high polarization, small beam size {sup 3}He atom beams have been successfully produced and used in surface science researches. By incorporating background reduction designs as combination shielding by μ-metal and superconductor and double beam paths, the precision of spin rotation angle per unit length could be improved by a factor of ∝ 10{sup 4}. By this precision, in combination with a high density and low magnetic susceptibility sample source mass, and reversing one beam path if necessary, sensitivities on three different types of spin dependent interactions could be improved by as much as ∝ 10{sup 2} to ∝ 10{sup 8} over the current experiments at the millimeter range. (orig.)

  20. Self—Trapping State and Atomic Tunnelling Current of an Atomic Bose—Einstein Condensate Interacting with a Laser Field in a Double—Well Potential

    Institute of Scientific and Technical Information of China (English)

    YUZhao-Xian; JIAOZhi-Yong

    2002-01-01

    We present a theoretical treatment of dynamics of an atomic Bose-Einstein condensation interacting with a single-mode quantized travelling-wave laser field in a double-well potential.When the atom-field system is initially in a coherent state,expressions for the energy exchange between atoms and photons are derived.It is revealed that atoms in the two wells can be in a self-trapping state when the tunnelling frequency satisfies two specific conditions,in which the resonant and far off-resonant cases are included.It is found that there is an alternating current with two different sinusoidal oscillations between the two wells,but no dc characteristic of the atomic tunnelling current occurs.It should be emphasized that when without the laser field,both the population difference and the atomic tunnelling current are only a single oscillation.But they will respectively become a superposition of two oscillations with different oscillatory frequencies in the presence of the laser field.For the two oscillations of the population difference,one always has an increment in the oscillatory frequency,the other can have an increment or a decrease under different cases.These conclusions are also suitable to those of the atomic tunnelling current.As a possible application,by measurement of the atomic tunnelling current between the two wells,the number of Bose-condensed atoms can be evaluated.By poperly selecting the laser field,the expected atomic tunnelling current can be obtained too.

  1. 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…

  2. 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.

  3. 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.

  4. GPGPU Approach: Simulation of the Interaction of Heavy Interstellar Atoms with the Heliosphere

    Science.gov (United States)

    DeStefano, A.

    2014-12-01

    Running simulations is an involved process taking many hours of computational time to complete. With the advent of cluster computing and parallel processing, problems may be solved in much less time compared to those run in serial. Specifically, NVIDIA released the parallel computing platform CUDA in 2007 giving researchers and programmers access to the GPU to solve generalized problems, and not those of just images.In current research, code has previously been developed to study the interaction of the heliosphere and heavy atoms from the local interstellar medium.Ionized species of hydrogen, helium and other heavy atoms are deflected by the heliosphere where as the neutral species are relatively unimpeded. Charge exchange of these neutral particles may occur between ionized species originating from the solar wind or other populations of pickup ions (PUI) modifying the shape and properties of the heliosphere, compared to one without neutrals. The details of the charge exchange interaction are element dependent and need to be investigated one by one. Current research has studied the interaction of local interstellar hydrogen with the heliosphere quite extensively with theory, simulations and modeling.Since hydrogen is the most abundant element care must be taken when coupling MHD equations with the charge exchange interactions. Simulation code has been developed to account for this dynamic problem and they have shown that the shape of the heliosphere is affected by this. Interstellar atoms heavier than hydrogen interacting with the heliosphere has been looked at as well, but not nearly with as much detail or sophisticated models as hydrogen. The heavy atom data collected by IBEX has in this sense been under-utilized by models.Previously, the simulation was computed with the use of MPI (Message Passing Interface) for parallelization. This approach provided a decrease in computational time. However, CUDA enables the programmer to take advantage of the computer

  5. Protein-protein interaction network of celiac disease

    Science.gov (United States)

    Zamanian Azodi, Mona; Peyvandi, Hassan; Rostami-Nejad, Mohammad; Safaei, Akram; Rostami, Kamran; Vafaee, Reza; Heidari, Mohammadhossein; Hosseini, Mostafa; Zali, Mohammad Reza

    2016-01-01

    Aim: The aim of this study is to investigate the Protein-Protein Interaction Network of Celiac Disease. Background: Celiac disease (CD) is an autoimmune disease with susceptibility of individuals to gluten of wheat, rye and barley. Understanding the molecular mechanisms and involved pathway may lead to the development of drug target discovery. The protein interaction network is one of the supportive fields to discover the pathogenesis biomarkers for celiac disease. Material and methods: In the present study, we collected the articles that focused on the proteomic data in celiac disease. According to the gene expression investigations of these articles, 31 candidate proteins were selected for this study. The networks of related differentially expressed protein were explored using Cytoscape 3.3 and the PPI analysis methods such as MCODE and ClueGO. Results: According to the network analysis Ubiquitin C, Heat shock protein 90kDa alpha (cytosolic and Grp94); class A, B and 1 member, Heat shock 70kDa protein, and protein 5 (glucose-regulated protein, 78kDa), T-complex, Chaperon in containing TCP1; subunit 7 (beta) and subunit 4 (delta) and subunit 2 (beta), have been introduced as hub-bottlnecks proteins. HSP90AA1, MKKS, EZR, HSPA14, APOB and CAD have been determined as seed proteins. Conclusion: Chaperons have a bold presentation in curtail area in network therefore these key proteins beside the other hub-bottlneck proteins may be a suitable candidates biomarker panel for diagnosis, prognosis and treatment processes in celiac disease. PMID:27895852

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

    Directory of Open Access Journals (Sweden)

    Brinda KV

    2005-12-01

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

  7. Lightweight Interactions for Reciprocal Cooperation in a Social Network Game

    CERN Document Server

    Takano, Masanori; Fukuda, Ichiro

    2016-01-01

    The construction of reciprocal relationships requires cooperative interactions during the initial meetings. However, cooperative behavior with strangers is risky because the strangers may be exploiters. In this study, we show that people increase the likelihood of cooperativeness of strangers by using lightweight non-risky interactions in risky situations based on the analysis of a social network game (SNG). They can construct reciprocal relationships in this manner. The interactions involve low-cost signaling because they are not generated at any cost to the senders and recipients. Theoretical studies show that low-cost signals are not guaranteed to be reliable because the low-cost signals from senders can lie at any time. However, people used low-cost signals to construct reciprocal relationships in an SNG, which suggests the existence of mechanisms for generating reliable, low-cost signals in human evolution.

  8. Interaction of interstitial atoms and configurational contribution to their thermodynamic activity in V, Nb, and Ta

    Science.gov (United States)

    Blanter, M. S.; Dmitriev, V. V.; Mogutnov, B. M.; Ruban, A. V.

    2017-02-01

    The pairwise interaction energies of O-O and N-N in bcc metals of group VB, which were calculated earlier using first-principles methods, have been employed to analyze the effect of the interatomic interactions on the configurational contribution to the thermodynamic activity. The strong effect of interstitial- interstitial interaction has been shown. The configurational contribution grows in the row (Nb-N) → (V-N) → (Ta-N) → (Nb-O) → (V-O) → (Ta-O), which is caused by a weakening of the mutual attraction of interstitial atoms in these solid solutions. The strong repulsion that characterizes the majority of coordination shells only weakly affects the thermodynamic activity. The character of the temperature dependence of the configurational contribution is defined by the strength of the mutual attraction of the interstitial atoms, i.e., upon strong attraction, the contribution increases with increasing temperature (Nb-N, V-N, Ta-N, and Nb-O) and, upon weak attraction, it decreases (V-O and Ta-O).

  9. Supramolecular assembly of 2,4,5-trifluorobenzoate complex based on weak interactions involving fluorine atoms

    Institute of Scientific and Technical Information of China (English)

    Chun-Hua Ge; Rui Zhang; Ping Fan; Xiang-Dong Zhang; Li-Juan Wang; Fang-Fang Wang

    2013-01-01

    The complex [Cd(tfbz)2(phen)]2 (1) (tfbz =2,4,5-trifluorobenzoate,phen =1,10-phenanthro-line) was synthesized using trifluorobenzoic acid ligand.The single-crystal structure of 1 has been determined by X-ray crystallography.The packing structure is characterized by the formation of an intricate three-dimensional supramolecular network that depends on the C-H…F,F…F, F(lp)…π (lp =lone pair) interactions.

  10. 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

  11. 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.

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

    Directory of Open Access Journals (Sweden)

    Paul Pawelzyk

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

  13. Interaction of atomic hydrogen with anthracene and polyacene from density functional theory

    Science.gov (United States)

    Ferullo, Ricardo M.; Castellani, Norberto J.; Belelli, Patricia G.

    2016-03-01

    The interaction of atomic hydrogen with two linear polycyclic aromatic hydrocarbons (PAHs), anthracene and polyacene (the polymer of benzene), was studied within the density functional theory (DFT). Using a proper dispersion-corrected method (DFT-D) the preferential physisorption sites were explored. The activation barrier for the bond formation between a peripheral C and the incoming H was calculated to be 58.5 and 34.1 meV with pure DFT on anthracene and polyacene at its antiferromagnetic ground state, respectively. DFT-D, although improves the description of the physisorbed state, tends to underestimate the chemisorption barriers due an artifact arising from the dispersion correction.

  14. Visualization of interaction between ribosome-inactivating proteins and supercoiled DNA with an atomic force microscope

    Institute of Scientific and Technical Information of China (English)

    吴晓华; 刘望夷; 欧阳振乾; 李民乾

    1997-01-01

    The interaction between ribosome-inactivating proteins (RIPs) and supercoiled DNA was observed with an atomic force microscope (AFM). It was found that RIPs can bind to both supercoiled DNA and the unwound double stranded loop region in supercoiled DNA. The RIPs hound to the supercoils can induce the conformational change of supercoiled DNA. Furthermore, the supercoiled DNA was relaxed and cleaved into nick or linear form by RIPs. It indicated that RIP seemed to be a supercoil-dependent DNA binding protein and exhibited the activity of su-percoil-dependent DNA endonuclease.

  15. Probing molecular interaction between transferrin and anti-transferrin by atomic force microscope

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    The interaction between transferrin (Tf) and its antibody was investigated by atomic force microscope. Tf-antibody was immobilized on the Au-coated glass slide, and the specific combination between antibody and antigen was also characterized by AFM. The results showed that holo-transferrin was jogged with anti-transferrin, and binded anti-tran- sferrin more tightly than apo-transferrin. The force- distance curves revealed that the affinity of anti-trans- ferrin and holo-transferrin was much stronger than that of apo-transferrin.

  16. Two interacting atoms in a cavity: exact solutions, entanglement and decoherence

    Energy Technology Data Exchange (ETDEWEB)

    Torres, J M; SadurnI, E; Seligman, T H, E-mail: mau@fis.unam.m [Instituto de Ciencias FIsicas, Universidad Nacional Autonoma de Mexico, CP 62210 Cuernavaca, Morelos (Mexico)

    2010-05-14

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

  17. Molecular ions in ultracold atomic gases: computed electronic interactions for \\MgHion with Rb

    CERN Document Server

    Tacconi, Mario

    2007-01-01

    The electronic structures of the manifold of potential energy surfaces generated in the lower energy range by the interaction of the MgH$^+$(X$^1\\Sigma^+$) cationic molecule with Rb($^2$S), neutral atom are obtained over a broad range of Jacobi coordinates from strongly correlated \\emph{ab initio} calculations which use a Multireference (MR) wavefunction within a Complete Active Space (CAS) approach. The relative features of the lowest five surfaces are analyzed in terms of possible collisional outcomes when employed to model the ultracold dynamics of ionic molecular partners.

  18. MiRTargetLink--miRNAs, Genes and Interaction Networks.

    Science.gov (United States)

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

    2016-04-14

    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.

  19. Interaction of atomic hydrogen with pico- and femtosecond laser pulses. Technical report

    Energy Technology Data Exchange (ETDEWEB)

    Parker, J.S.

    1989-12-01

    This thesis presents a theoretical study of the interaction of atomic hydrogen with coherent laser pulses in the 5 femtosecond to 10 picosecond range, in the weak-field limit, and in intense fields. We approach the problem in the weak-field limit by studying the relationship between the Fourier relation of the laser pulse (Delta omega Delta t) and the (Delta E Delta t) relation of the atomic Rydberg wave packet generated by the laser pulse. A derivation of the wave packet based on the WKB approximation is given, permitting the quantity Delta t to be derived for the quantum state, with the conclusion that under certain circumstances a transform-limited laser pulse (satisfying Delta omega Delta t = 1/2) can generate a transform-limited electron (satisfying Delta E Delta t/h = 1/2). A population-trapping effect is found numerically and modeled theoretically. Despite the high field intensities, population representing the excited electron is recaptured from the ionization continuum by bound states during the excitation. Population returns to the atom with just the right phase to strongly inhibit ionization. A theory is presented that models this effect for a variety of laser pulse shapes, with and without the rotating-wave approximation. The numerical integration reveals that a certain amount of above-threshold ionization (ATI) occurs.

  20. Dispersion C3 coefficients for the alkali-metal atoms interacting with a graphene layer and with a carbon nanotube

    CERN Document Server

    Arora, Bindiya; Sahoo, B K

    2013-01-01

    We evaluate separation dependent van der Waal dispersion ($C_3$) coefficients for the interactions of the Li, Na, K and Rb alkali 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 atoms. Accountability of these accurate values of dynamical polarizabilities of the alkali atoms in determination of the above $C_3$ coefficients are accentuated by comparing them with the coefficients evaluated using the dynamic dipole polarizabilities estimated from the single oscillator approximation which are typically employed in the earlier calculations. For practical description of the atom-surface interaction potentials the radial dependent $C_3$ coefficients are given for a wide range of separation distances between the ground states of the considered atoms and the wall surfaces and also for different values of nanotube radii. The coefficients for...

  1. Probing the interaction of individual amino acids with inorganic surfaces using atomic force spectroscopy.

    Science.gov (United States)

    Razvag, Yair; Gutkin, Vitaly; Reches, Meital

    2013-08-13

    This article describes single-molecule force spectroscopy measurements of the interaction between individual amino acid residues and inorganic surfaces in an aqueous solution. In each measurement, there is an amino acid residue, lysine, glutamate, phenylalanine, leucine, or glutamine, and each represents a class of amino acids (positively or negatively charged, aromatic, nonpolar, and polar). Force-distance curves measured the interaction of the individual amino acid bound to a silicon atomic force microscope (AFM) tip with a silcon substrate, cut from a single-crystal wafer, or mica. Using this method, we were able to measure low adhesion forces (below 300 pN) and could clearly determine the strength of interactions between the individual amino acid residues and the inorganic substrate. In addition, we observed how changes in the pH and ionic strength of the solution affected the adsorption of the residues to the substrates. Our results pinpoint the important role of hydrophobic interactions among the amino acids and the substrate, where hydrophobic phenylalanine exhibited the strongest adhesion to a silicon substrate. Additionally, electrostatic interactions also contributed to the adsorption of amino acid residues to inorganic substrates. A change in the pH or ionic strength values of the buffer altered the strength of interactions among the amino acids and the substrate. We concluded that the interplay between the hydrophobic forces and electrostatic interactions will determine the strength of adsorption among the amino acids and the surface. Overall, these results contribute to our understanding of the interaction at the organic-inorganic interface. These results may have implications for our perception of the specificity of peptide binding to inorganic surfaces. Consequently, it would possibly lead to a better design of composite materials and devices.

  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. 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.

  4. 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.

  5. Quantum Networks with Chiral-Light-Matter Interaction in Waveguides

    Science.gov (United States)

    Mahmoodian, Sahand; Lodahl, Peter; Sørensen, Anders S.

    2016-12-01

    We propose a scalable architecture for a quantum network based on a simple on-chip photonic circuit that performs loss-tolerant two-qubit measurements. The circuit consists of two quantum emitters positioned in the 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 perform high-fidelity intranode two-qubit parity measurements within a single chip and to emit photons to generate internode entanglement, 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 F ˜0.998 achievable in state-of-the-art quantum dot systems.

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

    Directory of Open Access Journals (Sweden)

    Martin H Schaefer

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

  7. [Novel Hyphenated Techniques of Atomic Spectrometry for Metal Species Interaction with Biomolecules].

    Science.gov (United States)

    Li, Yan; Yan, Xiu-ping

    2015-09-01

    Trace metals may be adopted by biological systems to assist in the syntheses and metabolic functions of genes (DNA and RNA) and proteins in the environment. These metals may be beneficial or may pose a risk to humans and other life forms. Novel hybrid techniques are required for studies on the interaction between different metal species and biomolecules, which is significant for biology, biochemistry, nutrition, agriculture, medicine, pharmacy, and environmental science. In recent years, our group dwells on new hyphenated techniques based on capillary electrophoresis (CE), electrothermal atomic absorption spectrometry (ETAAS), and inductively coupled plasma mass spectroscopy (ICP-MS), and their application for different metal species interaction with biomolecules such as DNA, HSA, and GSH. The CE-ETAAS assay and CE-ICP-MS assay allow sensitively probing the level of biomolecules such as DNA damage by different metal species and extracting the kinetic and thermodynamic information on the interactions of different metal species with biomolecules, provides direct evidences for the formation of different metal species--biomolecule adducts. In addition, the consequent structural information were extracted from circular dichroism (CD) and X-ray photoelectron spectroscopy (XPS), Raman spectroscopy, and Fourier transform infrared (FTIR) spectroscopy. The present works represent the most complete and extensive study to date on the interactions between different metal species with biomolecules, and also provide new evidences for and insights into the interactions of different metal species with biomolecules for further understanding of the toxicological effects of metal species.

  8. Aspects of the theory of atoms and coherent matter and their interaction with electromagnetic fields

    Energy Technology Data Exchange (ETDEWEB)

    Nilsen, Halvor Moell

    2002-07-01

    In the present work I have outlined and contributed to the time-dependent theory of the interaction between atoms and electromagnetic fields and the theory of Bose-Einstein condensates. New numerical methods and algorithms have been developed and applied in practice. Calculations have exhibited certain new dynamical features. All these calculations are in a regime where the applied field is of the same magnitude as the atomic field. In the case of BEC we have investigated the use of time-dependent methods to calculate the excitation frequencies. We also investigated the possibility of nonlinear coupling for a scissors mode and found no such contributions to damping which is consistent with other studies . Special emphasis has also been paid to the gyroscopic motion of rotating BEC where several models were investigated. Briefly, the main conclusions are: (1) Rydberg wave packets appear for direct excitations of Rydberg atoms for long pulses. (2) The survival of just a few states is decided by symmetry of the Hamiltonian. (3) For few cycle intense pulses classical and quantum mechanics show remarkable similarity. (4) Time-dependent methods for finding excitation frequencies have been shown to be very efficient. (5) New dynamical features is shown in gyroscopic motion of BEC. (6) It was shown that no nonlinear mixing of scissors modes occur in the standard Gross-Pitaevskii regime. As mentioned in the introduction, this work is a part of very active research fields and new progress is constantly reported. Thus, the present work cannot be concluded as a closed loop. The fast development of grid based numerical solutions for atoms in intense fields will surely make great contribution to solve many of today's problems. It is a very important area of research to understand both nonperturbative atomic response and highly nonlinear optics. In the field of Bose-Einstein condensation the new experimental achievements constantly drive the field forward. The new

  9. P ,T -odd electron-nucleus interaction in atomic systems as an exchange by Higgs bosons

    Science.gov (United States)

    Chubukov, D. V.; Labzowsky, L. N.

    2016-06-01

    Scalar-pseudoscalar P ,T -odd interaction between the electron and the nucleus in atomic systems is constructed within the standard model as an exchange by Higgs boson. The necessary P - and T -violating contribution is obtained at the three-loop level on the basis of Cabibbo-Kobayashi-Maskawa matrix. This contribution, unlike the corresponding contribution to the electron electric dipole moment (EDM), does not vanish since the "Higgs charges" of quarks, contrary to their electric charges, are flavor dependent. Order-of-magnitude estimates of the effect expressed as an "equivalent" electron EDM give the values within the range deeqv˜10-40-10-45e cm , depending on the known different estimates for the electron EDM. This can be compared with the known "benchmark" two-photon P ,T -odd electron-nucleus interaction effect, which provides deeqv˜10-38e cm .

  10. Indium-defect interactions in FCC and BCC metals studied using the modified embedded atom method

    Science.gov (United States)

    Zacate, M. O.

    2016-12-01

    With the aim of developing a transferable potential set capable of predicting defect formation, defect association, and diffusion properties in a wide range of intermetallic compounds, the present study was undertaken to test parameterization strategies for determining empirical pair-wise interaction parameters in the modified embedded atom method (MEAM) developed by Baskes and coworkers. This report focuses on indium-solute and indium-vacancy interactions in FCC and BCC metals, for which a large set of experimental data obtained from perturbed angular correlation measurements is available for comparison. Simulation results were found to be in good agreement with experimental values after model parameters had been adjusted to reproduce as best as possible the following two sets of quantities: (1) lattice parameters, formation enthalpies, and bulk moduli of hypothetical equiatomic compounds with the NaCl crystal structure determined using density functional theory and (2) dilute solution enthalpies in metals as predicted by Miedema's semi-empirical model.

  11. Multireference configuration interaction calculations of the first six ionization potentials of the uranium atom

    Energy Technology Data Exchange (ETDEWEB)

    Bross, David H.; Parmar, Payal; Peterson, Kirk A., E-mail: kipeters@wsu.edu [Department of Chemistry, Washington State University, Pullman, Washington 99164-4630 (United States)

    2015-11-14

    The first 6 ionization potentials (IPs) of the uranium atom have been calculated using multireference configuration interaction (MRCI+Q) with extrapolations to the complete basis set limit using new all-electron correlation consistent basis sets. The latter was carried out with the third-order Douglas-Kroll-Hess Hamiltonian. Correlation down through the 5s5p5d electrons has been taken into account, as well as contributions to the IPs due to the Lamb shift. Spin-orbit coupling contributions calculated at the 4-component Kramers restricted configuration interaction level, as well as the Gaunt term computed at the Dirac-Hartree-Fock level, were added to the best scalar relativistic results. The final ionization potentials are expected to be accurate to at least 5 kcal/mol (0.2 eV) and thus more reliable than the current experimental values of IP{sub 3} through IP{sub 6}.

  12. 2012 ATOMIC AND MOLECULAR INTERACTIONS GORDON RESEARCH CONFERENCE AND GORDON RESEARCH SEMINAR, JULY 15-20, 2012

    Energy Technology Data Exchange (ETDEWEB)

    Zwier, Timothy

    2012-07-20

    At the 2012 Atomic and Molecular Interactions Gordon Conference, there will be talks in several broadly defined and partially overlapping areas:  Intramolecular and single-collision reaction dynamics;  Photophysics and photochemistry of excited states;  Clusters, aerosols and solvation;  Interactions at interfaces;  Conformations and folding of large molecules;  Interactions under extreme conditions of temperature and pressure. The theme of the Gordon Research Seminar on Atomic & Molecular Interactions, in keeping with the tradition of the Atomic and Molecular Interactions Gordon Research Conference, is far-reaching and involves fundamental research in the gas and condensed phases along with application of these ideas to practical chemical fields. The oral presentations, which will contain a combination of both experiment and theory, will focus on four broad categories:  Ultrafast Phenomena;  Excited States, Photoelectrons, and Photoions;  Chemical Reaction Dynamics;  Biomolecules and Clusters.

  13. Human Dopamine Receptors Interaction Network (DRIN): a systems biology perspective on topology, stability and functionality of the network.

    Science.gov (United States)

    Podder, Avijit; Jatana, Nidhi; Latha, N

    2014-09-21

    Dopamine receptors (DR) are one of the major neurotransmitter receptors present in human brain. Malfunctioning of these receptors is well established to trigger many neurological and psychiatric disorders. Taking into consideration that proteins function collectively in a network for most of the biological processes, the present study is aimed to depict the interactions between all dopamine receptors following a systems biology approach. To capture comprehensive interactions of candidate proteins associated with human dopamine receptors, we performed a protein-protein interaction network (PPIN) analysis of all five receptors and their protein partners by mapping them into human interactome and constructed a human Dopamine Receptors Interaction Network (DRIN). We explored the topology of dopamine receptors as molecular network, revealing their characteristics and the role of central network elements. More to the point, a sub-network analysis was done to determine major functional clusters in human DRIN that govern key neurological pathways. Besides, interacting proteins in a pathway were characterized and prioritized based on their affinity for utmost drug molecules. The vulnerability of different networks to the dysfunction of diverse combination of components was estimated under random and direct attack scenarios. To the best of our knowledge, the current study is unique to put all five dopamine receptors together in a common interaction network and to understand the functionality of interacting proteins collectively. Our study pinpointed distinctive topological and functional properties of human dopamine receptors that have helped in identifying potential therapeutic drug targets in the dopamine interaction network.

  14. Nonlinear Dynamics of Cantilever-Sample Interactions in Atomic Force Microscopy

    Science.gov (United States)

    Cantrell, John H.; Cantrell, Sean A.

    2010-01-01

    The interaction of the cantilever tip of an atomic force microscope (AFM) with the sample surface is obtained by treating the cantilever and sample as independent systems coupled by a nonlinear force acting between the cantilever tip and a volume element of the sample surface. The volume element is subjected to a restoring force from the remainder of the sample that provides dynamical equilibrium for the combined systems. The model accounts for the positions on the cantilever of the cantilever tip, laser probe, and excitation force (if any) via a basis set of set of orthogonal functions that may be generalized to account for arbitrary cantilever shapes. The basis set is extended to include nonlinear cantilever modes. The model leads to a pair of coupled nonlinear differential equations that are solved analytically using a matrix iteration procedure. The effects of oscillatory excitation forces applied either to the cantilever or to the sample surface (or to both) are obtained from the solution set and applied to the to the assessment of phase and amplitude signals generated by various acoustic-atomic force microscope (A-AFM) modalities. The influence of bistable cantilever modes of on AFM signal generation is discussed. The effects on the cantilever-sample surface dynamics of subsurface features embedded in the sample that are perturbed by surface-generated oscillatory excitation forces and carried to the cantilever via wave propagation are accounted by the Bolef-Miller propagating wave model. Expressions pertaining to signal generation and image contrast in A-AFM are obtained and applied to amplitude modulation (intermittent contact) atomic force microscopy and resonant difference-frequency atomic force ultrasonic microscopy (RDF-AFUM). The influence of phase accumulation in A-AFM on image contrast is discussed, as is the effect of hard contact and maximum nonlinearity regimes of A-AFM operation.

  15. The Tip-Sample Interaction in Atomic Force Microscopy and its Implications for Biological Applications.

    Science.gov (United States)

    Baselt, David Randall

    This thesis describes the construction of an atomic force microscope and its application to the study of tip -sample interactions, primarily through the use of friction and hardness (elasticity) imaging. Part one describes the atomic force microscope, which consists of a scanned-cantilever stage (chapter 2); a versatile digital signal processor-based control system with self-optimizing feedback, lock-in amplifier emulation (for hardness imaging), and macro programmability (chapter 3); and image processing software (chapter 4). Part two describes a number of results that have helped to characterize the tip-sample interaction and the contact imaging modes used for its study. Meniscus forces act laterally as well as normally, and that they vary with position (chapter 5). Friction measurements couple with scanner position and feedback, and the meniscus effects friction images (chapter 6). Sliding of the tip over the sample surface introduces slope-dependence into hardness measurements (chapter 7). Dull tips can create prominent topography artifacts even on very flat surfaces (chapter 8). In an investigation of collagen fibrils, AFM has revealed the characteristic 65 nm banding pattern, a second, minor banding pattern, and microfibrils that run along the fibril axis. The distribution of proteoglycans along the fibrils creates a characteristic pattern in friction images. Although imaging in water reduces interaction forces, water can also make biological samples more sensitive to force. However, for robust biological samples imaged in air, tip shape presents a greater obstacle than tip -sample interaction forces to obtaining high-resolution images. Tip contamination increases tip-sample friction and can occasionally improve resolution (chapter 9). For a separate project I have designed a general -purpose nearfield scanning optical microscope (chapter 10).

  16. Interactions between solute atoms in Fe-Si-Al-C alloys as studied by mechanical spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Sinning, H.-R., E-mail: hr.sinning@tu-bs.de [Institut fuer Werkstoffe, Technische Universitaet Braunschweig, Braunschweig (Germany); Golovin, I.S. [Physics of Metals Department, Moscow Institute of Steel and Alloys, Moscow (Russian Federation); Physics of Metals and Materials Science Department, Tula State University, Tula (Russian Federation); Strahl, A. [Institut fuer Fachdidaktik der Naturwissenschaften, TU Braunschweig (Germany); Sokolova, O.A. [Physics of Metals and Materials Science Department, Tula State University, Tula (Russian Federation); Sazonova, T. [Institut fuer Werkstoffe, Technische Universitaet Braunschweig, Braunschweig (Germany)

    2009-09-15

    In Fe-Si-Al-C alloys, point-defect relaxation includes both the interstitial carbon Snoek-type relaxation, split into a 'pure iron' (Fe-C-Fe) Snoek peak and an 'interstitial-substitutional' (Fe-C-Me; Me = Al, Si) peak, and the substitutional Zener relaxation. The influence of Al and Si, with varying Al/Si ratio, on these effects is used to study the qualitative characteristics of substitutional-interstitial (Si-C, Al-C) and substitutional-substitutional (Al-Al, Si-Si, Al-Si) interactions in these alloys. Concerning the latter, there is a mutual compensation of the elastic distortion fields, produced in the Fe matrix by the relatively bigger Al and smaller Si atoms, respectively, which largely suppresses the Zener relaxation in the ternary Fe-Si-Al alloys, probably without affecting the elastic dipole strength of interstitial carbon. From the kinetic behavior of the two components of the Snoek-type relaxation, it is concluded that the substitutional-interstitial interaction is generally attractive and sufficient for modifying the distribution of the C atoms, but not for trapping to become dominant.

  17. Density functional theory study of nitrogen atoms and molecules interacting with Fe(1 1 1) surfaces

    Science.gov (United States)

    Nosir, M. A.; Martin-Gondre, L.; Bocan, G. A.; Díez Muiño, R.

    2016-09-01

    We present Density functional theory (DFT) calculations for the investigation of the structural relaxation of Fe(1 1 1), as well as for the study of the interaction of nitrogen atoms and molecules with this surface. We perform spin polarized DFT calculations using VASP (Vienna Ab-initio Simulation Package) code. We use the supercell approach and up to 19 slab layers for the relaxation of the Fe(1 1 1) surface. We find a contraction of the first two interlayer distances with a relative value of Δ12 = - 7.8 % and Δ23 = - 21.7 % with respect to the bulk reference. The third interlayer distance is however expanded with a relative change of Δ34 = 9.7 % . Early experimental studies of the surface relaxation using Low Energy Electron Diffraction (LEED) and Medium Energy Ion Scattering (MEIS) showed contradictory results, even on the relaxation general trend. Our current theoretical results support the LEED conclusions and are consistent qualitatively with other recent theoretical calculations. In addition, we study the interaction energy of nitrogen atoms and molecules on the Fe(1 1 1) surface. The nitrogen atoms are adsorbed in the hollow site of the unit cell, with an adsorption energy consistent with the one found in previous studies. In addition, we find the three molecularly adsorbed states that are observed experimentally. Two of them correspond to the adsorbed molecule oriented normal to the surface and a third one corresponds to the molecule adsorbed parallel to the surface. We conclude that our results are accurate enough to be used to build a full six-dimensional potential energy surface for the N2 system.

  18. Modeling dark energy through an Ising fluid with network interactions

    CERN Document Server

    Luongo, Orlando

    2013-01-01

    We show that the dark energy effects can be modeled by using an \\emph{Ising perfect fluid} with network interactions, whose low redshift equation of state, i.e. $\\omega_0$, becomes $\\omega_0=-1$ as in the $\\Lambda$CDM model. In our picture, dark energy is characterized by a barotropic fluid on a lattice in the equilibrium configuration. Thus, mimicking the spin interaction by replacing the spin variable with an occupational number, the pressure naturally becomes negative. We find that the corresponding equation of state mimics the effects of a variable dark energy term, whose limiting case reduces to the cosmological constant $\\Lambda$. This permits us to avoid the introduction of a vacuum energy as dark energy source by hand, alleviating the coincidence and fine tuning problems. We find fairly good cosmological constraints, by performing three tests with supernovae Ia, baryonic acoustic oscillation and cosmic microwave background measurements. Finally, we perform the AIC and BIC selection criteria, showing t...

  19. Messaging Performance of FIPA Interaction Protocols in Networked Embedded Controllers

    Directory of Open Access Journals (Sweden)

    García JoséAPérez

    2008-01-01

    Full Text Available Abstract Agent-based technologies in production control systems could facilitate seamless reconfiguration and integration of mechatronic devices/modules into systems. Advances in embedded controllers which are continuously improving computational capabilities allow for software modularization and distribution of decisions. Agent platforms running on embedded controllers could hide the complexity of bootstrap and communication. Therefore, it is important to investigate the messaging performance of the agents whose main motivation is the resource allocation in manufacturing systems (i.e., conveyor system. The tests were implemented using the FIPA-compliant JADE-LEAP agent platform. Agent containers were distributed through networked embedded controllers, and agents were communicating using request and contract-net FIPA interaction protocols. The test scenarios are organized in intercontainer and intracontainer communications. The work shows the messaging performance for the different test scenarios using both interaction protocols.

  20. Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network

    Directory of Open Access Journals (Sweden)

    Andrews Brenda

    2005-06-01

    Full Text Available Abstract Background Large-scale studies have revealed networks of various biological interaction types, such as protein-protein interaction, genetic interaction, transcriptional regulation, sequence homology, and expression correlation. Recurring patterns of interconnection, or 'network motifs', have revealed biological insights for networks containing either one or two types of interaction. Results To study more complex relationships involving multiple biological interaction types, we assembled an integrated Saccharomyces cerevisiae network in which nodes represent genes (or their protein products and differently colored links represent the aforementioned five biological interaction types. We examined three- and four-node interconnection patterns containing multiple interaction types and found many enriched multi-color network motifs. Furthermore, we showed that most of the motifs form 'network themes' – classes of higher-order recurring interconnection patterns that encompass multiple occurrences of network motifs. Network themes can be tied to specific biological phenomena and may represent more fundamental network design principles. Examples of network themes include a pair of protein complexes with many inter-complex genetic interactions – the 'compensatory complexes' theme. Thematic maps – networks rendered in terms of such themes – can simplify an otherwise confusing tangle of biological relationships. We show this by mapping the S. cerevisiae network in terms of two specific network themes. Conclusion Significantly enriched motifs in an integrated S. cerevisiae interaction network are often signatures of network themes, higher-order network structures that correspond to biological phenomena. Representing networks in terms of network themes provides a useful simplification of complex biological relationships.

  1. 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...

  2. Intrinsic Resolution of Molecular Electronic Wave Functions and Energies in Terms of Quasi-atoms and Their Interactions.

    Science.gov (United States)

    West, Aaron C; Schmidt, Michael W; Gordon, Mark S; Ruedenberg, Klaus

    2017-02-09

    A general intrinsic energy resolution has been formulated for strongly correlated wave functions in the full molecular valence space and its subspaces. The information regarding the quasi-atomic organization of the molecular electronic structure is extracted from the molecular wave function without introducing any additional postulated model state wave functions. To this end, the molecular wave function is expressed in terms of quasi-atomic molecular orbitals, which maximize the overlap between subspaces of the molecular orbital space and the free-atom orbital spaces. As a result, the molecular wave function becomes the superposition of a wave function representing the juxtaposed nonbonded quasi-atoms and a wave function describing the interatomic electron migrations that create bonds through electron sharing. The juxtaposed nonbonded quasi-atoms are shown to consist of entangled quasi-atomic states from different atoms. The binding energy is resolved as a sum of contributions that are due to quasi-atom formation, quasiclassical electrostatic interactions, and interatomic interferences caused by electron sharing. The contributions are further resolved according to orbital interactions. The various transformations that generate the analysis are determined by criteria that are independent of the working orbital basis used for calculating the molecular wave function. The theoretical formulation of the resolution is quantitatively validated by an application to the C2 molecule.

  3. MDM2–MDM4 molecular interaction investigated by atomic force spectroscopy and surface plasmon resonance

    Directory of Open Access Journals (Sweden)

    Moscetti I

    2016-08-01

    Full Text Available Ilaria Moscetti,1 Emanuela Teveroni,2,3 Fabiola Moretti,3 Anna Rita Bizzarri,1 Salvatore Cannistraro1 1Biophysics and Nanoscience Centre, Department DEB, Università della Tuscia, Viterbo, Italy; 2Department of Endocrinology and Metabolism, Università Cattolica di Roma, Roma, Italy; 3Institute of Cell Biology and Neurobiology, Consiglio Nazionale delle Ricerche (CNR, Roma, Italy Abstract: Murine double minute 2 (MDM2 and 4 (MDM4 are known as the main negative regulators of p53, a tumor suppressor. They are able to form heterodimers that are much more effective in the downregulation of p53. Therefore, the MDM2–MDM4 complex could be a target for promising therapeutic restoration of p53 function. To this aim, a deeper understanding of the molecular mechanisms underlining the heterodimerization is needed. The kinetic and thermodynamic characterization of the MDM2–MDM4 complex was performed with two complementary approaches: atomic force spectroscopy and surface plasmon resonance. Both techniques revealed an equilibrium dissociation constant (KD in the micromolar range for the MDM2–MDM4 heterodimer, similar to related complexes involved in the p53 network. Furthermore, the MDM2–MDM4 complex is characterized by a relatively high free energy, through a single energy barrier, and by a lifetime in the order of tens of seconds. New insights into the MDM2–MDM4 interaction could be highly important for developing innovative anticancer drugs focused on p53 reactivation. Keywords: MDM2, MDM4, atomic force spectroscopy, surface plasmon resonance

  4. 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.

  5. Accessing Wireless Sensor Networks Via Dynamically Reconfigurable Interaction Models

    Directory of Open Access Journals (Sweden)

    Maria Cecília Gomes

    2012-12-01

    Full Text Available The Wireless Sensor Networks (WSNs technology is already perceived as fundamental for science across many domains, since it provides a low cost solution for environment monitoring. WSNs representation via the service concept and its inclusion in Web environments, e.g. through Web services, supports particularly their open/standard access and integration. Although such Web enabled WSNs simplify data access, network parameterization and aggregation, the existing interaction models and run-time adaptation mechanisms available to clients are still scarce. Nevertheless, applications increasingly demand richer and more flexible accesses besides the traditional client/server. For instance, applications may require a streaming model in order to avoid sequential data requests, or the asynchronous notification of subscribed data through the publish/subscriber. Moreover, the possibility to automatically switch between such models at runtime allows applications to define flexible context-based data acquisition. To this extent, this paper discusses the relevance of the session and pattern abstractions on the design of a middleware prototype providing richer and dynamically reconfigurable interaction models to Web enabled WSNs.

  6. Coevolving complex networks in the model of social interactions

    Science.gov (United States)

    Raducha, Tomasz; Gubiec, Tomasz

    2017-04-01

    We analyze Axelrod's model of social interactions on coevolving complex networks. We introduce four extensions with different mechanisms of edge rewiring. The models are intended to catch two kinds of interactions-preferential attachment, which can be observed in scientists or actors collaborations, and local rewiring, which can be observed in friendship formation in everyday relations. Numerical simulations show that proposed dynamics can lead to the power-law distribution of nodes' degree and high value of the clustering coefficient, while still retaining the small-world effect in three models. All models are characterized by two phase transitions of a different nature. In case of local rewiring we obtain order-disorder discontinuous phase transition even in the thermodynamic limit, while in case of long-distance switching discontinuity disappears in the thermodynamic limit, leaving one continuous phase transition. In addition, we discover a new and universal characteristic of the second transition point-an abrupt increase of the clustering coefficient, due to formation of many small complete subgraphs inside the network.

  7. The role of hydrogen atoms in interactions involving imidazolium-based ionic liquids

    Science.gov (United States)

    Kempter, V.; Kirchner, B.

    2010-05-01

    In the first part of this report experimental results are discussed which focus onto the importance of hydrogen atoms in the interaction of imidazolium-based ionic liquids. These include examples for the cation-anion interaction in neat ionic liquids as well as the interactions between ionic liquids and their molecular environment, water in particular. Most of the studies emphasize the importance of the C(2)-H group of the imidazolium ring for the intra- and intermolecular interactions; commonly, the interactions of the type C-H … X (X =: O, halide) are attributed to "hydrogen bonding". In the second part it is analyzed whether these interactions and their consequences fulfill the criteria set by standard definitions of hydrogen bonding. Two cation-anion co-conformations at the C(2)-H group are found. One co-conformer (in-plane) often resembles a hydrogen bond while the other one (on-top) points to a non-hydrogen bonding behavior. Furthermore, the degree of hydrogen bonding for the in-plane structure is very dependent on the anion. Spatial distribution functions show that, in general, both co-conformations are occupied. However, the question of how long a particular co-conformer is populated in the liquid state has yet to be answered. Therefore, it is concluded that the term "hydrogen bond" should, at present, be treated with care to characterize the cation-anion contacts, because of the above-mentioned difficulties. Once more it must be stressed that oversimplifications and generalizations, even for this subclass of ionic liquids have to be avoided, because these liquids are more complicated than it appears from first sight.

  8. High Intensity Femtosecond XUV Pulse Interactions with Atomic Clusters: Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Ditmire, Todd [Univ. of Texas, Austin, TX (United States). Center for High Energy Density Science

    2016-10-12

    We propose to expand our recent studies on the interactions of intense extreme ultraviolet (XUV) femtosecond pulses with atomic and molecular clusters. The work described follows directly from work performed under BES support for the past grant period. During this period we upgraded the THOR laser at UT Austin by replacing the regenerative amplifier with optical parametric amplification (OPA) using BBO crystals. This increased the contrast of the laser, the total laser energy to ~1.2 J , and decreased the pulse width to below 30 fs. We built a new all reflective XUV harmonic beam line into expanded lab space. This enabled an increase influence by a factor of 25 and an increase in the intensity by a factor of 50. The goal of the program proposed in this renewal is to extend this class of experiments to available higher XUV intensity and a greater range of wavelengths. In particular we plan to perform experiments to confirm our hypothesis about the origin of the high charge states in these exploding clusters, an effect which we ascribe to plasma continuum lowering (ionization potential depression) in a cluster nano-­plasma. To do this we will perform experiments in which XUV pulses of carefully chosen wavelength irradiate clusters composed of only low-Z atoms and clusters with a mixture of this low-­Z atom with higher Z atoms. The latter clusters will exhibit higher electron densities and will serve to lower the ionization potential further than in the clusters composed only of low Z atoms. This should have a significant effect on the charge states produced in the exploding cluster. We will also explore the transition of explosions in these XUV irradiated clusters from hydrodynamic expansion to Coulomb explosion. The work proposed here will explore clusters of a wider range of constituents, including clusters from solids. Experiments on clusters from solids will be enabled by development we performed during the past grant period in which we constructed and

  9. Entropy evolvement properties in a system of Schr(o)dinger cat state light field interacting with two entangled atoms

    Institute of Scientific and Technical Information of China (English)

    Liu Tang-Kun

    2006-01-01

    The field entropy can be regarded as a measurement of the degree of entanglement between the light field and the atoms of a system which is composed of two-level atoms initially in an entangled state interacting with the Schr(o)dinger cat state. The influences of the strength of light field and the phase angle between the two coherent states on the field entropy are discussed by using numerical calculations. The result shows that when the strength of light field is large enough the field entropy is not zero and the degrees of entanglement between the atoms and the three different states of the light fields are equal. When the strength of the light field is small, the degree of entanglement is maximum in a system of the two entangled atoms interacting with an odd coherent state; it is intermediate for a system of the two entangled atoms interacting with the Yurke-Stoler coherent state, and it is minimum in a system of the two entangled atoms interacting with an even coherent state.

  10. Dynamic polarizabilities of rare-earth-metal atoms and dispersion coefficients for their interaction with helium atoms

    NARCIS (Netherlands)

    Chu, X.; Dalgarno, A.; Groenenboom, G.C.

    2007-01-01

    The dynamic scalar and tensor polarizabilities of the rare-earth-metal atoms are calculated with time-dependent density functional theory. The frequency-dependent polarizabilities at imaginary frequencies are used to determine the isotropic and orientation-dependent van der Waals coefficients for th

  11. 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…

  12. Prediction of drug-target interaction by label propagation with mutual interaction information derived from heterogeneous network.

    Science.gov (United States)

    Yan, Xiao-Ying; Zhang, Shao-Wu; Zhang, Song-Yao

    2016-02-01

    The identification of potential drug-target interaction pairs is very important, which is useful not only for providing greater understanding of protein function, but also for enhancing drug research, especially for drug function repositioning. Recently, numerous machine learning-based algorithms (e.g. kernel-based, matrix factorization-based and network-based inference methods) have been developed for predicting drug-target interactions. All these methods implicitly utilize the assumption that similar drugs tend to target similar proteins and yield better results for predicting interactions between drugs and target proteins. To further improve the accuracy of prediction, a new method of network-based label propagation with mutual interaction information derived from heterogeneous networks, namely LPMIHN, is proposed to infer the potential drug-target interactions. LPMIHN separately performs label propagation on drug and target similarity networks, but the initial label information of the target (or drug) network comes from the drug (or target) label network and the known drug-target interaction bipartite network. The independent label propagation on each similarity network explores the cluster structure in its network, and the label information from the other network is used to capture mutual interactions (bicluster structures) between the nodes in each pair of the similarity networks. As compared to other recent state-of-the-art methods on the four popular benchmark datasets of binary drug-target interactions and two quantitative kinase bioactivity datasets, LPMIHN achieves the best results in terms of AUC and AUPR. In addition, many of the promising drug-target pairs predicted from LPMIHN are also confirmed on the latest publicly available drug-target databases such as ChEMBL, KEGG, SuperTarget and Drugbank. These results demonstrate the effectiveness of our LPMIHN method, indicating that LPMIHN has a great potential for predicting drug-target interactions.

  13. 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

  14. Novel recurrent neural network for modelling biological networks: oscillatory p53 interaction dynamics.

    Science.gov (United States)

    Ling, Hong; Samarasinghe, Sandhya; Kulasiri, Don

    2013-12-01

    Understanding the control of cellular networks consisting of gene and protein interactions and their emergent properties is a central activity of Systems Biology research. For this, continuous, discrete, hybrid, and stochastic methods have been proposed. Currently, the most common approach to modelling accurate temporal dynamics of networks is ordinary differential equations (ODE). However, critical limitations of ODE models are difficulty in kinetic parameter estimation and numerical solution of a large number of equations, making them more suited to smaller systems. In this article, we introduce a novel recurrent artificial neural network (RNN) that addresses above limitations and produces a continuous model that easily estimates parameters from data, can handle a large number of molecular interactions and quantifies temporal dynamics and emergent systems properties. This RNN is based on a system of ODEs representing molecular interactions in a signalling network. Each neuron represents concentration change of one molecule represented by an ODE. Weights of the RNN correspond to kinetic parameters in the system and can be adjusted incrementally during network training. The method is applied to the p53-Mdm2 oscillation system - a crucial component of the DNA damage response pathways activated by a damage signal. Simulation results indicate that the proposed RNN can successfully represent the behaviour of the p53-Mdm2 oscillation system and solve the parameter estimation problem with high accuracy. Furthermore, we presented a modified form of the RNN that estimates parameters and captures systems dynamics from sparse data collected over relatively large time steps. We also investigate the robustness of the p53-Mdm2 system using the trained RNN under various levels of parameter perturbation to gain a greater understanding of the control of the p53-Mdm2 system. Its outcomes on robustness are consistent with the current biological knowledge of this system. As more

  15. Consistent structures and interactions by density functional theory with small atomic orbital basis sets.

    Science.gov (United States)

    Grimme, Stefan; Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas

    2015-08-07

    A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of "low-cost" electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT methods

  16. Consistent structures and interactions by density functional theory with small atomic orbital basis sets

    Energy Technology Data Exchange (ETDEWEB)

    Grimme, Stefan, E-mail: grimme@thch.uni-bonn.de; Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas [Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn (Germany)

    2015-08-07

    A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of “low-cost” electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT

  17. Influence of tip indentation depth on the adhesive behavior of viscoelastic polydimethylsiloxane networks studied by atomic force microscopy

    NARCIS (Netherlands)

    Pickering, J.P.; Vancso, G.J.

    2001-01-01

    A commercial atomic force microscope (AFM) outfitted with a custom control and data acquisition system was used to investigate the adhesive nature of a viscoelastic polydimethylsiloxane (PDMS) network. Due to the complex dependence of the adhesion of this sample on factors such as indentation, surfa

  18. Dynamic patterns and their interactions in networks of excitable elements.

    Science.gov (United States)

    Gong, Pulin; Steel, Harrison; Robinson, Peter; Qi, Yang

    2013-10-01

    Formation of localized propagating patterns is a fascinating self-organizing phenomenon that happens in a wide range of spatially extended, excitable systems in which individual elements have resting, activated, and refractory states. Here we study a type of stochastic three-state excitable network model that has been recently developed; this model is able to generate a rich range of pattern dynamics, including localized wandering patterns and localized propagating patterns with crescent shapes and long-range propagation. The collective dynamics of these localized patterns have anomalous subdiffusive dynamics before symmetry breaking and anomalous superdiffusive dynamics after that, showing long-range spatiotemporal coherence in the system. In this study, the stability of the localized wandering patterns is analyzed by treating an individual localized pattern as a subpopulation to develop its average response function. This stability analysis indicates that when the average refractory period is greater than a certain value, there are too many elements in the refractory state after being activated to allow the subpopulation to support a self-sustained pattern; this is consistent with symmetry breaking identified by using an order parameter. Furthermore, in a broad parameter space, the simple network model is able to generate a range of interactions between different localized propagating patterns including repulsive collisions and partial and full annihilations, and interactions between localized propagating patterns and the refractory wake behind others; in this study, these interaction dynamics are systematically quantified based on their relative propagation directions and the resultant angles between them before and after their collisions. These results suggest that the model potentially provides a modeling framework to understand the formation of localized propagating patterns in a broad class of systems with excitable properties.

  19. Interaction of Rydberg atoms in circular states with the alkaline-earth Ca(4s{sup 2}) and Sr(5s{sup 2}) atoms

    Energy Technology Data Exchange (ETDEWEB)

    Mironchuk, E. S.; Narits, A. A.; Lebedev, V. S., E-mail: vlebedev@sci.lebedev.ru [Russian Academy of Sciences, Lebedev Physical Institute (Russian Federation)

    2015-11-15

    The resonant mechanism of interaction of alkaline-earth atoms having a low electron affinity to Rydberg atoms in circular (l = vertical bar m vertical bar = n–1) and near-circular states has been studied. To describe the dynamics of resonant processes accompanied by nonadiabatic transitions between ionic and Rydberg covalent terms of a quasimolecule, an approach based on the integration of coupled equations for the probability amplitudes has been developed taking into account the possibility of the decay of an anion in the Coulomb field of the positive ionic core of a highly excited atom. The approach involves the specific features of the problem associated with the structure of the wavefunction of a Rydberg electron in states with high orbital angular momenta l ∼ n–1. This approach provides a much more accurate description of the dynamics of electronic transitions at collisions between atoms than that within the modified semiclassical Landau–Zener model. In addition, this approach makes it possible to effectively take into account many channels of the problem. The cross sections for resonant quenching of Rydberg states of the Li(nlm) atom with given principal n, orbital l = n–1, and magnetic m quantum numbers at thermal collisions with the Ca(4s{sup 2}) and Sr(5s{sup 2}) atoms have been calculated. The dependences of the results on n, m, and angle α between the relative velocity of the atoms and the normal to the plane of the orbit of the Rydberg electron have been obtained. The influence of orientational effects on the efficiency of the collisional destruction of circular and near-circular states has been studied. The results indicate a higher stability of such states to their perturbations by neutral particles as compared to usually studied nl states with low values of l (l ≪ n)

  20. Interaction of Rydberg atoms in circular states with the alkaline-earth Ca(4 s 2) and Sr(5 s 2) atoms

    Science.gov (United States)

    Mironchuk, E. S.; Narits, A. A.; Lebedev, V. S.

    2015-11-01

    The resonant mechanism of interaction of alkaline-earth atoms having a low electron affinity to Rydberg atoms in circular ( l = | m| = n-1) and near-circular states has been studied. To describe the dynamics of resonant processes accompanied by nonadiabatic transitions between ionic and Rydberg covalent terms of a quasimolecule, an approach based on the integration of coupled equations for the probability amplitudes has been developed taking into account the possibility of the decay of an anion in the Coulomb field of the positive ionic core of a highly excited atom. The approach involves the specific features of the problem associated with the structure of the wavefunction of a Rydberg electron in states with high orbital angular momenta l ~ n-1. This approach provides a much more accurate description of the dynamics of electronic transitions at collisions between atoms than that within the modified semiclassical Landau-Zener model. In addition, this approach makes it possible to effectively take into account many channels of the problem. The cross sections for resonant quenching of Rydberg states of the Li( nlm) atom with given principal n, orbital l = n-1, and magnetic m quantum numbers at thermal collisions with the Ca(4 s 2) and Sr(5 s 2) atoms have been calculated. The dependences of the results on n, m, and angle α between the relative velocity of the atoms and the normal to the plane of the orbit of the Rydberg electron have been obtained. The influence of orientational effects on the efficiency of the collisional destruction of circular and near-circular states has been studied. The results indicate a higher stability of such states to their perturbations by neutral particles as compared to usually studied nl states with low values of l ( l ≪ n).

  1. Approximate and Conditional Teleportation of an Unknown Atomic State Without Bell-State Measurement with Two-Photon Interaction

    Institute of Scientific and Technical Information of China (English)

    CHEN Chang-Yong

    2006-01-01

    A scheme for approximately and conditionally teleporting an unknown atomic state via two-photon interaction in cavity QED is proposed. It is the extension of the scheme of Ref. [11] [Phys. Rev. A 69 (2004) 064302], which is based on Jaynes-Cummings model in QED and where only a time point of system evolution and the corresponding fidelity implementing the teleportation are given. In our scheme, the two-photon interaction Jaynes-Cummings model is used to realize the approximate and conditional teleportation. Our scheme does not involve the Bell-state measurement and an additional atom, only requiring two atoms and one single-mode cavity. The fidelity of the scheme is higher than that of Ref. [11]. The scheme may be generalized to not only the teleportation of the state of a cavity mode to another mode by means of a single atom but also the teleportation of the state of a trapped ion.

  2. Entropy squeezing of the field interacting with a nearly degenerate V-type three-level atom

    Institute of Scientific and Technical Information of China (English)

    Zhou Qing-Chun; Zhu Shi-Ning

    2005-01-01

    The position- and momentum-entopic squeezing properties of the optical field in the system of a nearly degenerate three-level atom interacting with a single-mode field are investigated. Calculation results indicate that when the field is initially in the vacuum state, it may lead to squeezing of the position entropy or the momentum entropy of the field if the atom is prepared properly. The effects of initial atomic state and the splitting of the excited levels of the atom on field entropies are discussed in this case. When the initial field is in a coherent state, we find that position-entropy squeezing of the field is present even if the atom is prepared in the ground state. By comparing the variance squeezing and entropy squeezing of the field we confirm that entropy is more sensitive than variance in measuring quantum fluctuations.

  3. Dynamics of bell-nonlocality for two atoms interacting with a vacuum multi-mode noise field

    Science.gov (United States)

    Liu, Yu-Jie; Zheng, Li; Han, Dong-Mei; Lü, Huan-Lin; Zheng, Tai-Yu

    2016-06-01

    We investigate the internal-state Bell nonlocal entanglement dynamics, as measured by CHSH inequality of two atoms interacting with a vacuum multi-mode noise field by taking into account the spatial degrees of freedom of the two atoms. The dynamics of Bell nonlocality of the atoms with the atomic internal states being initially in a Werner-type state is studied, by deriving the analytical solutions of the Schrödinger equation, and tracing over the degrees of freedom of the field and the external motion of the two atoms. In addition, through comparison with entanglement as measured by concurrence, we find that the survival time of entanglement is much longer than that of the Bell-inequality violation. And the comparison of the quantum correlation time between two Werner-type states is discussed.

  4. Probing anisotropic surface properties and interaction forces of chrysotile rods by atomic force microscopy and rheology.

    Science.gov (United States)

    Yang, Dingzheng; Xie, Lei; Bobicki, Erin; Xu, Zhenghe; Liu, Qingxia; Zeng, Hongbo

    2014-09-16

    Understanding the surface properties and interactions of nonspherical particles is of both fundamental and practical importance in the rheology of complex fluids in various engineering applications. In this work, natural chrysotile, a phyllosilicate composed of 1:1 stacked silica and brucite layers which coil into cylindrical structure, was chosen as a model rod-shaped particle. The interactions of chrysotile brucite-like basal or bilayered edge planes and a silicon nitride tip were measured using an atomic force microscope (AFM). The force-distance profiles were fitted using the classical Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, which demonstrates anisotropic and pH-dependent surface charge properties of brucite-like basal plane and bilayered edge surface. The points of zero charge (PZC) of the basal and edge planes were estimated to be around pH 10-11 and 6-7, respectively. Rheology measurements of 7 vol % chrysotile (with an aspect ratio of 14.5) in 10 mM NaCl solution showed pH-dependent yield stress with a local maximum around pH 7-9, which falls between the two PZC values of the edge and basal planes of the rod particles. On the basis of the surface potentials of the edge and basal planes obtained from AFM measurements, theoretical analysis of the surface interactions of edge-edge, basal-edge, and basal-basal planes of the chrysotile rods suggests the yield stress maximum observed could be mainly attributed to the basal-edge attractions. Our results indicate that the anisotropic surface properties (e.g., charges) of chrysotile rods play an important role in the particle-particle interaction and rheological behavior, which also provides insight into the basic understanding of the colloidal interactions and rheology of nonspherical particles.

  5. Laser-material interaction during atom probe tomography of oxides with embedded metal nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Shinde, D.; Arnoldi, L.; Devaraj, A.; Vella, A.

    2016-10-28

    Oxide-supported metal nano-particles are of great interest in catalysis but also in the development of new large-spectrum-absorption materials. The design of such nano materials requires three-dimensional characterization with a high spatial resolution and elemental selectivity. The laser assisted Atom Probe Tomography (La-APT) presents both these capacities if an accurate understanding of laser-material interaction is developed. In this paper, we focus on the fundamental physics of field evaporation as a function of sample geometry, laser power, and DC electric field for Au nanoparticles embedded in MgO. By understanding the laser-material interaction through experiments and a theoretical model of heat diffusion inside the sample after the interaction with laser pulse, we point out the physical origin of the noise and determine the conditions to reduce it by more than one order of magnitude, improving the sensitivity of the La-APT for metal-dielectric composites. Published by AIP Publishing.

  6. Direct force measurement of single DNA-peptide interactions using atomic force microscopy.

    Science.gov (United States)

    Chung, Ji W; Shin, Dongjin; Kwak, June M; Seog, Joonil

    2013-06-01

    The selective interactions between DNA and miniature (39 residues) engineered peptide were directly measured at the single-molecule level by using atomic force microscopy. This peptide (p007) contains an α-helical recognition site similar to leucine zipper GCN4 and specifically recognizes the ATGAC sequence in the DNA with nanomolar affinity. The average rupture force was 42.1 pN, which is similar to the unbinding forces of the digoxigenin-antidigoxigenin complex, one of the strongest interactions in biological systems. The single linear fit of the rupture forces versus the logarithm of pulling rates showed a single energy barrier with a transition state located at 0.74 nm from the bound state. The smaller koff compared with that of other similar systems was presumably due to the increased stability of the helical structure by putative folding residues in p007. This strong sequence-specific DNA-peptide interaction has a potential to be utilized to prepare well-defined mechanically stable DNA-protein hybrid nanostructures.

  7. Nanobiosensors exploiting specific interactions between an enzyme and herbicides in atomic force spectroscopy.

    Science.gov (United States)

    da Silva, Aline C N; Deda, Daiana K; Bueno, Carolina C; Moraes, Ariana S; Da Roz, Alessandra L; Yamaji, Fabio M; Prado, Rogilene A; Viviani, Vadim; Oliveira, Osvaldo N; Leite, Fábio L

    2014-09-01

    The development of sensitive methodologies for detecting agrochemicals has become important in recent years due to the increasingly indiscriminate use of these substances. In this context, nanosensors based on atomic force microscopy (AFM) tips are useful because they provide higher sensitivity with operation at the nanometer scale. In this paper we exploit specific interactions between AFM tips functionalized with the enzyme acetolactate synthase (ALS) to detect the ALS-inhibitor herbicides metsulfuron-methyl and imazaquin. Using atomic force spectroscopy (AFS) we could measure the adhesion force between tip and substrate, which was considerably higher when the ALS-functionalized tip (nanobiosensor) was employed. The increase was approximately 250% and 160% for metsulfuron-methyl and imazaquin, respectively, in comparison to unfunctionalized probes. We estimated the specific enzyme-herbicide force by assuming that the measured force comprises an adhesion force according to the Johnson-Kendall-Roberts (JKR) model, the capillary force and the specific force. We show that the specific, biorecognition force plays a crucial role in the higher sensitivity of the nanobiosensor, thus opening the way for the design of similarly engineered tips for detecting herbicides and other analytes.

  8. Dynamics of gas-surface interactions atomic-level understanding of scattering processes at surfaces

    CERN Document Server

    Díez Muniño, Ricardo

    2013-01-01

    This book gives a representative survey of the state of the art of research on gas-surface interactions. It provides an overview of the current understanding of gas surface dynamics and, in particular, of the reactive and non-reactive processes of atoms and small molecules at surfaces. Leading scientists in the field, both from the theoretical and the experimental sides, write in this book about their most recent advances. Surface science grew as an interdisciplinary research area over the last decades, mostly because of new experimental technologies (ultra-high vacuum, for instance), as well as because of a novel paradigm, the ‘surface science’ approach. The book describes the second transformation which is now taking place pushed by the availability of powerful quantum-mechanical theoretical methods implemented numerically. In the book, experiment and theory progress hand in hand with an unprecedented degree of accuracy and control. The book presents how modern surface science targets the atomic-level u...

  9. Nonclasssical Properties in Two-Mode Fields Resonantly Interacting with a Three-Level [Ⅰ]-Type Atom

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Some noclassical properties in electromagnetic Reid are investigated for the interaction of two-modes initially taken in coherent-state representation with the three-level [Ⅰ]-type atom, such as squeezing properties and violation of the Cauchy-Schwartz inequality. The enhancement of Geld squeezing is found by selective atomic measurement. The Cauchy-Schwartz inequality is violated by the application of the classical Geld followed by detection in excited state.

  10. Theory of metal atom-water interactions and alkali halide dimers

    Science.gov (United States)

    Jordan, K. D.; Kurtz, H. A.

    1982-01-01

    Theoretical studies of the interactions of metal atoms with water and some of its isoelectronic analogs, and of the properties of alkali halides and their aggregates are discussed. Results are presented of ab initio calculations of the heats of reaction of the metal-water adducts and hydroxyhydrides of Li, Be, B, Na, Mg, and Al, and of the bond lengths and angles an; the heats of reaction for the insertion of Al into HF, H2O, NH3, H2S and CH3OH, and Be and Mg into H2O. Calculations of the electron affinities and dipole moments and polarizabilities of selected gas phase alkali halide monomers and dimers are discussed, with particular attention given to results of calculations of the polarizability of LiF taking into account electron correlation effects, and the polarizability of the dimer (LiF)2.

  11. Quantitative characterization of biomolecular assemblies and interactions using atomic force microscopy.

    Science.gov (United States)

    Yang, Yong; Wang, Hong; Erie, Dorothy A

    2003-02-01

    Atomic force microscopy (AFM) has been applied in many biological investigations in the past 15 years. This review focuses on the application of AFM for quantitatively characterizing the structural and thermodynamic properties of protein-protein and protein-nucleic acid complexes. AFM can be used to determine the stoichiometries and association constants of multiprotein assemblies and to quantify changes in conformations of proteins and protein-nucleic acid complexes. In addition, AFM in solution permits the observation of the dynamic properties of biomolecular complexes and the measurement of intermolecular forces between biomolecules. Recent advances in cryogenic AFM, AFM on two-dimensional crystals, carbon nanotube probes, solution imaging, high-speed AFM, and manipulation capabilities enhance these applications by improving AFM resolution and the dynamic and operative capabilities of the AFM. These developments make AFM a powerful tool for investigating the biomolecular assemblies and interactions that govern gene regulation.

  12. Shifted Tietz-Wei oscillator for simulating the atomic interaction in diatomic molecules

    CERN Document Server

    Falaye, Babatunde J; Hamzavi, Majid

    2015-01-01

    The shifted Tietz-Wei (sTW) oscillator is as good as traditional Morse potential in simulating the atomic interaction in diatomic molecules. By using the Pekeris-type approximation to deal with the centrifugal term, we obtain the bound-state solutions of the radial Schr\\"odinger equation with this typical molecular model via the exact quantization rule (EQR). The energy spectrum for a set of diatomic molecules ($NO \\left(a^4\\Pi_i\\right)$, $NO \\left(B^2\\Pi_r\\right)$, $NO \\left(L'^2\\phi\\right)$, $NO \\left(b^4\\Sigma^{-}\\right)$, $ICl\\left(X^1\\Sigma_g^{+}\\right)$, $ICl\\left(A^3\\Pi_1\\right)$ and $ICl\\left(A'^3\\Pi_2\\right)$ for arbitrary values of $n$ and $\\ell$ quantum numbers are obtained. For the sake of completeness, we study the corresponding wavefunctions using the formula method.

  13. A Partitioned Correlation Function Interaction approach for describing electron correlation in atoms

    CERN Document Server

    Verdebout, S; Jönsson, P; Gaigalas, G; Fischer, C Froese; Godefroid, M

    2013-01-01

    Traditional multiconfiguration Hartree-Fock (MCHF) and configuration interaction (CI) methods are based on a single orthonormal orbital basis (OB). For atoms with complicated shell structures, a large OB is needed to saturate all the electron correlation effects. The large OB leads to massive configuration state function (CSF) expansions that are difficult to handle. We show that it is possible to relax the orthonormality restriction on the OB and break down the originally large calculations to a set of smaller ones that can be run in parallel. Each calculation determines a partitioned correlation function (PCF) that accounts for a specific correlation effect. The PCFs are built on optimally localized orbital sets and are added to a zero-order multireference (MR) function to form a total wave function. The mixing coefficients of the PCFs are fixed from a small generalized eigenvalue problem. The required matrices are computed using a biorthonormal transformation technique. The new method, called partitioned c...

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

    CERN Document Server

    Khusnutdinov, Nail R

    2012-01-01

    The van der Waals and Casimir-Polder interaction energy of an atom with an infinitely thin sphere with finite conductivity is investigated in the framework of the hydrodynamic approach at finite temperature. The Lifshits approach is used to find the free energy. We find the close expression for the free energy and make the analysis of it for i) high and low temperatures, ii) large radii of sphere and ii) short distance from sphere. At low temperatures the thermal part of the free energy tends to zero as forth power of the temperature while for high temperatures it is proportional to the first degree of the temperature. We show that the entropy of this system is positive for small radii of sphere and it becomes negative at low temperatures and for large radii of the sphere.

  15. Van der Waals-Casimir-Polder interaction of an atom with a composite surface

    CERN Document Server

    Eizner, Elad; Henkel, Carsten

    2012-01-01

    We study the dispersion interaction of the van der Waals and Casimir-Polder (vdW-CP) type between a neutral atom and the surface of a metal by allowing for nonlocal electrodynamics, i.e. electron diffusion. We consider two models: (i) bulk diffusion, and (ii) diffusion in a surface charge layer. In both cases the transition to a semiconductor is continuous as a function of the conductivity, unlike the case of a local model. The relevant parameter is the electric screening length and depends on the carrier diffusion constant. We find that for distances comparable to the screening length, vdW-CP data can distinguish between bulk and surface diffusion, hence it can be a sensitive probe for surface states.

  16. Phage-bacteria interaction network in human oral microbiome.

    Science.gov (United States)

    Wang, Jinfeng; Gao, Yuan; Zhao, Fangqing

    2016-07-01

    Although increasing knowledge suggests that bacteriophages play important roles in regulating microbial ecosystems, phage-bacteria interaction in human oral cavities remains less understood. Here we performed a metagenomic analysis to explore the composition and variation of oral dsDNA phage populations and potential phage-bacteria interaction. A total of 1,711 contigs assembled with more than 100 Gb shotgun sequencing data were annotated to 104 phages based on their best BLAST matches against the NR database. Bray-Curtis dissimilarities demonstrated that both phage and bacterial composition are highly diverse between periodontally healthy samples but show a trend towards homogenization in diseased gingivae samples. Significantly, according to the CRISPR arrays that record infection relationship between bacteria and phage, we found certain oral phages were able to invade other bacteria besides their putative bacterial hosts. These cross-infective phages were positively correlated with commensal bacteria while were negatively correlated with major periodontal pathogens, suggesting possible connection between these phages and microbial community structure in oral cavities. By characterizing phage-bacteria interaction as networks rather than exclusively pairwise predator-prey relationships, our study provides the first insight into the participation of cross-infective phages in forming human oral microbiota.

  17. 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.

  18. Laser spectroscopy with nanometric gas cells distance dependence of atom-surface interaction and collisions under confinement

    CERN Document Server

    Hamdi, I; Yarovitski, A; Dutier, G; Maurin, I; Saltiel, S; Li, Y; Lezama, A; Vartapetyan, T; Sarkisyan, D; Gorza, M P; Fichet, M; Bloch, D; Ducloy, M; Hamdi, Ismah\\`{e}ne; Todorov, Petko; Yarovitski, Alexander; Dutier, Gabriel; Maurin, Isabelle; Saltiel, Solomon; Li, Yuanyuan; Lezama, Arturo; Varzhapetyan, Tigran; Sarkisyan, David; Gorza, Marie-Pascale; Fichet, Mich\\`{e}le; Bloch, Daniel; Ducloy, Martial

    2005-01-01

    The high sensitivity of Laser Spectroscopy has made possible the exploration of atomic resonances in newly designed "nanometric" gas cells, whose local thickness varies from 20nm to more than 1000 nm. Following the initial observation of the optical analogous of the coherent Dicke microwave narrowing, the newest prospects include the exploration of long-range atom surface van der Waals interaction with spatial resolution in an unprecedented range of distances, modification of atom dielectric resonant coupling under the influence of the coupling between the two neighbouring dielectric media, and even the possible modification of interatomic collisions processes under the effect of confinement.

  19. 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...

  20. Continuous flow atomic force microscopy imaging reveals fluidity and time-dependent interactions of antimicrobial dendrimer with model lipid membranes.

    Science.gov (United States)

    Lind, Tania Kjellerup; Zielińska, Paulina; Wacklin, Hanna Pauliina; Urbańczyk-Lipkowska, Zofia; Cárdenas, Marité

    2014-01-28

    In this paper, an amphiphilic peptide dendrimer with potential applications against multi-resistant bacteria such as Staphylococcus aureus was synthesized and studied on model cell membranes. The combination of quartz crystal microbalance and atomic force microscopy imaging during continuous flow allowed for in situ monitoring of the very initial interaction processes and membrane transformations on longer time scales. We used three different membrane compositions of low and high melting temperature phospholipids to vary the membrane properties from a single fluid phase to a pure gel phase, while crossing the phase coexistence boundaries at room temperature. The interaction mechanism of the dendrimer was found to be time-dependent and to vary remarkably with the fluidity and coexistence of liquid-solid phases in the membrane. Spherical micelle-like dendrimer-lipid aggregates were formed in the fluid-phase bilayer and led to partial solubilization of the membrane, while in gel-phase membranes, the dendrimers caused areas of local depressions followed by redeposition of flexible lipid patches. Domain coexistence led to a sequence of events initiated by the formation of a ribbon-like network and followed by membrane solubilization via spherical aggregates from the edges of bilayer patches. Our results show that the dendrimer molecules were able to destroy the membrane integrity through different mechanisms depending on the lipid phase and morphology and shed light on their antimicrobial activity. These findings could have an impact on the efficacy of the dendrimers since lipid membranes in certain bacteria have transition temperatures very close to the host body temperature.

  1. 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...

  2. Drug-Drug Interaction Extraction via Convolutional Neural Networks.

    Science.gov (United States)

    Liu, Shengyu; Tang, Buzhou; Chen, Qingcai; Wang, Xiaolong

    2016-01-01

    Drug-drug interaction (DDI) extraction as a typical relation extraction task in natural language processing (NLP) has always attracted great attention. Most state-of-the-art DDI extraction systems are based on support vector machines (SVM) with a large number of manually defined features. Recently, convolutional neural networks (CNN), a robust machine learning method which almost does not need manually defined features, has exhibited great potential for many NLP tasks. It is worth employing CNN for DDI extraction, which has never been investigated. We proposed a CNN-based method for DDI extraction. Experiments conducted on the 2013 DDIExtraction challenge corpus demonstrate that CNN is a good choice for DDI extraction. The CNN-based DDI extraction method achieves an F-score of 69.75%, which outperforms the existing best performing method by 2.75%.

  3. 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%.

  4. 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.

  5. Efficient quantum transport in disordered interacting many-body networks

    Science.gov (United States)

    Ortega, Adrian; Stegmann, Thomas; Benet, Luis

    2016-10-01

    The coherent transport of n fermions in disordered networks of l single-particle states connected by k -body interactions is studied. These networks are modeled by embedded Gaussian random matrix ensemble (EGE). The conductance bandwidth and the ensemble-averaged total current attain their maximal values if the system is highly filled n ˜l -1 and k ˜n /2 . For the cases k =1 and k =n the bandwidth is minimal. We show that for all parameters the transport is enhanced significantly whenever centrosymmetric embedded Gaussian ensemble (csEGE) are considered. In this case the transmission shows numerous resonances of perfect transport. Analyzing the transmission by spectral decomposition, we find that centrosymmetry induces strong correlations and enhances the extrema of the distributions. This suppresses destructive interference effects in the system and thus causes backscattering-free transmission resonances that enhance the overall transport. The distribution of the total current for the csEGE has a very large dominating peak for n =l -1 , close to the highest observed currents.

  6. Topological robustness analysis of protein interaction networks reveals key targets for overcoming chemotherapy resistance in glioma

    OpenAIRE

    Hátylas Azevedo; Carlos Alberto Moreira-Filho

    2015-01-01

    Biological networks display high robustness against random failures but are vulnerable to targeted attacks on central nodes. Thus, network topology analysis represents a powerful tool for investigating network susceptibility against targeted node removal. Here, we built protein interaction networks associated with chemoresistance to temozolomide, an alkylating agent used in glioma therapy, and analyzed their modular structure and robustness against intentional attack. These networks showed fu...

  7. Atomic resolution model of the antibody Fc interaction with the complement C1q component.

    Science.gov (United States)

    Schneider, Sebastian; Zacharias, Martin

    2012-05-01

    The globular C1q heterotrimer is a subunit of the C1 complement factor. Binding of the C1q subunit to the constant (Fc) part of antibody molecules is a first step and key event of complement activation. Although three-dimensional structures of C1q and antibody Fc subunits have been determined experimentally no atomic resolution structure of the C1q-Fc complex is known so far. Based on systematic protein-protein docking searches and Molecular Dynamics simulations a structural model of the C1q-IgG1-Fc-binding geometry has been obtained. The structural model is compatible with available experimental data on the interaction between the two partner proteins. It predicts a binding geometry that involves mainly the B-subunit of the C1q-trimer and both subunits of the IgG1-Fc-dimer with small conformational adjustments with respect to the unbound partners to achieve high surface complementarity. In addition to several charge-charge and polar contacts in the rim region of the interface it also involves nonpolar contacts between the two proteins and is compatible with the carbohydrate moiety of the Fc subunit. The model for the complex structure provides a working model for rationalizing available biochemical data on this important interaction and can form the basis for the design of Fc variants with a greater capacity to activate the complement system for example on binding to cancer cells or other target structures.

  8. Unraveling protein-protein interactions in clathrin assemblies via atomic force spectroscopy.

    Science.gov (United States)

    Jin, Albert J; Lafer, Eileen M; Peng, Jennifer Q; Smith, Paul D; Nossal, Ralph

    2013-03-01

    Atomic force microscopy (AFM), single molecule force spectroscopy (SMFS), and single particle force spectroscopy (SPFS) are used to characterize intermolecular interactions and domain structures of clathrin triskelia and clathrin-coated vesicles (CCVs). The latter are involved in receptor-mediated endocytosis (RME) and other trafficking pathways. Here, we subject individual triskelia, bovine-brain CCVs, and reconstituted clathrin-AP180 coats to AFM-SMFS and AFM-SPFS pulling experiments and apply novel analytics to extract force-extension relations from very large data sets. The spectroscopic fingerprints of these samples differ markedly, providing important new information about the mechanism of CCV uncoating. For individual triskelia, SMFS reveals a series of events associated with heavy chain alpha-helix hairpin unfolding, as well as cooperative unraveling of several hairpin domains. SPFS of clathrin assemblies exposes weaker clathrin-clathrin interactions that are indicative of inter-leg association essential for RME and intracellular trafficking. Clathrin-AP180 coats are energetically easier to unravel than the coats of CCVs, with a non-trivial dependence on force-loading rate.

  9. Weyl spin-orbit-coupling-induced interactions in uniform and trapped atomic quantum fluids

    Science.gov (United States)

    Gupta, Reena; Singh, G. S.; Bosse, Jürgen

    2013-11-01

    We establish through analytical and numerical studies of thermodynamic quantities for noninteracting atomic gases that the isotropic three-dimensional spin-orbit coupling, the Weyl coupling, induces interaction which counters “effective” attraction (repulsion) of the exchange symmetry present in zero-coupling Bose (Fermi) gas. The exact analytical expressions for the grand potential and hence for several thermodynamic quantities have been obtained for this purpose in both uniform and trapped cases. It is enunciated that many interesting features of spin-orbit-coupled systems revealed theoretically can be understood in terms of coupling-induced modifications in statistical interparticle potential. The temperature dependence of the chemical potential, specific heat, and isothermal compressibility for a uniform Bose gas is found to have signature of the incipient Bose-Einstein condensation in the very weak coupling regime although the system does not really go in the Bose-condensed phase. The transition temperature in the harmonically trapped case decreases with an increase of coupling strength consistent with the weakening of the statistical attractive interaction. Anomalous behavior of some thermodynamic quantities, partly akin to that in dimensions less than two, appears for uniform fermions as soon as the Fermi level goes down the Dirac point on increasing the coupling strength. It is suggested that the fluctuation-dissipation theorem can be utilized to verify anomalous behaviors from studies of long-wavelength fluctuations in bunching and antibunching effects.

  10. The Fueling Diagram: Linking Galaxy Molecular-to-Atomic Gas Ratios to Interactions and Accretion

    CERN Document Server

    Stark, David V; Wei, Lisa H; Baker, Andrew J; Leroy, Adam K; Eckert, Kathleen D; Vogel, Stuart N

    2013-01-01

    To assess how external factors such as local interactions and fresh gas accretion influence the global ISM of galaxies, we analyze the relationship between recent enhancements of central star formation and total molecular-to-atomic (H2/HI) gas ratios, using a broad sample of field galaxies spanning early-to-late type morphologies, stellar masses of 10^(7.2-11.2) Msun, and diverse stages of evolution. We find that galaxies occupy several loci in a "fueling diagram" that plots H2/HI vs. mass-corrected blue-centeredness, a metric tracing the degree to which galaxies have bluer centers than the average galaxy at their stellar mass. Spiral galaxies show a positive correlation between H2/HI and mass-corrected blue-centeredness. When combined with previous results linking mass-corrected blue-centeredness to external perturbations, this correlation suggests a link between local galaxy interactions and molecular gas inflow/replenishment. Intriguingly, E/S0 galaxies show a more complex picture: some follow the same cor...

  11. Interaction of cationic hydrophobic surfactants at negatively charged surfaces investigated by atomic force microscopy.

    Science.gov (United States)

    McNamee, Cathy E; Butt, Hans-Jürgen; Higashitani, Ko; Vakarelski, Ivan U; Kappl, Michael

    2009-10-06

    Atomic force microscopy was used to study the adsorption of the surfactant octadecyl trimethyl ammonium chloride (C18TAC) at a low concentration (0.03 mM) to negatively charged surfaces in water. Atomic force microscopy tips were functionalized with dimethyloctadecyl(3-tripropyl)ammonium chloride (C18TAC-si) or N-trimethoxysilylpropyl-N,N,N-trimethylammomium chloride (hydrophilpos-si) to facilitate imaging of the adsorbed surfactant without artifacts. Tapping mode images and force measurements revealed C18TAC patches, identified as partial surfactant bilayers or hemimicelles. The forces controlling the adsorption process of the C18TAC to a negatively charged surface were investigated by measuring the forces between a C18TAC-si or a hydrophilpos-si tip and a silica surface in the presence of varying concentrations of either NaCl or NaNO3. Screening of forces with an increasing NaCl concentration was observed for the C18TAC-si and hydrophilpos-si tips, proving an electrostatic contribution. Screening was also observed for the hydrophilpos-si tip in NaNO3, whereas a long-range attraction was observed for the C18TAC-si tip for all NaNO3 concentrations. These results indicate that screening of the forces for the C18TAC-si tip depended on the type and/or size of the anion, possibly due to a different probability of the anions to enter the silane layers. The interaction of C18TAC patches with C18TAC-si tips in the presence of NaCl and the interaction of the patches with hydrophilpos-si tips in either NaCl or NaNO3 were repulsive and independent of the number of force curves measured, indicating a stable, positively charged C18TAC patch. However, the forces measured between the patches and a C18TAC-si tip in NaNO3 depended on the number of force curves measured, indicating a change in patch structure induced by the first interaction.

  12. Single Molecule Science for Personalized Nanomedicine: Atomic Force Microscopy of Biopolymer-Protein Interactions

    Science.gov (United States)

    Hsueh, Carlin

    Nanotechnology has a unique and relatively untapped utility in the fields of medicine and dentistry at the level of single-biopolymer and -molecule diagnostics. In recent years atomic force microscopy (AFM) has garnered much interest due to its ability to obtain atomic-resolution of molecular structures and probe biophysical behaviors of biopolymers and proteins in a variety of biologically significant environments. The work presented in this thesis focuses on the nanoscale manipulation and observation of biopolymers to develop an innovative technology for personalized medicine while understanding complex biological systems. These studies described here primarily use AFM to observe biopolymer interactions with proteins and its surroundings with unprecedented resolution, providing a better understanding of these systems and interactions at the nanoscale. Transcriptional profiling, the measure of messenger RNA (mRNA) abundance in a single cell, is a powerful technique that detects "behavior" or "symptoms" at the tissue and cellular level. We have sought to develop an alternative approach, using our expertise in AFM and single molecule nanotechnology, to achieve a cost-effective high throughput method for sensitive detection and profiling of subtle changes in transcript abundance. The technique does not require amplification of the mRNA sample because the AFM provides three-dimensional views of molecules with unprecedented resolution, requires minimal sample preparation, and utilizes a simple tagging chemistry on cDNA molecules. AFM images showed collagen polymers in teeth and of Drebrin-A remodeling of filamentous actin structure and mechanics. AFM was used to image collagen on exposed dentine tubules and confirmed tubule occlusion with a desensitizing prophylaxis paste by Colgate-Palmolive. The AFM also superseded other microscopy tools in resolving F-actin helix remodeling and possible cooperative binding by a neuronal actin binding protein---Drebrin-A, an

  13. Project LINK: ``A Live and Interactive Network of Knowledge"

    Science.gov (United States)

    Hawkins, I.; Welsh, B.

    1995-05-01

    Project LINK (A Live and Interactive Network of Knowledge), a collaboration among Eureka Scientific, Inc., the Exploratorium, and NASA/Ames Research Center will demonstrate video-conferencing capabilities from the Kuiper Airborne Observatory (KAO) to the San Francisco Exploratorium in the context of science education outreach to K--12 teachers and students. The project is intended to pilot-test strategies for facilitating the live interface between scientists aboard the KAO and K-12 teachers and students through the resources and technical expertise available at science museums and private industry. The interface will be based on Internet/CuSeeMe videoconferencing capabilities which will allow teachers and students at the Exploratorium to collaborate in a live and interactive manner with teachers and scientists aboard the KAO. The teacher teams chosen for the on-board experiments represent rural and urban school districts in California. The teachers will interface with colleagues as part of the NASA-Funded Project FOSTER (Flight Opportunities for Science Teacher EnRichment). Our project will serve to demonstrate live interface capabilities in preparation for the ``Live from the Stratosphere" Project. Teachers from Project LINK will participate on two flights aboard the KAO during the Summer of 1995. Lesson plans, classroom activities, project description and lessons learned will be disseminated through the World Wide Web. Project LINK is made possible by a grant from NASA to Eureka Scientific, Inc.

  14. 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.

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

    Science.gov (United States)

    Quattrociocchi, Walter; Caldarelli, Guido; Scala, Antonio

    2014-05-27

    The inner dynamics of the multiple actors of the informations systems - i.e, T.V., newspapers, blogs, social network platforms, - play a fundamental role on the evolution of the public opinion. Coherently with the recent history of the information system (from few main stream media to the massive diffusion of socio-technical system), in this work we investigate how main stream media signed interaction might shape the opinion space. In particular we focus on how different size (in the number of media) and interaction patterns of the information system may affect collective debates and thus the opinions' distribution. We introduce a sophisticated computational model of opinion dynamics which accounts for the coexistence of media and gossip as separated mechanisms and for their feedback loops. The model accounts also for the effect of the media communication patterns by considering both the simple case where each medium mimics the behavior of the most successful one (to maximize the audience) and the case where there is polarization and thus competition among media memes. We show that plurality and competition within information sources lead to stable configurations where several and distant cultures coexist.

  16. Investigating the importance of Delaunay-based definition of atomic interactions in scoring of protein-protein docking results.

    Science.gov (United States)

    Jafari, Rahim; Sadeghi, Mehdi; Mirzaie, Mehdi

    2016-05-01

    The approaches taken to represent and describe structural features of the macromolecules are of major importance when developing computational methods for studying and predicting their structures and interactions. This study attempts to explore the significance of Delaunay tessellation for the definition of atomic interactions by evaluating its impact on the performance of scoring protein-protein docking prediction. Two sets of knowledge-based scoring potentials are extracted from a training dataset of native protein-protein complexes. The potential of the first set is derived using atomic interactions extracted from Delaunay tessellated structures. The potential of the second set is calculated conventionally, that is, using atom pairs whose interactions were determined by their separation distances. The scoring potentials were tested against two different docking decoy sets and their performances were compared. The results show that, if properly optimized, the Delaunay-based scoring potentials can achieve higher success rate than the usual scoring potentials. These results and the results of a previous study on the use of Delaunay-based potentials in protein fold recognition, all point to the fact that Delaunay tessellation of protein structure can provide a more realistic definition of atomic interaction, and therefore, if appropriately utilized, may be able to improve the accuracy of pair potentials.

  17. Spin filtering and switching action in a diamond network with magnetic-nonmagnetic atomic distribution

    Science.gov (United States)

    Pal, Biplab; Dutta, Paramita

    2016-09-01

    We propose a simple model quantum network consisting of diamond-shaped plaquettes with deterministic distribution of magnetic and non-magnetic atoms in presence of a uniform external magnetic flux in each plaquette and predict that such a simple model can be a prospective candidate for spin filter as well as flux driven spintronic switch. The orientations and the amplitudes of the substrate magnetic moments play a crucial role in the energy band engineering of the two spin channels which essentially gives us a control over the spin transmission leading to a spin filtering effect. The externally tunable magnetic flux plays an important role in inducing a switch on-switch off effect for both the spin states indicating the behavior like a spintronic switch. Even a correlated disorder configuration in the on-site potentials and in the magnetic moments may lead to disorder-induced spin filtering phenomenon where one of the spin channel gets entirely blocked leaving the other one transmitting over the entire allowed energy regime. All these features are established by evaluating the density of states and the two terminal transmission probabilities using the transfer-matrix formalism within a tight-binding framework. Experimental realization of our theoretical study may be helpful in designing new spintronic devices.

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

    Science.gov (United States)

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

    2014-05-01

    Cancer risk at low doses of ionizing radiation remains poorly defined because of ambiguity in the quantitative link to doses below 0.2 Sv in atomic bomb survivors in Hiroshima and Nagasaki arising from limitations in the statistical power and information available on overall radiation dose. To deal with these difficulties, a novel nonparametric statistics based on the 'integrate-and-fire' algorithm of artificial neural networks was developed and tested in cancer databases established by the Radiation Effects Research Foundation. The analysis revealed unique features at low doses that could not be accounted for by nominal exposure dose, including (i) the presence of a threshold that varied with organ, gender and age at exposure, and (ii) a small but significant bumping increase in cancer risk at low doses in Nagasaki that probably reflects internal exposure to (239)Pu. The threshold was distinct from the canonical definition of zero effect in that it was manifested as negative excess relative risk, or suppression of background cancer rates. Such a unique tissue response at low doses of radiation exposure has been implicated in the context of the molecular basis of radiation-environment interplay in favor of recently emerging experimental evidence on DNA double-strand break repair pathway choice and its epigenetic memory by histone marking.

  19. Influence of Halide Solutions on Collagen Networks: Measurements of Physical Properties by Atomic Force Microscopy

    Science.gov (United States)

    Kempe, André; Lackner, Maximilian

    2016-01-01

    The influence of aqueous halide solutions on collagen coatings was tested. The effects on resistance against indentation/penetration on adhesion forces were measured by atomic force microscopy (AFM) and the change of Young's modulus of the coating was derived. Comparative measurements over time were conducted with halide solutions of various concentrations. Physical properties of the mesh-like coating generally showed large variability. Starting with a compact set of physical properties, data disperse after minutes. A trend of increase in elasticity and permeability was found for all halide solutions. These changes were largest in NaI, displaying a logical trend with ion size. However a correlation with concentration was not measured. Adhesion properties were found to be independent of mechanical properties. The paper also presents practical experience for AFM measurements of soft tissue under liquids, particularly related to data evaluation. The weakening in physical strength found after exposure to halide solutions may be interpreted as widening of the network structure or change in the chemical properties in part of the collagen fibres (swelling). In order to design customized surface coatings at optimized conditions also for medical applications, halide solutions might be used as agents with little impact on the safety of patients.

  20. Homology modeling, molecular dynamics and atomic level interaction study of snake venom 5' nucleotidase.

    Science.gov (United States)

    Arafat, A Syed Yasir; Arun, A; Ilamathi, M; Asha, J; Sivashankari, P R; D'Souza, Cletus J M; Sivaramakrishnan, V; Dhananjaya, B L

    2014-03-01

    5' Nucleotidase (5' NUC) is a ubiquitously distributed enzyme known to be present in snake venoms (SV) that is responsible primarily for causing dysregulation of physiological homeostasis in humans by inducing anticoagulant effects and by inhibiting platelet aggregation. It is also known to act synergistically with other toxins to exert a more pronounced anti-coagulant effect during envenomation. Its structural and functional role is not yet ascertained clearly. The 3D structure of snake venom 5' nucleotidase (SV-5' NUC) is not yet known and was predicted by us for the first time using a comparative homology modeling approach using Demansia vestigiata protein sequence. The accuracy and stability of the predicted SV-5' NUC structure were validated using several computational approaches. Key interactions of SV-5' NUC were studied using experimental studies/molecular docking analysis of the inhibitors vanillin, vanillic acid and maltol. All these inhibitors were found to dock favorably following pharmacologically relevant absorption, distribution, metabolism and excretion (ADME) profiles. Further, atomic level docking interaction studies using inhibitors of the SV-5' NUC active site revealed amino acid residues Y65 and T72 as important for inhibitor-(SV-5' NUC) interactions. Our in silico analysis is in good agreement with experimental inhibition results of SV-5' NUC with vanillin, vanillic acid and maltol. The present study should therefore play a guiding role in the experimental design of new SV-5' NUC inhibitors for snake bite management. We also identified a few pharmacophoric features essential for SV-5' NUC inhibitory activity that can be utilized further for the discovery of putative anti-venom agents of therapeutic value for snake bite management.

  1. Conformational Preference and Donor Atom Interaction Leading to Hexacoordination vs Pentacoordination in Bicyclic Tetraoxyphosphoranes(1).

    Science.gov (United States)

    Sherlock, David J.; Chandrasekaran, A.; Prakasha, T. K.; Day, Roberta O.; Holmes, Robert R.

    1998-01-12

    New bicyclic tetraoxyphosphoranes all containing a six-membered oxaphosphorinane ring, C(6)H(8)(CH(2)O)(2)P(OC(12)H(8))(OXyl) (1), (C(6)H(4)O)(2)P(OC(12)H(8))(OXyl) (2), CH(2)[(t-Bu)(2)C(6)H(2)O](2)P(OC(12)H(8))(OXyl) (3), O(2)S[(t-Bu)MeC(6)H(2)O](2)P(OC(12)H(8))(OXyl) (4), and S[(t-Bu)MeC(6)H(2)O](2)P(OC(12)H(8))(OXyl) (5), were synthesized by the oxidative addition reaction of the cyclic phosphine P(OC(12)H(8))(OXyl) (6) with an appropriate diol in the presence of N-chlorodiisopropylamine. X-ray analysis revealed trigonal bipyramidal (TBP) geometries for 1-4 where the dioxa ring varied in size from six- to eight-membered. With a sulfur donor atom as part of an eight-membered ring in place of a potential oxygen donor atom of a sulfone group as in 4, the X-ray study of 5 showed the formation of a hexacoordinated structure via a P-S interaction. Ring constraints are evaluated to give an order of conformational flexibility associated with the (TBP) tetraoxyphosphoranes 4 > 3 approximately 1 > 2 which parallels the degree of shielding from (31)P NMR chemical shifts: 4 > 3 > 1 > 2. The six- and seven-membered dioxa rings in 1 and 2, respectively, are positioned at axial-equatorial sites, whereas the eight-membered dioxa ring in 3 and 4 occupies diequatorial sites of a TBP. V-T (1)H NMR data give barriers to xylyl group rotation about the C-OXyl bond. The geometry of 5 is located along a coordinate from square pyramidal toward octahedral to the extent of 60.7%. Achieving hexacoordination in bicyclic tetraoxyphosphoranes of reduced electrophilicity relative to bicyclic pentaoxyphosphoranes appears to be dependent on the presence of a sufficiently strong donor atom.

  2. Interaction of a two-level atom with single-mode optical field beyond the rotating wave approximation.

    Science.gov (United States)

    Liu, Ju; Li, Zhi-Yuan

    2014-11-17

    One of the simplest models involving the atom-field interaction is the coupling of a single two-level atom with single-mode optical field. Under the rotating wave approximation, this problem is reduced to a form that can be solved exactly. But the approximation is only valid when the two levels are resonant or nearly resonant with the applied electromagnetic radiation. Here we present an analytical solution without the rotating wave approximation and applicable to general atom-field interaction far away from the resonance. We find that there exists remarkable influence of the initial phase of optical field on the Rabi oscillations and Rabi splitting, and this issue cannot be explored in the context of the rotating wave approximation. Due to the retention of the counter-rotating terms, higher-order harmonic appears during the Rabi splitting. The analytical solution suggests a way to regulate and control the quantum dynamics of a two-level atom and allows for exploring more essential features of the atom-field interaction.

  3. Drug-target interaction prediction by random walk on the heterogeneous network.

    Science.gov (United States)

    Chen, Xing; Liu, Ming-Xi; Yan, Gui-Ying

    2012-07-01

    Predicting potential drug-target interactions from heterogeneous biological data is critical not only for better understanding of the various interactions and biological processes, but also for the development of novel drugs and the improvement of human medicines. In this paper, the method of Network-based Random Walk with Restart on the Heterogeneous network (NRWRH) is developed to predict potential drug-target interactions on a large scale under the hypothesis that similar drugs often target similar target proteins and the framework of Random Walk. Compared with traditional supervised or semi-supervised methods, NRWRH makes full use of the tool of the network for data integration to predict drug-target associations. It integrates three different networks (protein-protein similarity network, drug-drug similarity network, and known drug-target interaction networks) into a heterogeneous network by known drug-target interactions and implements the random walk on this heterogeneous network. When applied to four classes of important drug-target interactions including enzymes, ion channels, GPCRs and nuclear receptors, NRWRH significantly improves previous methods in terms of cross-validation and potential drug-target interaction prediction. Excellent performance enables us to suggest a number of new potential drug-target interactions for drug development.

  4. Refining ensembles of predicted gene regulatory networks based on characteristic interaction sets.

    Directory of Open Access Journals (Sweden)

    Lukas Windhager

    Full Text Available Different ensemble voting approaches have been successfully applied for reverse-engineering of gene regulatory networks. They are based on the assumption that a good approximation of true network structure can be derived by considering the frequencies of individual interactions in a large number of predicted networks. Such approximations are typically superior in terms of prediction quality and robustness as compared to considering a single best scoring network only. Nevertheless, ensemble approaches only work well if the predicted gene regulatory networks are sufficiently similar to each other. If the topologies of predicted networks are considerably different, an ensemble of all networks obscures interesting individual characteristics. Instead, networks should be grouped according to local topological similarities and ensemble voting performed for each group separately. We argue that the presence of sets of co-occurring interactions is a suitable indicator for grouping predicted networks. A stepwise bottom-up procedure is proposed, where first mutual dependencies between pairs of interactions are derived from predicted networks. Pairs of co-occurring interactions are subsequently extended to derive characteristic interaction sets that distinguish groups of networks. Finally, ensemble voting is applied separately to the resulting topologically similar groups of networks to create distinct group-ensembles. Ensembles of topologically similar networks constitute distinct hypotheses about the reference network structure. Such group-ensembles are easier to interpret as their characteristic topology becomes clear and dependencies between interactions are known. The availability of distinct hypotheses facilitates the design of further experiments to distinguish between plausible network structures. The proposed procedure is a reasonable refinement step for non-deterministic reverse-engineering applications that produce a large number of candidate

  5. Van der Waals interaction between microparticle and uniaxial crystal with application to hydrogen atoms and multiwall carbon nanotubes

    CERN Document Server

    Blagov, E V; Mostepanenko, V M

    2005-01-01

    The Lifshitz theory of the van der Waals force is extended for the case of an atom (molecule) interacting with a plane surface of an uniaxial crystal or with a long solid cylinder or cylindrical shell made of isotropic material or uniaxial crystal. For a microparticle near a semispace or flat plate made of an uniaxial crystal the exact expressions for the free energy of the van der Waals and Casimir-Polder interaction are presented. An approximate expression for the free energy of microparticle- cylinder interaction is obtained which becomes precise for microparticle-cylinder separations much smaller than cylinder radius. The obtained expressions are used to investigate the van der Waals interaction between hydrogen atoms (molecules) and graphite plates or multiwall carbon nanotubes. To accomplish this the behavior of graphite dielectric permittivities along the imaginary frequency axis is found using the optical data for the complex refractive index of graphite for the ordinary and extraordinary rays. It is ...

  6. Generation of GHZ entangled states of photons in multiple cavities via a superconucting qubit or an atom through resonant interaction

    CERN Document Server

    Yang, Chui-Ping

    2012-01-01

    We propose a method to generate a GHZ entangled state of n photons in n microwave cavities (or resonators) via resonant interaction to a single superconducting qubit. By performing local operations on a qubit (e.g., a solid-state qubit, an atom, etc.) placed in each cavity, the created GHZ states of n photons can be transferred to qubits for storage. The proposed scheme greatly reduces effect of decoherence since only resonant qubit-cavity interaction and resonant qubit-pulse interaction are involved, and no measurement is required. In addition, we show that the method can be applied to create a GHZ state of photons in multiple cavities via an atom through resonant interaction with no measurement needed.

  7. Functional features and protein network of human sperm-egg interaction.

    Science.gov (United States)

    Sabetian, Soudabeh; Shamsir, Mohd Shahir; Abu Naser, Mohammed

    2014-12-01

    Elucidation of the sperm-egg interaction at the molecular level is one of the unresolved problems in sexual reproduction, and understanding the molecular mechanism is crucial in solving problems in infertility and failed in vitro fertilization (IVF). Many molecular interactions in the form of protein-protein interactions (PPIs) mediate the sperm-egg membrane interaction. Due to the complexity of the problem such as difficulties in analyzing in vivo membrane PPIs, many efforts have failed to comprehensively elucidate the fusion mechanism and the molecular interactions that mediate sperm-egg membrane fusion. The main purpose of this study was to reveal possible protein interactions and associated molecular function during sperm-egg interaction using a protein interaction network approach. Different databases have been used to construct the human sperm-egg interaction network. The constructed network revealed new interactions. These included CD151 and CD9 in human oocyte that interact with CD49 in sperm, and CD49 and ITGA4 in sperm that interact with CD63 and CD81, respectively, in the oocyte. These results showed that the different integrins in sperm may be involved in human sperm-egg interaction. It was also suggested that sperm ADAM2 plays a role as a protein candidate involved in sperm-egg membrane interaction by interacting with CD9 in the oocyte. Interleukin-4 receptor activity, receptor signaling protein tyrosine kinase activity, and manganese ion transmembrane transport activity are the major molecular functions in sperm-egg interaction protein network. The disease association analysis indicated that sperm-egg interaction defects are also reflected in other disease networks such as cardiovascular, hematological, and breast cancer diseases. By analyzing the network, we identified the major molecular functions and disease association genes in sperm-egg interaction protein. Further experimental studies will be required to confirm the significance of these new

  8. Energy Landscape of Alginate-Epimerase Interactions Assessed by Optical Tweezers and Atomic Force Microscopy.

    Directory of Open Access Journals (Sweden)

    Armend Gazmeno Håti

    Full Text Available Mannuronan C-5 epimerases are a family of enzymes that catalyze epimerization of alginates at the polymer level. This group of enzymes thus enables the tailor-making of various alginate residue sequences to attain various functional properties, e.g. viscosity, gelation and ion binding. Here, the interactions between epimerases AlgE4 and AlgE6 and alginate substrates as well as epimerization products were determined. The interactions of the various epimerase-polysaccharide pairs were determined over an extended range of force loading rates by the combined use of optical tweezers and atomic force microscopy. When studying systems that in nature are not subjected to external forces the access to observations obtained at low loading rates, as provided by optical tweezers, is a great advantage since the low loading rate region for these systems reflect the properties of the rate limiting energy barrier. The AlgE epimerases have a modular structure comprising both A and R modules, and the role of each of these modules in the epimerization process were examined through studies of the A- module of AlgE6, AlgE6A. Dynamic strength spectra obtained through combination of atomic force microscopy and the optical tweezers revealed the existence of two energy barriers in the alginate-epimerase complexes, of which one was not revealed in previous AFM based studies of these complexes. Furthermore, based on these spectra estimates of the locations of energy transition states (xβ, lifetimes in the absence of external perturbation (τ0 and free energies (ΔG# were determined for the different epimerase-alginate complexes. This is the first determination of ΔG# for these complexes. The values determined were up to 8 kBT for the outer barrier, and smaller values for the inner barriers. The size of the free energies determined are consistent with the interpretation that the enzyme and substrate are thus not tightly locked at all times but are able to relocate

  9. Gene regulatory network interactions in sea urchin endomesoderm induction.

    Directory of Open Access Journals (Sweden)

    Aditya J Sethi

    2009-02-01

    Full Text Available A major goal of contemporary studies of embryonic development is to understand large sets of regulatory changes that accompany the phenomenon of embryonic induction. The highly resolved sea urchin pregastrular endomesoderm-gene regulatory network (EM-GRN provides a unique framework to study the global regulatory interactions underlying endomesoderm induction. Vegetal micromeres of the sea urchin embryo constitute a classic endomesoderm signaling center, whose potential to induce archenteron formation from presumptive ectoderm was demonstrated almost a century ago. In this work, we ectopically activate the primary mesenchyme cell-GRN (PMC-GRN that operates in micromere progeny by misexpressing the micromere determinant Pmar1 and identify the responding EM-GRN that is induced in animal blastomeres. Using localized loss-of -function analyses in conjunction with expression of endo16, the molecular definition of micromere-dependent endomesoderm specification, we show that the TGFbeta cytokine, ActivinB, is an essential component of this induction in blastomeres that emit this signal, as well as in cells that respond to it. We report that normal pregastrular endomesoderm specification requires activation of the Pmar1-inducible subset of the EM-GRN by the same cytokine, strongly suggesting that early micromere-mediated endomesoderm specification, which regulates timely gastrulation in the sea urchin embryo, is also ActivinB dependent. This study unexpectedly uncovers the existence of an additional uncharacterized micromere signal to endomesoderm progenitors, significantly revising existing models. In one of the first network-level characterizations of an intercellular inductive phenomenon, we describe an important in vivo model of the requirement of ActivinB signaling in the earliest steps of embryonic endomesoderm progenitor specification.

  10. Using Concept Maps as Instructional Materials to Foster the Understanding of the Atomic Model and Matter-Energy Interaction

    Science.gov (United States)

    Aguiar, Joana G.; Correia, Paulo R. M.

    2016-01-01

    In this paper, we explore the use of concept maps (Cmaps) as instructional materials prepared by teachers, to foster the understanding of chemistry. We choose fireworks as a macroscopic event to teach basic chemical principles related to the Bohr atomic model and matter-energy interaction. During teachers' Cmap navigation, students can experience…

  11. Use of a PhET Interactive Simulation in General Chemistry Laboratory: Models of the Hydrogen Atom

    Science.gov (United States)

    Clark, Ted M.; Chamberlain, Julia M.

    2014-01-01

    An activity supporting the PhET interactive simulation, Models of the Hydrogen Atom, has been designed and used in the laboratory portion of a general chemistry course. This article describes the framework used to successfully accomplish implementation on a large scale. The activity guides students through a comparison and analysis of the six…

  12. Development and implementation of an algorithm for detection of protein complexes in large interaction networks

    Directory of Open Access Journals (Sweden)

    Kanaya Shigehiko

    2006-04-01

    Full Text Available Abstract Background After complete sequencing of a number of genomes the focus has now turned to proteomics. Advanced proteomics technologies such as two-hybrid assay, mass spectrometry etc. are producing huge data sets of protein-protein interactions which can be portrayed as networks, and one of the burning issues is to find protein complexes in such networks. The enormous size of protein-protein interaction (PPI networks warrants development of efficient computational methods for extraction of significant complexes. Results This paper presents an algorithm for detection of protein complexes in large interaction networks. In a PPI network, a node represents a protein and an edge represents an interaction. The input to the algorithm is the associated matrix of an interaction network and the outputs are protein complexes. The complexes are determined by way of finding clusters, i. e. the densely connected regions in the network. We also show and analyze some protein complexes generated by the proposed algorithm from typical PPI networks of Escherichia coli and Saccharomyces cerevisiae. A comparison between a PPI and a random network is also performed in the context of the proposed algorithm. Conclusion The proposed algorithm makes it possible to detect clusters of proteins in PPI networks which mostly represent molecular biological functional units. Therefore, protein complexes determined solely based on interaction data can help us to predict the functions of proteins, and they are also useful to understand and explain certain biological processes.

  13. Fading characterization for context aware body area networks (CABAN) in interactive smart environments

    NARCIS (Netherlands)

    Heaney, S.F.; Scanlon, W.G.; Garcia-Palacios, E.; Cotton, S.L.

    2010-01-01

    Body Area Networks are unique in that the large-scale mobility of users allows the network itself to travel across a diverse range of operating domains. This presents the possibility of creating interactive smart environments where Context Aware Body Area Networks can sense and co-operate with nearb

  14. New experimental results on the interference of the states of the hydrogen atom due to long-range interaction with the metal surface

    NARCIS (Netherlands)

    Kucheryaev, YA; Pal'chikov, VG; Pchelin, YA; Sokolov, YL; Yakovlev, VP

    2005-01-01

    The interference of the 2P state of the hydrogen atom due to unknown long-range interaction with the metal surface (Sokolov effect) has been studied by an atomic interferometer. In contrast to previous experiments, where an atomic beam passed through slits in metal plates, a beam in the presented ex

  15. Modes of Escherichia coli Dps Interaction with DNA as Revealed by Atomic Force Microscopy.

    Directory of Open Access Journals (Sweden)

    Vladislav V Melekhov

    Full Text Available Multifunctional protein Dps plays an important role in iron assimilation and a crucial role in bacterial genome packaging. Its monomers form dodecameric spherical particles accumulating ~400 molecules of oxidized iron ions within the protein cavity and applying a flexible N-terminal ends of each subunit for interaction with DNA. Deposition of iron is a well-studied process by which cells remove toxic Fe2+ ions from the genetic material and store them in an easily accessible form. However, the mode of interaction with linear DNA remained mysterious and binary complexes with Dps have not been characterized so far. It is widely believed that Dps binds DNA without any sequence or structural preferences but several lines of evidence have demonstrated its ability to differentiate gene expression, which assumes certain specificity. Here we show that Dps has a different affinity for the two DNA fragments taken from the dps gene regulatory region. We found by atomic force microscopy that Dps predominantly occupies thermodynamically unstable ends of linear double-stranded DNA fragments and has high affinity to the central part of the branched DNA molecule self-assembled from three single-stranded oligonucleotides. It was proposed that Dps prefers binding to those regions in DNA that provide more contact pads for the triad of its DNA-binding bundle associated with one vertex of the protein globule. To our knowledge, this is the first study revealed the nucleoid protein with an affinity to branched DNA typical for genomic regions with direct and inverted repeats. As a ubiquitous feature of bacterial and eukaryotic genomes, such structural elements should be of particular care, but the protein system evolutionarily adapted for this function is not yet known, and we suggest Dps as a putative component of this system.

  16. Measurement of the parity nonconserving neutral weak interaction in atomic thallium

    Energy Technology Data Exchange (ETDEWEB)

    Bucksbaum, P.H.

    1980-11-01

    This thesis describes an experiment to measure parity nonconservation in atomic thallium. A frequency doubled, flashlamp pumped tunable dye laser is used to excite the 6P/sub 1/2/(F = 0) ..-->.. 7P/sub 1/2/(F = 1) transition at 292.7 nm, with circularly polarized light. An electrostatic field E of 100 to 300 V/cm causes this transition to occur via Stark induced electric dipole. Two field free transitions may also occur: a highly forbidden magnetic dipole M, and a parity nonconserving electric dipole epsilon/sub P/. The latter is presumed to be due to the presence of a weak neutral current interaction between the 6p valence electron and the nucleus, as predicted by gauge theories which unite the electromagnetic and weak interactions. Both M and epsilon/sub P/ interfere with the Stark amplitude ..beta..E to produce a polarization of the 7P/sub 1/2/ state. This is measured with a circularly polarized infrared laser beam probe, tuned to the 7P/sub 1/2/ ..-->.. 8S/sub 1/2/ transition. This selectively excites m/sub F/ = +1 or -1 components of the 7P/sub 1/2/ state, and the polarization is seen as an asymmetry in 8S ..-->.. 6P/sub 3/2/ fluorescence when the probe helicity is reversed. The polarization due to M is ..delta../sub M/ = -2M/(BETAE). It is used to calibrate the analyzing efficiency. The polarization due to epsilon/sub P/ is ..delta../sub P/ = 2i epsilon/sub P//(..beta..E), and can be distinguished from ..delta../sub M/ by its properties under reversal of the 292.7 nm photon helicity and reversal of the laser direction. A preliminary measurement yielded a parity violation in agreement with the gauge theory of Weinberg and Salam.

  17. Predict drug-protein interaction in cellular networking.

    Science.gov (United States)

    Xiao, Xuan; Min, Jian-Liang; Wang, Pu; Chou, Kuo-Chen

    2013-01-01

    Involved with many diseases such as cancer, diabetes, neurodegenerative, inflammatory and respiratory disorders, GPCRs (G-protein-coupled receptors) are the most frequent targets for drug development: over 50% of all prescription drugs currently on the market are actually acting by targeting GPCRs directly or indirectly. Found in every living thing and nearly all cells, ion channels play crucial roles for many vital functions in life, such as heartbeat, sensory transduction, and central nervous system response. Their dysfunction may have significant impact to human health, and hence ion channels are deemed as "the next GPCRs". To develop GPCR-targeting or ion-channel-targeting drugs, the first important step is to identify the interactions between potential drug compounds with the two kinds of protein receptors in the cellular networking. In this minireview, we are to introduce two predictors. One is called iGPCR-Drug accessible at http://www.jci-bioinfo.cn/iGPCR-Drug/; the other called iCDI-PseFpt at http://www.jci-bioinfo.cn/iCDI-PseFpt. The former is for identifying the interactions of drug compounds with GPCRs; while the latter for that with ion channels. In both predictors, the drug compound was formulated by the two-dimensional molecular fingerprint, and the protein receptor by the pseudo amino acid composition generated with the grey model theory, while the operation engine was the fuzzy K-nearest neighbor algorithm. For the convenience of most experimental pharmaceutical and medical scientists, a step-bystep guide is provided on how to use each of the two web-servers to get the desired results without the need to follow the complicated mathematics involved originally for their establishment.

  18. A scored human protein-protein interaction network to catalyze genomic interpretation

    DEFF Research Database (Denmark)

    Li, Taibo; Wernersson, Rasmus; Hansen, Rasmus B;

    2017-01-01

    Genome-scale human protein-protein interaction networks are critical to understanding cell biology and interpreting genomic data, but challenging to produce experimentally. Through data integration and quality control, we provide a scored human protein-protein interaction network (In...

  19. Topology association analysis in weighted protein interaction network for gene prioritization

    Science.gov (United States)

    Wu, Shunyao; Shao, Fengjing; Zhang, Qi; Ji, Jun; Xu, Shaojie; Sun, Rencheng; Sun, Gengxin; Du, Xiangjun; Sui, Yi

    2016-11-01

    Although lots of algorithms for disease gene prediction have been proposed, the weights of edges are rarely taken into account. In this paper, the strengths of topology associations between disease and essential genes are analyzed in weighted protein interaction network. Empirical analysis demonstrates that compared to other genes, disease genes are weakly connected with essential genes in protein interaction network. Based on this finding, a novel global distance measurement for gene prioritization with weighted protein interaction network is proposed in this paper. Positive and negative flow is allocated to disease and essential genes, respectively. Additionally network propagation model is extended for weighted network. Experimental results on 110 diseases verify the effectiveness and potential of the proposed measurement. Moreover, weak links play more important role than strong links for gene prioritization, which is meaningful to deeply understand protein interaction network.

  20. Elemental Analysis of Nanomaterial Using Photon-Atom Interaction Based EDXRF Technique

    Directory of Open Access Journals (Sweden)

    Sanjeev Kumar

    2013-08-01

    Full Text Available Presence of trace amount of foreign impurities (both metallic and non-metallic in standard salts used for sample preparation and during the synthesis process can alter the physical and chemical behavior of the pure and doped nano-materials. Therefore, it becomes important to determine concentration of various elements present in synthesized nano-material sample. In present work, the elemental and compositional analysis of nano-materials synthesized using various methods has been performed using photon-atom interaction based energy dispersive x-ray fluorescence (EDXRF technique. This technique due to its multielement analytical capability, lower detection limit, capability to analyze metals and non-metals alike and almost no sample preparation requirements can be utilized for analysis of nano-materials. The EDXRF spectrometer involves a 2.4 kW Mo anode x-ray tube (Pananalytic, Netherland equipped with selective absorbers as an excitation source and an LEGe detector (FWHM = 150 eV at 5.895 keV, Canberra, US coupled with PC based multichannel analyzer used to collect the fluorescentx-ray spectra. The analytical results showed good agreements with the expected values calculated on the basis of the precursor used in preparation of nano-materials.

  1. Interactions and low energy collisions between an alkali ion and an alkali atom of different nucleus

    CERN Document Server

    Rakshit, Arpita; Berriche, Hamid; Deb, Bimalendu

    2015-01-01

    We study theoretically interaction potentials and low energy collisions between different alkali atoms and alkali ions. Specifically, we consider systems like X + Y$^{+}$, where X(Y$^{+})$ is either Li(Cs$^+$) or Cs((Li$^+$), Na(Cs$^+$) or Cs(Na$^+$) and Li(Rb$^+$) or Rb(Li$^+$). We calculate the molecular potentials of the ground and first two excited states of these three systems using pseudopotential method and compare our results with those obtained by others. We calculate ground-state scattering wave functions and cross sections of these systems for a wide range of energies. We find that, in order to get convergent results for the total scattering cross sections for energies of the order $1$ K, one needs to take into account at least 60 partial waves. In the low energy limit ($< 1 \\mu$K), elastic scattering cross sections exhibit Wigner law threshold behavior while in the high energy limit the cross sections go as $E^{-1/3}$. We discuss qualitatively the possibilities of forming cold molecular ion by ...

  2. Use of Hilbert Curves in Parallelized CUDA code: Interaction of Interstellar Atoms with the Heliosphere

    Science.gov (United States)

    Destefano, Anthony; Heerikhuisen, Jacob

    2015-04-01

    Fully 3D particle simulations can be a computationally and memory expensive task, especially when high resolution grid cells are required. The problem becomes further complicated when parallelization is needed. In this work we focus on computational methods to solve these difficulties. Hilbert curves are used to map the 3D particle space to the 1D contiguous memory space. This method of organization allows for minimized cache misses on the GPU as well as a sorted structure that is equivalent to an octal tree data structure. This type of sorted structure is attractive for uses in adaptive mesh implementations due to the logarithm search time. Implementations using the Message Passing Interface (MPI) library and NVIDIA's parallel computing platform CUDA will be compared, as MPI is commonly used on server nodes with many CPU's. We will also compare static grid structures with those of adaptive mesh structures. The physical test bed will be simulating heavy interstellar atoms interacting with a background plasma, the heliosphere, simulated from fully consistent coupled MHD/kinetic particle code. It is known that charge exchange is an important factor in space plasmas, specifically it modifies the structure of the heliosphere itself. We would like to thank the Alabama Supercomputer Authority for the use of their computational resources.

  3. Fermi and Coulomb correlation effects upon the interacting quantum atoms energy partition

    CERN Document Server

    Ruiz, Isela; Holguín-Gallego, Fernando José; Francisco, Evelio; Pendás, Ángel Martín; Rocha-Rinza, Tomás

    2016-01-01

    The Interacting Quantum Atoms (IQA) electronic energy partition is an important method in the field of quantum chemical topology which has given important insights of different systems and processes in physical chemistry. There have been several attempts to include Electron Correlation (EC) in the IQA approach, for example, through DFT and Hartree-Fock/Coupled-Cluster (HF/CC) transition densities. This work addresses the separation of EC in Fermi and Coulomb correlation and its effect upon the IQA analysis by taking into account spin-dependent one- and two-electron matrices $D^{\\mathrm{HF/CC}}_{p\\sigma q \\sigma}$ and $d^{\\mathrm{HF/CC}}_{p\\sigma q\\sigma r\\tau s\\tau}$ wherein $\\sigma$ and $\\tau$ represent either of the $\\alpha$ and $\\beta$ spin projections. We illustrate this approach by considering BeH$_2$,BH, CN$^-$, HF, LiF, NO$^+$, LiH, H$_2$O$\\cdots$H$_2$O and C$_2$H$_2$, which comprise non-polar covalent, polar covalent, ionic and hydrogen bonded systems. The same and different spin contributions to ($i$...

  4. Sulphur Atoms from Methionines Interacting with Aromatic Residues Are Less Prone to Oxidation

    Science.gov (United States)

    Aledo, Juan C.; Cantón, Francisco R.; Veredas, Francisco J.

    2015-11-01

    Methionine residues exhibit different degrees of susceptibility to oxidation. Although solvent accessibility is a relevant factor, oxidation at particular sites cannot be unequivocally explained by accessibility alone. To explore other possible structural determinants, we assembled different sets of oxidation-sensitive and oxidation-resistant methionines contained in human proteins. Comparisons of the proteins containing oxidized methionines with all proteins in the human proteome led to the conclusion that the former exhibit a significantly higher mean value of methionine content than the latter. Within a given protein, an examination of the sequence surrounding the non-oxidized methionine revealed a preference for neighbouring tyrosine and tryptophan residues, but not for phenylalanine residues. However, because the interaction between sulphur atoms and aromatic residues has been reported to be important for the stabilization of protein structure, we carried out an analysis of the spatial interatomic distances between methionines and aromatic residues, including phenylalanine. The results of these analyses uncovered a new determinant for methionine oxidation: the S-aromatic motif, which decreases the reactivity of the involved sulphur towards oxidants.

  5. Recurrent Interactions in Spiking Networks with Arbitrary Topology

    OpenAIRE

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

    2011-01-01

    The population activity of random networks of excitatory and inhibitory leaky integrate-and-fire (LIF) 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...

  6. The atom-surface interaction potential for He-NaCl: A model based on pairwise additivity

    Science.gov (United States)

    Hutson, Jeremy M.; Fowler, P. W.

    1986-08-01

    The recently developed semi-empirical model of Fowler and Hutson is applied to the He-NaCl atom-surface interaction potential. Ab initio self-consistent field calculations of the repulsive interactions between He atoms and in-crystal Cl - and Na + ions are performed. Dispersion coefficients involving in-crystal ions are also calculated. The atom-surface potential is constructed using a model based on pairwise additivity of atom-ion forces. With a small adjustment of the repulsive part, this potential gives good agreement with the experimental bound state energies obtained from selective adsorption resonances in low-energy atom scattering experiments. Close-coupling calculations of the resonant scattering are performed, and good agreement with the experimental peak positions and intensity patterns is obtained. It is concluded that there are no bound states deeper than those observed in the selective adsorption experiments, and that the well depth of the He-NaCl potential is 6.0 ± 0.2 meV.

  7. External Heavy-Atom Effect via Orbital Interactions Revealed by Single-Crystal X-ray Diffraction.

    Science.gov (United States)

    Sun, Xingxing; Zhang, Baicheng; Li, Xinyang; Trindle, Carl O; Zhang, Guoqing

    2016-07-28

    Enhanced spin-orbit coupling through external heavy-atom effect (EHE) has been routinely used to induce room-temperature phosphorescence (RTP) for purely organic molecular materials. Therefore, understanding the nature of EHE, i.e., the specific orbital interactions between the external heavy atom and the luminophore, is of essential importance in molecular design. For organic systems, halogens (e.g., Cl, Br, and I) are the most commonly seen heavy atoms serving to realize the EHE-related RTP. In this report, we conduct an investigation on how heavy-atom perturbers and aromatic luminophores interact on the basis of data obtained from crystallography. We synthesized two classes of molecular systems including N-haloalkyl-substituted carbazoles and quinolinium halides, where the luminescent molecules are considered as "base" or "acid" relative to the heavy-atom perturbers, respectively. We propose that electron donation from a π molecular orbital (MO) of the carbazole to the σ* MO of the C-X bond (π/σ*) and n electron donation to a π* MO of the quinolinium moiety (n/π*) are responsible for the EHE (RTP) in the solid state, respectively.

  8. Expression Profiling of Human Genetic and Protein Interaction Networks in Type 1 Diabetes

    DEFF Research Database (Denmark)

    Brunak, Søren; Bergholdt, R; Brorsson, C;

    2009-01-01

    previously identified sets of genes, likely to represent distinct cellular pathways involved in T1D risk. Here we evaluate the candidate genes involved in these putative interaction networks not only at the single gene level, but also in the context of the networks of which they form an integral part. m...... in each of the four interaction networks to evaluate evidence of significant association at network level. This method provided additional support, in an independent data set, that two of the interaction networks could be involved in T1D and highlights the following processes as risk factors: oxidative......Proteins contributing to a complex disease are often members of the same functional pathways. Elucidation of such pathways may provide increased knowledge about functional mechanisms underlying disease. By combining genetic interactions in Type 1 Diabetes (T1D) with protein interaction data we have...

  9. Ultracold magnetically tunable interactions without radiative charge transfer losses between Ca$^+$, Sr$^+$, Ba$^+$, and Yb$^+$ ions and Cr atoms

    CERN Document Server

    Tomza, Michał

    2015-01-01

    The Ca$^+$, Sr$^+$, Ba$^+$, and Yb$^+$ ions immersed in an ultracold gas of the Cr atoms are proposed as experimentally feasible heteronuclear systems in which ion-atom interactions at ultralow temperatures can be controlled with magnetically tunable Feshbach resonances without charge transfer and radiative losses. \\textit{Ab initio} techniques are applied to investigate electronic-ground-state properties of the (CaCr)$^+$, (SrCr)$^+$, (BaCr)$^+$, and (YbCr)$^+$ molecular ions. The potential energy curves, permanent electric dipole moments, and static electric dipole polarizabilities are computed. The spin restricted open-shell coupled cluster method restricted to single, double, and noniterative triple excitations, RCCSD(T), and the multireference configuration interaction method restricted to single and double excitations, MRCISD, are employed. The scalar relativistic effects are included within the small-core energy-consistent pseudopotentials. The leading long-range induction and dispersion interaction co...

  10. Simulated evolution of protein-protein interaction networks with realistic topology.

    Science.gov (United States)

    Peterson, G Jack; Pressé, Steve; Peterson, Kristin S; Dill, Ken A

    2012-01-01

    We model the evolution of eukaryotic protein-protein interaction (PPI) networks. In our model, PPI networks evolve by two known biological mechanisms: (1) Gene duplication, which is followed by rapid diversification of duplicate interactions. (2) Neofunctionalization, in which a mutation leads to a new interaction with some other protein. Since many interactions are due to simple surface compatibility, we hypothesize there is an increased likelihood of interacting with other proteins in the target protein's neighborhood. We find good agreement of the model on 10 different network properties compared to high-confidence experimental PPI networks in yeast, fruit flies, and humans. Key findings are: (1) PPI networks evolve modular structures, with no need to invoke particular selection pressures. (2) Proteins in cells have on average about 6 degrees of separation, similar to some social networks, such as human-communication and actor networks. (3) Unlike social networks, which have a shrinking diameter (degree of maximum separation) over time, PPI networks are predicted to grow in diameter. (4) The model indicates that evolutionarily old proteins should have higher connectivities and be more centrally embedded in their networks. This suggests a way in which present-day proteomics data could provide insights into biological evolution.

  11. Interaction network of vascular epiphytes and trees in a subtropical forest

    Science.gov (United States)

    Ceballos, Sergio Javier; Chacoff, Natacha Paola; Malizia, Agustina

    2016-11-01

    The commensalistic interaction between vascular epiphytes and host trees is a type of biotic interaction that has been recently analysed with a network approach. This approach is useful to describe the network structure with metrics such as nestedness, specialization and interaction evenness, which can be compared with other vascular epiphyte-host tree networks from different forests of the world. However, in several cases these comparisons showed different and inconsistent patterns between these networks, and their possible ecological and evolutionary determinants have been scarcely studied. In this study, the interactions between vascular epiphytes and host trees of a subtropical forest of sierra de San Javier (Tucuman, Argentina) were analysed with a network approach. We calculated metrics to characterize the network and we analysed factors such as the abundance of species, tree size, tree bark texture, and tree wood density in order to predict interaction frequencies and network structure. The interaction network analysed exhibited a nested structure, an even distribution of interactions, and low specialization, properties shared with other obligated vascular epiphyte-host tree networks with a different assemblage structure. Interaction frequencies were predicted by the abundance of species, tree size and tree bark texture. Species abundance and tree size also predicted nestedness. Abundance indicated that abundant species interact more frequently; and tree size was an important predictor, since larger-diameter trees hosted more vascular epiphyte species than small-diameter trees. This is one of the first studies analyzing interactions between vascular epiphytes and host trees using a network approach in a subtropical forest, and taking the whole vascular epiphyte assemblage of the sampled community into account.

  12. Classical and quantum aspects of spin interaction in 3 d chains on a C u3N -Cu(110) molecular network

    Science.gov (United States)

    Bazhanov, D. I.; Stepanyuk, O. V.; Farberovich, O. V.; Stepanyuk, V. S.

    2016-01-01

    We present a study of the magnetic states and exchange coupling in transition-metal Mn, Fe, and Co atomic chains deposited on a self-corrugated C u3N -Cu(110) molecular network by means of first-principles calculations based on the density functional theory. The various adsorption sites on a bumping area of a self-corrugated C u3N layer are investigated where the atomic chains are formed at the initial stage of nanowire growth. We demonstrate, by calculating the ground-state magnetic configurations, that the exchange coupling, magnetic order, and anisotropies in atomic chains depend sensitively on their chemical composition and adsorption sites on the C u3N network. We find that the exchange interactions in atomic chains could lead to ferromagnetic or antiferromagnetic coupling of atomic spins depending on the position of the chain on the surface. The classical spin dynamics is investigated by means of the kinetic Monte Carlo method based on transition-state theory. Moreover we evaluate the Heisenberg-Dirac-Van Vleck quantum spin Hamiltonian for calculations of the magnetic susceptibility, in order to demonstrate the existence of quantum entanglement in the antiferromagnetic atomic chains at low temperatures.

  13. Analytical Model of the Nonlinear Dynamics of Cantilever Tip-Sample Surface Interactions for Various Acoustic-Atomic Force Microscopies

    Science.gov (United States)

    Cantrell, John H., Jr.; Cantrell, Sean A.

    2008-01-01

    A comprehensive analytical model of the interaction of the cantilever tip of the atomic force microscope (AFM) with the sample surface is developed that accounts for the nonlinearity of the tip-surface interaction force. The interaction is modeled as a nonlinear spring coupled at opposite ends to linear springs representing cantilever and sample surface oscillators. The model leads to a pair of coupled nonlinear differential equations that are solved analytically using a standard iteration procedure. Solutions are obtained for the phase and amplitude signals generated by various acoustic-atomic force microscope (A-AFM) techniques including force modulation microscopy, atomic force acoustic microscopy, ultrasonic force microscopy, heterodyne force microscopy, resonant difference-frequency atomic force ultrasonic microscopy (RDF-AFUM), and the commonly used intermittent contact mode (TappingMode) generally available on AFMs. The solutions are used to obtain a quantitative measure of image contrast resulting from variations in the Young modulus of the sample for the amplitude and phase images generated by the A-AFM techniques. Application of the model to RDF-AFUM and intermittent soft contact phase images of LaRC-cp2 polyimide polymer is discussed. The model predicts variations in the Young modulus of the material of 24 percent from the RDF-AFUM image and 18 percent from the intermittent soft contact image. Both predictions are in good agreement with the literature value of 21 percent obtained from independent, macroscopic measurements of sheet polymer material.

  14. Screened Coulomb interactions in metallic alloys. II. Screening beyond the single-site and atomic-sphere approximations

    DEFF Research Database (Denmark)

    Ruban, Andrei; Simak, S.I.; Korzhavyi, P.A.

    2002-01-01

    -electron potential and energy. In the case of a random alloy such interactions can be accounted for only by lifting the atomic-sphere and single-site approximations, in order to include the polarization due to local environment effects. Nevertheless, a simple parametrization of the screened Coulomb interactions...... for the ordinary single-site methods, including the generalized perturbation method, is still possible. We obtained such a parametrization for bulk and surface NiPt alloys, which allows one to obtain quantitatively accurate effective interactions in this system....

  15. Semantic integration to identify overlapping functional modules in protein interaction networks

    Directory of Open Access Journals (Sweden)

    Ramanathan Murali

    2007-07-01

    Full Text Available Abstract Background The systematic analysis of protein-protein interactions can enable a better understanding of cellular organization, processes and functions. Functional modules 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 functional module detection algorithms. Results We have developed novel metrics, called semantic similarity and semantic interactivity, which use Gene Ontology (GO annotations to measure the reliability of protein-protein interactions. The protein interaction networks can be converted into a weighted graph representation by assigning the reliability values to each interaction as a weight. We presented a flow-based modularization algorithm to efficiently identify overlapping modules in the weighted interaction networks. The experimental results show that the semantic similarity and semantic interactivity of interacting pairs were positively correlated with functional co-occurrence. The effectiveness of the algorithm for identifying modules was evaluated using functional categories from the MIPS database. We demonstrated that our algorithm had higher accuracy compared to other competing approaches. Conclusion The integration of protein interaction networks with GO annotation data and the capability of detecting overlapping modules substantially improve the accuracy of module identification.

  16. Non-Markovian Dynamics for a Two-Atom-Coupled System Interacting with Local Reservoir at Finite Temperature

    Science.gov (United States)

    Jiang, Li; Zhang, Guo-Feng

    2017-03-01

    By using the effective non-Markovian measure (Breuer et al., Phys. Rev. Lett. 103, 210401 2009) we investigate non-Markovian dynamics of a pair of two-level atoms (TLAs) system, each of which interacting with a local reservoir. We show that subsystem dynamics can be controlled by manipulating the coupling between TLAs, temperature and relaxation rate of the atoms. Moreover, the correlation between non-Markovianity of subsystem and entanglement between the subsystem and the structured bath is investigated, the results show that the emergence of non-Markovianity has a negative effect on the entanglement.

  17. Interaction of gas phase atomic hydrogen with Pt(111): Direct evidence for the formation of bulk hydrogen species

    Institute of Scientific and Technical Information of China (English)

    JIANG ZhiQuan; HUANG WeiXin; BAO XinHe

    2007-01-01

    Employing hot tungsten filament to thermal dissociate molecular hydrogen, we generated gas phase atomic hydrogen under ultra-high vacuum (UHV) conditions and investigated its interaction with Pt(111) surface. Thermal desorption spectroscopy (TDS) results demonstrate that adsorption of molecular hydrogen on Pt(111) forms surface Had species whereas adsorption of atomic hydrogen forms not only surface Had species but also bulk Had species. Bulk Had species is more thermal-unstable than surface Had species on Pt(111), suggesting that bulk Had species is more energetic. This kind of weakly- adsorbed bulk Had species might be the active hydrogen species in the Pt-catalyzed hydrogenation reactions.

  18. A coarse-grained elastic network atom contact model and its use in the simulation of protein dynamics and the prediction of the effect of mutations.

    Directory of Open Access Journals (Sweden)

    Vincent Frappier

    2014-04-01

    Full Text Available Normal mode analysis (NMA methods are widely used to study dynamic aspects of protein structures. Two critical components of NMA methods are coarse-graining in the level of simplification used to represent protein structures and the choice of potential energy functional form. There is a trade-off between speed and accuracy in different choices. In one extreme one finds accurate but slow molecular-dynamics based methods with all-atom representations and detailed atom potentials. On the other extreme, fast elastic network model (ENM methods with Cα-only representations and simplified potentials that based on geometry alone, thus oblivious to protein sequence. Here we present ENCoM, an Elastic Network Contact Model that employs a potential energy function that includes a pairwise atom-type non-bonded interaction term and thus makes it possible to consider the effect of the specific nature of amino-acids on dynamics within the context of NMA. ENCoM is as fast as existing ENM methods and outperforms such methods in the generation of conformational ensembles. Here we introduce a new application for NMA methods with the use of ENCoM in the prediction of the effect of mutations on protein stability. While existing methods are based on machine learning or enthalpic considerations, the use of ENCoM, based on vibrational normal modes, is based on entropic considerations. This represents a novel area of application for NMA methods and a novel approach for the prediction of the effect of mutations. We compare ENCoM to a large number of methods in terms of accuracy and self-consistency. We show that the accuracy of ENCoM is comparable to that of the best existing methods. We show that existing methods are biased towards the prediction of destabilizing mutations and that ENCoM is less biased at predicting stabilizing mutations.

  19. The influence of atomic coherence and dipole–dipole interaction on entanglement of two qubits with nondegenerate two-photon transitions

    Indian Academy of Sciences (India)

    E K Bashkirov; M S Mastyugin

    2015-01-01

    Considering two artificial identical atoms interacting with two-mode thermal field through non-degenerate two-photon transitions, this paper studies the influence of atomic coherence and dipole–dipole interaction on the entanglement of two qubits. It is found that the entanglement is greatly enhanced by these mechanisms.

  20. The management of interaction networks. The ???in-between??? concept within social work and counseling

    OpenAIRE

    Hern??ndez-Aristu, Jes??s

    2015-01-01

    We are familiar with the field of group interaction through the traditional work of Kurt Lewin and also systemic thinking talks about network interaction that builds up the system. Martin Buber also discusses the ???in-between??? concept as the third element.The therapist or counselor, social worker and clients are part of an interaction network, representing therapeutic and social working situations. Success in treatment and reflective processes, depends on the perception and managemen...