WorldWideScience

Sample records for atomic interaction networks

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

    Directory of Open Access Journals (Sweden)

    Rodrigo L. Oréfice

    1998-12-01

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

  2. Atomic and Molecular Interactions

    International Nuclear Information System (INIS)

    2002-01-01

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 Emphasis was placed on current unpublished research and discussion of the future target areas in this field

  3. Neuromorphic atomic switch networks.

    Directory of Open Access Journals (Sweden)

    Audrius V Avizienis

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

  4. Elementary Atom Interaction with Matter

    OpenAIRE

    Mrowczynski, Stanislaw

    1998-01-01

    The calculations of the elementary atom (the Coulomb bound state of elementary particles) interaction with the atom of matter, which are performed in the Born approximation, are reviewed. We first discuss the nonrelativistic approach and then its relativistic generalization. The cross section of the elementary atom excitation and ionization as well as the total cross section are considered. A specific selection rule, which applies for the atom formed as positronium by particle-antiparticle pa...

  5. Correlations between interacting Rydberg atoms

    DEFF Research Database (Denmark)

    Paris-Mandoki, Asaf; Braun, Christoph; Hofferberth, Sebastian

    2018-01-01

    This paper is a short introduction to Rydberg physics and quantum nonlinear optics using Rydberg atoms. It has been prepared as a compliment to a series of lectures delivered during the Latin American School of Physics "Marcos Moshinsky" 2017. We provide a short introduction to the properties...... of individual Rydberg atoms and discuss in detail how the interaction potential between Rydberg atom pairs is calculated. We then discuss how this interaction gives rise to the Rydberg blockade mechanism. With the aid of hallmark experiments in the field applications of the blockade for creating correlated...

  6. Quantum network with individual atoms and photons

    International Nuclear Information System (INIS)

    Rempe, G.

    2013-01-01

    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. (authors)

  7. Lasers, light-atom interaction

    International Nuclear Information System (INIS)

    Cagnac, B.; Faroux, J.P.

    2002-01-01

    This book has a double purpose: first to explain in a way as simple as possible the interaction processes occurring between atoms and light waves, and secondly to help any scientist that needs further information to improve his knowledge of lasers. The content of this book has been parted into 3 more or less independent sections: 1) effect of an electromagnetic field on a 2-quantum state system, 2) operating mode of lasers in the framework of transition probabilities, and 3) calculation of the emitted wave. Einstein's phenomenological hypothesis has led to probability equations called rate equations, these equations do not give a true representation of the interaction process at the scale of the atom but this representation appears to be true on an average over a large population of atoms. Only quantum mechanics can describe accurately the light-atom interaction but at the cost of a far higher complexity. In the first part of the book quantum mechanics is introduced and applied under 2 simplifying hypothesis: -) the atom system has only 2 non-degenerate states and -) the intensity of the light wave is high enough to involve a large population of photons. Under these hypothesis, Rabi oscillations, Ramsey pattern and the splitting of Autler-Townes levels are explained. The second part is dedicated to the phenomenological model of Einstein that gives good results collectively. In the third part of the book, Maxwell equations are used to compute field spatial distribution that are currently found in experiments involving lasers. (A.C.)

  8. Correlations between interacting Rydberg atoms

    Science.gov (United States)

    Paris-Mandoki, Asaf; Braun, Christoph; Hofferberth, Sebastian

    2018-04-01

    This paper is a short introduction to Rydberg physics and quantum nonlinear optics using Rydberg atoms. It has been prepared as a compliment to a series of lectures delivered during the Latin American School of Physics "Marcos Moshinsky" 2017. We provide a short introduction to the properties of individual Rydberg atoms and discuss in detail how the interaction potential between Rydberg atom pairs is calculated. We then discuss how this interaction gives rise to the Rydberg blockade mechanism. With the aid of hallmark experiments in the field applications of the blockade for creating correlated quantum systems are discussed. Our aim is to give an overview of this exciting and rapidly evolving field. The interested reader is referred to original work and more comprehensive reviews and tutorials for further details on these subjects.

  9. Strongly interacting photons and atoms

    International Nuclear Information System (INIS)

    Alge, W.

    1999-05-01

    This thesis contains the main results of the research topics I have pursued during the my PhD studies at the University of Innsbruck and partly in collaboration with the Institut d' Optique in Orsay, France. It is divided into three parts. The first and largest part discusses the possibility of using strong standing waves as a tool to cool and trap neutral atoms in optical cavities. This is very important in the field of nonlinear optics where several successful experiments with cold atoms in cavities have been performed recently. A discussion of the optical parametric oscillator in a regime where the nonlinearity dominates the evolution is the topic of the second part. We investigated mainly the statistical properties of the cavity output of the three interactive cavity modes. Very recently a system has been proposed which promises fantastic properties. It should exhibit a giant Kerr nonlinearity with negligible absorption thus leading to a photonic turnstile device based on cold atoms in cavity. We have shown that this model suffers from overly simplistic assumptions and developed several more comprehensive approaches to study the behavior of this system. Apart from the division into three parts of different contents the thesis is divided into publications, supplements and invisible stuff. The intention of the supplements is to reach researchers which work in related areas and provide them with more detailed information about the concepts and the numerical tools we used. It is written especially for diploma and PhD students to give them a chance to use the third part of our work which is actually the largest one. They consist of a large number of computer programs we wrote to investigate the behavior of the systems in parameter regions where no hope exists to solve the equations analytically. (author)

  10. Atomic switch networks as complex adaptive systems

    Science.gov (United States)

    Scharnhorst, Kelsey S.; Carbajal, Juan P.; Aguilera, Renato C.; Sandouk, Eric J.; Aono, Masakazu; Stieg, Adam Z.; Gimzewski, James K.

    2018-03-01

    Complexity is an increasingly crucial aspect of societal, environmental and biological phenomena. Using a dense unorganized network of synthetic synapses it is shown that a complex adaptive system can be physically created on a microchip built especially for complex problems. These neuro-inspired atomic switch networks (ASNs) are a dynamic system with inherent and distributed memory, recurrent pathways, and up to a billion interacting elements. We demonstrate key parameters describing self-organized behavior such as non-linearity, power law dynamics, and multistate switching regimes. Device dynamics are then investigated using a feedback loop which provides control over current and voltage power-law behavior. Wide ranging prospective applications include understanding and eventually predicting future events that display complex emergent behavior in the critical regime.

  11. Strong interaction effects in hadronic atoms

    International Nuclear Information System (INIS)

    Kaufmann, W.B.

    1977-01-01

    The WKB method is applied to the calculation of strong interaction-induced level widths and shifts of hadronic atoms. The calculation, while elementary enough for undergraduate quantum mechanics students, gives a good account of kaonic and antiprotonic atom data

  12. Simulation of coherent interactions between Rydberg atoms

    International Nuclear Information System (INIS)

    Robicheaux, F.; Hernandez, J.V.; Topcu, T.; Noordam, L.D.

    2004-01-01

    The results of a theoretical investigation of the coherent interaction between many Rydberg atoms are reported. The atoms are assumed to move very little during the time range we investigate. We describe the basic interaction between atoms and show that (contrary to previous theoretical studies) the interaction between the atoms can be coherent. The band structure for a perfect lattice of atoms and the density of states for an amorphous distribution of atoms are presented. We also give results for when the atoms are roughly positioned in a lattice. Finally, we performed detailed calculations to understand when the Rydberg interactions are too strong for an essential states type of approximation. The relevance of our results to previous measurements in a Rydberg gas and to possible future experiments is discussed

  13. Optically polarized atoms understanding light-atom interactions

    CERN Document Server

    Auzinsh, Marcis; Rochester, Simon M

    2010-01-01

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

  14. Design of atomic energy information network system

    International Nuclear Information System (INIS)

    Kim, Y. T.; Lee, E. J.; Han, K. W.; Lee, H. C.; Chang, J. H.

    2004-01-01

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

  15. 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.

  16. Interaction of strong electromagnetic fields with atoms

    International Nuclear Information System (INIS)

    Brandi, H.S.; Davidovich, L.; Zagury, N.

    1982-06-01

    Several non-linear processes involvoing the interaction of atoms with strong laser fields are discussed, with particular emphasis on the ionization problem. Non-perturbative methods which have been proposed to tackle this problem are analysed, and shown to correspond to an expansion in the intra-atomic potential. The relation between tunneling and multiphoton absorption as ionization mechanisms, and the generalization of Einstein's photoelectric equation to the strong-field case are discussed. (Author) [pt

  17. Interacting neural networks

    Science.gov (United States)

    Metzler, R.; Kinzel, W.; Kanter, I.

    2000-08-01

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

  18. Inter-atomic interaction between electrons, 2

    International Nuclear Information System (INIS)

    Haga, Eijiro; Kato, Tomohiko; Aisaka, Tsuyoshi.

    1978-01-01

    Intra- and inter-atomic interactions in the exchange process are defined with respect to the Wannier function rather than the atomic function. In relation to the neutron scattering data for nickel, the behavior for the effective exchange parameter I(q) in the q-dependent susceptibility is, in RPA, investigated by taking into account the main types of the nearest neighbor interactions and by extending our previous treatment. The different types of interactions lead to different behavior for the q-dependence of I(q). The contribution to I(q) from inter-atomic interactions other than the exchange type decreases as the surface area of the Fermi surface becomes large. For the exchange type, the l-th neighbor interaction with l<=4 is taken into account, and, from the comparison with the empirical result for I(q), it is found that the inter-atomic contribution to I(0) is about thirty percent with a reasonable decrease against l. (author)

  19. Atom interferometry with trapped Bose-Einstein condensates: impact of atom-atom interactions

    International Nuclear Information System (INIS)

    Grond, Julian; Hohenester, Ulrich; Mazets, Igor; Schmiedmayer, Joerg

    2010-01-01

    Interferometry with ultracold atoms promises the possibility of ultraprecise and ultrasensitive measurements in many fields of physics, and is the basis of our most precise atomic clocks. Key to a high sensitivity is the possibility to achieve long measurement times and precise readout. Ultracold atoms can be precisely manipulated at the quantum level and can be held for very long times in traps; they would therefore be an ideal setting for interferometry. In this paper, we discuss how the nonlinearities from atom-atom interactions, on the one hand, allow us to efficiently produce squeezed states for enhanced readout and, on the other hand, result in phase diffusion that limits the phase accumulation time. We find that low-dimensional geometries are favorable, with two-dimensional (2D) settings giving the smallest contribution of phase diffusion caused by atom-atom interactions. Even for time sequences generated by optimal control, the achievable minimal detectable interaction energy ΔE min is of the order of 10 -4 μ, where μ is the chemical potential of the Bose-Einstein condensate (BEC) in the trap. From these we have to conclude that for more precise measurements with atom interferometers, more sophisticated strategies, or turning off the interaction-induced dephasing during the phase accumulation stage, will be necessary.

  20. 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

  1. Atomic and Molecular Manipulation of Chemical Interactions

    National Research Council Canada - National Science Library

    Ho, Wilson

    2007-01-01

    .... In effect, the goal is to carry out chemical changes by manipulating individual atoms and molecules to induce different bonding geometry and to create new interactions with their environment. These studies provide the scientific basis for the advancement of technology in catalysis, molecular electronics, optics, chemical and biological sensing, and magnetic storage.

  2. 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.

  3. Muonic atom-light nucleus interaction

    International Nuclear Information System (INIS)

    Kuz'michev, V.E.; Peresypkin, V.V.; Efetov, A.V.

    1991-01-01

    The effective potential of the interaction between light nucleus and two-particle atom at distances greater than its Bohr radius is obtained in the analytic form on the basis of a correct account of three Coulomb particle problem. Features of the interaction between p, t, 4 He, 7 Be nuclei and mesonic atoms μp, μt, μ 4 He and μ 7 Be, that arising from the differences in masses and charges of interacting particles, are studied. The corresponding potentials in the pre-threshold energy range are given. The coefficients of the symptotic formula for the effective are calculated in adiabatic approximation and with regard for the main off-shell corrections. 16 refs.; 4 figs

  4. Anti pp interactions in anti p atoms

    International Nuclear Information System (INIS)

    Poth, H.

    1975-01-01

    The x-rays of anti p atoms were recorded to trace out a strong interaction shift and width to the electromagnetic energy and the radiation width of the low-lying levels. The energy of the levels and consequently the energy of the transitions was calculated by solving numerically the Dirac equation with an electromagnetic potential, taking into account the finite size of the nucleus and the vacuum polarization. Due to the lack of sufficient data, the antiproton-nucleon interaction was not well understood at low energies. In order to separate antiproton-proton from antiproton-neutron interactions, the studies of isotope effects were proposed. (L.M.K.)

  5. Interactions of atomic hydrogen with amorphous SiO2

    Science.gov (United States)

    Yue, Yunliang; Wang, Jianwei; Zhang, Yuqi; Song, Yu; Zuo, Xu

    2018-03-01

    Dozens of models are investigated by the first-principles calculations to simulate the interactions of an atomic hydrogen with a defect-free random network of amorphous SiO2 (a-SiO2) and oxygen vacancies. A wide variety of stable configurations are discovered due to the disorder of a-SiO2, and their structures, charges, magnetic moments, spin densities, and density of states are calculated. The atomic hydrogen interacts with the defect-free a-SiO2 in positively or negatively charged state, and produces the structures absent in crystalline SiO2. It passivates the neutral oxygen vacancies and generates two neutral hydrogenated E‧ centers with different Si dangling bond projections. Electron spin resonance parameters, including Fermi contacts, and g-tensors, are calculated for these centers. The atomic hydrogen interacts with the positive oxygen vacancies in dimer configuration, and generate four different positive hydrogenated defects, two of which are puckered like the Eγ‧ centers. This research helps to understand the interactions between an atomic hydrogen, and defect-free a-SiO2 and oxygen vacancies, which may generate the hydrogen-complexed defects that play a key role in the degeneration of silicon/silica-based microelectronic devices.

  6. Networks and Interactivity

    DEFF Research Database (Denmark)

    Considine, Mark; Lewis, Jenny

    2012-01-01

    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......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......, but not The Netherlands. Networking appears to be mediated by policy and regulatory imperatives....

  7. Ab initio calculation atomics ground state wave function for interactions Ion- Atom

    International Nuclear Information System (INIS)

    Shojaee, F.; Bolori zadeh, M. A.

    2007-01-01

    Ab initio calculation atomics ground state wave function for interactions Ion- Atom Atomic wave function expressed in a Slater - type basis obtained within Roothaan- Hartree - Fock for the ground state of the atoms He through B. The total energy is given for each atom.

  8. The Interaction between Graphene and Oxygen Atom

    Directory of Open Access Journals (Sweden)

    Hao Yifan

    2016-01-01

    Full Text Available Based on the density function theory (DFT method, the interaction between the graphene and oxygen atom is simulated by the B3LYP functional with the 6-31G basis set. Due to the symmetry of graphene (C54H18, D6h, a representative patch is put forward to represent the whole graphene to simplify the description. The representative patch on the surface is considered to gain the potential energy surface (PES. By the calculation of the PES, four possible stable isomers of the C54H18-O radical can be obtained. Meanwhile, the structures and energies of the four possible stable isomers, are further investigated thermodynamically, kinetically, and chemically. According to the transition states, the possible reaction mechanism between the graphene and oxygen atom is given.

  9. Online Social Network Interactions:

    Directory of Open Access Journals (Sweden)

    Hui-Jung Chang

    2018-01-01

    Full Text Available A cross-cultural comparison of social networking structure on McDonald’s Facebook fan sites between Taiwan and the USA was conducted utilizing the individualism/collectivism dimension proposed by Hofstede. Four network indicators are used to describe the network structure of McDonald’s Facebook fan sites: size, density, clique and centralization. Individuals who post on both Facebook sites for the year of 2012 were considered as network participants for the purpose of the study. Due to the huge amount of data, only one thread of postings was sampled from each month of the year of 2012. The final data consists of 1002 postings written by 896 individuals and 5962 postings written by 5532 individuals from Taiwan and the USA respectively. The results indicated that the USA McDonald’s Facebook fan network has more fans, while Taiwan’s McDonald’s Facebook fan network is more densely connected. Cliques did form among the overall multiplex and within the individual uniplex networks in two countries, yet no significant differences were found between them. All the fan networks in both countries are relatively centralized, mostly on the site operators.

  10. Interaction potential for two different atoms

    International Nuclear Information System (INIS)

    Kuzmichev, V.E.; Peresypkin, V.V.

    1991-01-01

    Using the rigorous approach to the nonrelativistic four Coulomb particle problem the interaction potentials between an ordinary hydrogen and muonic-hydrogen atoms at large: R>a e +a μ (1), and intermediate: a e >R>>a μ (2) distances, where a e and a μ are the Bohr radii, are calculated in the adiabatic approximation. The van der Waals potential constants in the region (1) and an explicit potential form in the region (2) taking into account both the polarization effects and the electron screening corrections are determined. 10 refs

  11. First-Order Quantum Phase Transition for Dicke Model Induced by Atom-Atom Interaction

    International Nuclear Information System (INIS)

    Zhao Xiu-Qin; Liu Ni; Liang Jiu-Qing

    2017-01-01

    In this article, we use the spin coherent state transformation and the ground state variational method to theoretically calculate the ground function. In order to consider the influence of the atom-atom interaction on the extended Dicke model’s ground state properties, the mean photon number, the scaled atomic population and the average ground energy are displayed. Using the self-consistent field theory to solve the atom-atom interaction, we discover the system undergoes a first-order quantum phase transition from the normal phase to the superradiant phase, but a famous Dicke-type second-order quantum phase transition without the atom-atom interaction. Meanwhile, the atom-atom interaction makes the phase transition point shift to the lower atom-photon collective coupling strength. (paper)

  12. Interaction of slow pions with atomic nuclei

    International Nuclear Information System (INIS)

    Troitskij, M.A.; Tsybul'nikov, A.V.; Chekunaev, N.I.

    1984-01-01

    Interactions of slow pions with atomic nuclei near to pion condensation are investigated. From comparison of experimental data with the theoretical calculation results on the basis of precise microscopic approach not bound with the random phase approximation (RPA) nuclear matter fundamental parameters near a critical point can be found. Optical potential of slow pions in nuclei, πN-scattering amplitudes and lengths, π-atom level isotopic shift, phenomenon of single-nucleon pion absorption by nucleus, phenomenon of nuclear critical opalescence are considered. The results of πN-scattering lengths calculation, sup(40-44)Ca, sup(24-29)Mg, sup(16-18)O π-atom level shift are presented. It is shown that the presence of π-condensate in nuclei can explain the observed suppression of p-wave potential terms. The phenomenon of single-nucleon pion absorption by nucleus is one of direct experiments which permits to reveal the π-condensate. The nuclear opalescence phenomenon is manifested in increase of pion photoproduction reaction cross section for account of nucleus proximity to π-condensation as compared with the calculated in the Fermi-gas model. The suggested method for calculating precondensate phenomena operates the better, the nearer is the system to the condensation threshold whereas the RPA method in this region is inapplicable

  13. Topology of molecular interaction networks

    NARCIS (Netherlands)

    Winterbach, W.; Van Mieghem, P.; Reinders, M.; Wang, H.; De Ridder, D.

    2013-01-01

    Molecular interactions are often represented as network models which have become the common language of many areas of biology. Graphs serve as convenient mathematical representations of network models and have themselves become objects of study. Their topology has been intensively researched over

  14. Interaction of relativistic elementary atoms with matter. I. General formulas

    International Nuclear Information System (INIS)

    Mrowczyn'ski, S.

    1987-01-01

    The problem of the interaction of relativistic elementary atoms (Coulomb bound states of elementary particles such as positronium, pionium, etc.) with matter is studied in the reference frame where the atom is initially at rest. An atom of matter is treated as a spinless structureless fast particle. The amplitudes of elementary-atom interaction are derived in the Born approximation under the assumption that a momentum transfer to the atom does not significantly exceed an inverse Bohr radius of the atom. The elementary-atom excitation and ionization processes are considered. The transitions where the spin projection of the atom component is reversed are also studied. In particular the matrix elements for para-ortho and ortho-para transitions are given. The spin structure of the amplitudes is discussed in detail. The sum rules, which allow the calculation of the cross sections summed over atom final states are found. Finally the formulas of the atom interaction cross sections are presented

  15. 2010 Atomic & Molecular Interactions Gordon Research Conference

    Energy Technology Data Exchange (ETDEWEB)

    Todd Martinez

    2010-07-23

    The Atomic and Molecular Interactions Gordon Conferences is justifiably recognized for its broad scope, touching on areas ranging from fundamental gas phase and gas-condensed matter collision dynamics, to laser-molecule interactions, photophysics, and unimolecular decay processes. The meeting has traditionally involved scientists engaged in fundamental research in gas and condensed phases and those who apply these concepts to systems of practical chemical and physical interest. A key tradition in this meeting is the strong mixing of theory and experiment throughout. The program for 2010 conference continues these traditions. At the 2010 AMI GRC, there will be talks in 5 broadly defined and partially overlapping areas of intermolecular interactions and chemical dynamics: (1) Photoionization and Photoelectron Dynamics; (2) Quantum Control and Molecules in Strong Fields; (3) Photochemical Dynamics; (4) Complex Molecules and Condensed Phases; and (5) Clusters and Reaction Dynamics. These areas encompass many of the most productive and exciting areas of chemical physics, including both reactive and nonreactive processes, intermolecular and intramolecular energy transfer, and photodissociation and unimolecular processes. Gas phase dynamics, van der Waals and cluster studies, laser-matter interactions and multiple potential energy surface phenomena will all be discussed.

  16. 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.

  17. 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.

  18. The antiproton-hydrogen atom interaction

    International Nuclear Information System (INIS)

    Morgan, D.L. Jr.

    1994-07-01

    The bar p-H interaction is the most important aspect of the bar ppe system. While this interaction is worthy of study in itself, it is also relevant to a number of bar p applications, both practical and in the area of fundamental physics. Theoretical study of p-H commenced more than 20 years ago and has continued with growing interest through the present. Experimental study has been limited, but recently measurements have been made of bar p's slowing in hydrogen at KeV energies, which shed light on their interaction with hydrogen atoms. Theoretical work involving various kinds and levels of approximation has now been carried out for a variety of bar p energy domains. Particular attention has been given to bar p capture at low and sub eV energies, in which a bound bar p-p state is formed, and to H excitation and ionization at KeV energies. Such calculations now extend into the sub Kelvin domain of energies. It is beginning to be possible to make comparisons between experiment and calculation and to compare calculations to one another. These comparisons suggest that theoretical work needs to be carried out in some intermediate energy domains and that some past calculations have to be repeated with more accurate methods

  19. Long-range interactions among three alkali-metal atoms

    International Nuclear Information System (INIS)

    Marinescu, M.; Starace, A.F.

    1996-01-01

    The long-range asymptotic form of the interaction potential surface for three neutral alkali-metal atoms in their ground states may be expressed as an expansion in inverse powers of inter-nuclear distances. The first leading powers are proportional to the dispersion coefficients for pairwise atomic interactions. They are followed by a term responsible for a three body dipole interaction. The authors results consist in evaluation of the three body dipole interaction coefficient between three alkali-metal atoms. The generalization to long-range n atom interaction terms will be discussed qualitatively

  20. A study of atomic interaction between suspended nanoparticles and sodium atoms in liquid sodium

    International Nuclear Information System (INIS)

    Saito, Jun-ichi; Ara, Kuniaki

    2010-01-01

    A feasibility study of suppression of the chemical reactivity of sodium itself using an atomic interaction between nanoparticles and sodium atoms has been carried out. We expected that the atomic interaction strengthens when the nanoparticle metal is the transition element which has a major difference in electronegativity from sodium. We also calculated the atomic interaction between nanoparticle and sodium atoms. It became clear that the atomic bond between the nanoparticle atom and the sodium atom is larger than that between sodium atoms, and the charge transfer takes place to the nanoparticle atom from the sodium atom. Using sodium with suspended nanoparticles, the fundamental physical properties related to the atomic interaction were investigated to verify the atomic bond. The surface tension of sodium with suspended nanoparticles increased, and the evaporation rate of sodium with suspended nanoparticles also decreased compared with that of sodium. Therefore the presence of the atomic interaction between nanoparticles and sodium was verified from these experiments. Because the fundamental physical property changes by the atomic interaction, we expected changes in the chemical reactivity characteristics. The chemical reaction properties of sodium with suspended nanoparticles with water were investigated experimentally. The released reaction heat and the reaction rate of sodium with suspended nanoparticles were reduced than those of sodium. The influence of the charge state of nanoparticle on the chemical process with water was theoretically investigated to speculate on the cause of reaction suppression. The potential energy in both primary and side reactions changed by the charge transfer, and the free energy of activation of the reaction with water increased. Accordingly, the reaction barrier also increased. This suggests there is a possibility of the reduction in the reaction of sodium by the suspension of nanoparticles. Consequently the possibility of the

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

    International Nuclear Information System (INIS)

    Liu Tang-Kun; Zhang Kang-Long; Tao Yu; Shan Chuan-Jia; Liu Ji-Bing

    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. (paper)

  2. Dynamic and interacting complex networks

    Science.gov (United States)

    Dickison, Mark E.

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

  3. Interaction of rare gas metastable atoms

    International Nuclear Information System (INIS)

    Wang, A.Z.F.

    1977-11-01

    The physical and chemical properties of metastable rare gas atoms are discussed and summarized. This is followed by a detailed examination of the various possible pathways whereby the metastable's excess electronic energy can be dissipated. The phenomenon of chemi-ionization is given special emphasis, and a theoretical treatment based on the use of complex (optical) potential is presented. This is followed by a discussion on the unique advantages offered by elastic differential cross section measurements in the apprehension of the fundamental forces governing the ionization process. The methodology generally adopted to extract information about the interaction potential for scattering data is also systematically outlined. Two widely studied chemi-ionization systems are then closely examined in the light of accurate differential cross section measurements obtained in this work. The first system is He(2 3 S) + Ar for which one can obtain an interaction potential which is in good harmony with the experimental results of other investigators. The validity of using the first-order semiclassical approximation for the phase shifts calculation in the presence of significant opacities is also discussed. The second reaction studied is He*+D 2 for which measurements were made on both spin states of the metastable helium. A self-consistent interaction potential is obtained for the triplet system, and reasons are given for not being able to do likewise for the singlet system. The anomalous hump proposed by a number of laboratories is analyzed. Total elastic and ionization cross sections as well as rate constants are calculated for the triplet case. Good agreement with experimental data is found. Finally, the construction and operation of a high power repetitively pulsed nitrogen laser pumped dye laser system is described in great details. Details for the construction and operation of a flashlamp pumped dye laser are likewise given

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

    International Nuclear Information System (INIS)

    Perreault, John D.; Cronin, Alexander D.

    2005-01-01

    The development of nanotechnology and atom optics relies on understanding how atoms behave and interact with their environment. Isolated atoms can exhibit wavelike (coherent) behavior with a corresponding de Broglie wavelength and phase which can be affected by nearby surfaces. Here an atom interferometer is used to measure the phase shift of Na atom waves induced by the walls of a 50 nm wide cavity. To our knowledge this is the first direct measurement of the de Broglie wave phase shift caused by atom-surface interactions. The magnitude of the phase shift is in agreement with that predicted by Lifshitz theory for a nonretarded van der Waals interaction. This experiment also demonstrates that atom waves can retain their coherence even when atom-surface distances are as small as 10 nm

  5. Interaction of complex atoms with radiation

    International Nuclear Information System (INIS)

    Amus'ya, M.Ya.

    1984-01-01

    Different manifestations of multielectron atomic structure under photoionization are discussed. Collectivization of external electron shells essential both in production cross section and in angular distribution as well as in photoelectron polarization are noted. In a wide range of quantum energies (of the order of ionization potential) an incident electron scattering on the atom irradiates quite differently than on the potential. It polarizes atoms mainly dipolarly, and virtually excited atom emits ''bremsstrahlung'' quantum. With energy growth of the incident electron at small momentum transferred to it by the atom the role of the second mechanism turns to be determinant

  6. 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.

  7. Ionization due to the interaction between two Rydberg atoms

    International Nuclear Information System (INIS)

    Robicheaux, F

    2005-01-01

    Using a classical trajectory Monte Carlo method, we have computed the ionization resulting from the interaction between two cold Rydberg atoms. We focus on the products resulting from close interaction between two highly excited atoms. We give information on the distribution of ejected electron energies, the distribution of internal atom energies and the velocity distribution of the atoms and ions after the ionization. If the potential for the atom is not purely Coulombic, the average interaction between two atoms can change from attractive to repulsive giving a Van de Graaff-like mechanism for accelerating atoms. In a small fraction of ionization cases, we find that the ionization leads to a positive molecular ion where all of the distances are larger than 1000 Bohr radii

  8. Depletion interaction measured by colloidal probe atomic force microscopy

    NARCIS (Netherlands)

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

    2004-01-01

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

  9. Basic atomic interactions of accelerated heavy ions in matter atomic interactions of heavy ions

    CERN Document Server

    Tolstikhina, Inga; Winckler, Nicolas; Shevelko, Viacheslav

    2018-01-01

    This book provides an overview of the recent experimental and theoretical results on interactions of heavy ions with gaseous, solid and plasma targets from the perspective of atomic physics. The topics discussed comprise stopping power, multiple-electron loss and capture processes, equilibrium and non-equilibrium charge-state fractions in penetration of fast ion beams through matter including relativistic domain. It also addresses mean charge-states and equilibrium target thickness in ion-beam penetrations, isotope effects in low-energy electron capture, lifetimes of heavy ion beams, semi-empirical formulae for effective cross sections. The book is intended for researchers and graduate students working in atomic, plasma and accelerator physics.

  10. Dependences of the van der Waals atom-wall interaction on atomic and material properties

    International Nuclear Information System (INIS)

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

    2005-01-01

    The 1%-accurate calculations of the van der Waals interaction between an atom and a cavity wall are performed in the separation region from 3 nm to 150 nm. The cases of metastable He * and Na atoms near metal, semiconductor, and dielectric walls are considered. Different approximations to the description of wall material and atomic dynamic polarizability are carefully compared. The smooth transition to the Casimir-Polder interaction is verified. It is shown that to obtain accurate results for the atom-wall van der Waals interaction at short separations with an error less than 1% one should use the complete optical-tabulated data for the complex refractive index of the wall material and the accurate dynamic polarizability of an atom. The obtained results may be useful for the theoretical interpretation of recent experiments on quantum reflection and Bose-Einstein condensation of ultracold atoms on or near surfaces of different kinds

  11. Statistical Mechanics of Temporal and Interacting Networks

    Science.gov (United States)

    Zhao, Kun

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

  12. Atomic processes in matter-antimatter interactions

    International Nuclear Information System (INIS)

    Morgan, D.L.

    1988-01-01

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

  13. Muon, positron and antiproton interactions with atoms and molecules

    Energy Technology Data Exchange (ETDEWEB)

    Armour, Edward A G, E-mail: edward.armour@nottingham.ac.u [School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD (United Kingdom)

    2010-04-01

    In this paper, a description is given of some interesting processes involving the interaction of a muon, a positron, or an antiproton with atoms and molecules. The process involving a muon is the resonant formation of the muonic molecular ion, dt{mu}, in the muon catalyzed fusion cycle. In the case of a positron, the process considered is positron annihilation in low-energy positron scattering by the hydrogen molecule. The antiproton is considered as the nucleus of an antihydrogen atom interacting with simple atoms. Attention is given to antiproton annihilation through the strong interaction. An outline is given of proposed tests of fundamental physics to be carried out using antihydrogen.

  14. 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.

  15. Exotic atoms and the kaon-nucleon interaction

    International Nuclear Information System (INIS)

    Batty, C.J.

    1989-12-01

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

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

    International Nuclear Information System (INIS)

    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 8 . The atoms of several tens of μK degree have been trapped by controlling the intensity of trapping laser and intensity gradient of magnetic field. EIT phenomena caused by atomic coherent interaction has been studied for the development of atom optical elements. For the investigation of the focusing phenomena induced by the coherent interaction, experimental measurements and theoretical analysis have been performed. Spatial dependency of spectrum and double distribution signal of coupling laser have been obtained. The deflection of laser beams utilizing the EIT effects has also been considered. (author)

  17. A Quantum Network with Atoms and Photons

    Science.gov (United States)

    2016-09-01

    98, 111115. 5. Karmakar, S, Shih, Y. Two- color ghost imaging with enhanced angular resolving power. Physical Review A. 2010; 81, 033845. 6. Karmakar...information. We constructed the rubidium (⁸⁷Rb) atomic memory magneto optical trap (MOT) cell and laser controls, and developed protocols, hardware, and...software to control the secure teleportation of information between quantum memories at ARL and JQI. Notably, we performed successful in-laboratory

  18. Photonic and Quantum Interactions of Atomic-Scale Junctions

    Data.gov (United States)

    National Aeronautics and Space Administration — In this proposal, the fundamental quantum and photonic interactions of bimetallic atomic-scale junctions (ASJs) will be explored, with three major space...

  19. 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.

  20. 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

  1. Collisional interaction between metastable neon atoms

    International Nuclear Information System (INIS)

    Drunen, Wouter Johannes van

    2008-01-01

    In this thesis, the study of cold gases of neon atoms in different metastable states is described. It contains measurements of the collisional parameters for both the 3s[3/2] 2 and the 3s'[1/2] 0 metastable state and the dependence of the inelastic loss on external fields. Furthermore, the investigation of frequency dependent laser-induced collisions, and the possibility to excite photoassociation resonances is presented. For the measurements described here, neon atoms have been confined in a magnetooptical trap, in a magnetostatic trap, or in an optical dipole trap, respectively. By laser cooling inside the magnetic trap, atomic samples with more than 95 percent occupation of the magnetic substate m J = +2 could be prepared. They have a typical temperature of 0.5 mK, central densities up to 10 11 cm -3 , and a central phase-space density of up to 2.2.10 -7 . After loading the optical dipole trap from the magnetic trap, 2.5.10 6 atoms with typical temperatures of 0.1 mK, and central densities up to 5.10 10 cm -3 were trapped. By evaporative cooling of the atoms in the magnetic trap we could increase the phase-space density by a factor of 200 to 5.10 -5 . Investigating the frequency dependence of laser-induced collisions did not reveal an experimental signature for the excitation of photoassociation resonances. For the 3 D 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 3 P 0 metastable state. From the trap loss measurements we determined the two-body loss coefficient of the 3 P 0 metastable state for both bosonic isotopes 20 Ne and 22 Ne. For 20 Ne we obtained β=6 +5 -4 .10 -10 cm 3 /s and for 22 Ne β = 11 +7 -6 .10 -10 cm 3 /s. (orig.)

  2. Casimir interaction between gas media of excited atoms

    International Nuclear Information System (INIS)

    Sherkunov, Yury

    2007-01-01

    The retarded dispersion interaction (Casimir interaction) between two dilute dielectric media at high temperatures is considered. The excited atoms are taken into account. It is shown that the perturbation technique cannot be applied to this problem due to divergence of integrals. A non-perturbative approach based on kinetic Green functions is implemented. We consider the interaction between two atoms (one of them is excited) embedded in an absorbing dielectric medium. We take into account the possible absorption of photons in the medium, which solves the problem of divergence. The force between two plane dilute dielectric media is calculated at pair interaction approximation. We show that the result of quantum electrodynamics differs from the Lifshitz formula for dilute gas media at high temperatures (if the number of excited atoms is significant). According to quantum electrodynamics, the interaction may be either attractive or repulsive depending on the temperature and the density numbers of the media

  3. Single-atom gating and magnetic interactions in quantum corrals

    Energy Technology Data Exchange (ETDEWEB)

    Ngo, Anh T.; Kim, Eugene H.; Ulloa, Sergio E.

    2017-04-01

    Single-atom gating, achieved by manipulation of adatoms on a surface, has been shown in experiments to allow precise control over superposition of electronic states in quantum corrals. Using a Green's function approach, we demonstrate theoretically that such atom gating can also be used to control the coupling between magnetic degrees of freedom in these systems. Atomic gating enables control not only on the direct interaction between magnetic adatoms, but also over superpositions of many-body states which can then control long distance interactions. We illustrate this effect by considering the competition between direct exchange between magnetic impurities and the Kondo screening mediated by the host electrons, and how this is affected by gating. These results suggest that both magnetic and nonmagnetic single-atom gating may be used to investigate magnetic impurity systems with tailored interactions, and may allow the control of entanglement of different spin states.

  4. Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks

    Science.gov (United States)

    Haraldsdóttir, Hulda S.; Fleming, Ronan M. T.

    2016-01-01

    Conserved moieties are groups of atoms that remain intact in all reactions of a metabolic network. Identification of conserved moieties gives insight into the structure and function of metabolic networks and facilitates metabolic modelling. All moiety conservation relations can be represented as nonnegative integer vectors in the left null space of the stoichiometric matrix corresponding to a biochemical network. Algorithms exist to compute such vectors based only on reaction stoichiometry but their computational complexity has limited their application to relatively small metabolic networks. Moreover, the vectors returned by existing algorithms do not, in general, represent conservation of a specific moiety with a defined atomic structure. Here, we show that identification of conserved moieties requires data on reaction atom mappings in addition to stoichiometry. We present a novel method to identify conserved moieties in metabolic networks by graph theoretical analysis of their underlying atom transition networks. Our method returns the exact group of atoms belonging to each conserved moiety as well as the corresponding vector in the left null space of the stoichiometric matrix. It can be implemented as a pipeline of polynomial time algorithms. Our implementation completes in under five minutes on a metabolic network with more than 4,000 mass balanced reactions. The scalability of the method enables extension of existing applications for moiety conservation relations to genome-scale metabolic networks. We also give examples of new applications made possible by elucidating the atomic structure of conserved moieties. PMID:27870845

  5. Atomic interactions of charged particles with matter

    International Nuclear Information System (INIS)

    Bichsel, H.

    1993-01-01

    Ideas about the interactions of charged particles with matter are discussed. First, some experimental information is presented. Concepts related to collision cross sections and the Bethe model for them are given. The stopping power is derived and applied to the discussion of depth dose functions ('Bragg curves'). Some details of the energy loss in microscopic volumes are discussed

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

    Science.gov (United States)

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

    2016-05-27

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

  7. ENDF/B-6 Photon Atomic Interaction Data Library

    International Nuclear Information System (INIS)

    Lemmel, H.D.

    1990-09-01

    The ENDF/B-6 version of the Photo-Atomic Interaction Data Library of the Livermore Evaluated Photon Data Library (EPDL) contains pair and triplet cross-sections, photoelectric cross-sections, atom form factors, coherent scattering cross-sections and some other data for all the elements from Z=1 to 100. The data library is available on magnetic tape costfree from the IAEA Nuclear Data Section. The library supersedes the earlier photo-atomic data library by the US Radiation Shielding Information Center RSIC that was included in the data libraries ENDF/B-5 and JEF-1. (author). Refs, figs and tabs

  8. Total cross section for relativistic positronium interaction with atom

    International Nuclear Information System (INIS)

    Pak, A.S.; Tarasov, A.V.

    1985-01-01

    Total cross sections of interaction of positronium relativistic atoms with atoms are calculated. Calculations are conducted within the framework of potential theory in Born approximaton. Contributions in total cross section of coherent (σsub(coh)) and incoherent (σsub(inc)) parts are analyzed. It is shown that for light elements σsub(inc) value is comparable with σsub(coh), and for heavy ones the ratio σsub(inc)/σsub(coh) sufficiently exceeds Zsup(-1) (Z-charge of the atomic nucleus. Numerical calculation results are presented. A conclusion is made on importance of the coherent part account during the calculation of total cross sections

  9. 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.

  10. 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. PMID:26555073

  11. Vulnerability of networks of interacting Markov chains.

    Science.gov (United States)

    Kocarev, L; Zlatanov, N; Trajanov, D

    2010-05-13

    The concept of vulnerability is introduced for a model of random, dynamical interactions on networks. In this model, known as the influence model, the nodes are arranged in an arbitrary network, while the evolution of the status at a node is according to an internal Markov chain, but with transition probabilities that depend not only on the current status of that node but also on the statuses of the neighbouring nodes. Vulnerability is treated analytically and numerically for several networks with different topological structures, as well as for two real networks--the network of infrastructures and the EU power grid--identifying the most vulnerable nodes of these networks.

  12. 2004 Atomic and Molecular Interactions Gordon Research Conference

    International Nuclear Information System (INIS)

    Dr. Paul J. Dagdigian

    2004-01-01

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

  13. Van der Waals interaction between metal and atom

    International Nuclear Information System (INIS)

    Rao, P.R.; Mukhopadhyay, G.

    1984-07-01

    A dielectric response approach to the Van der Waals interaction between an atom and a planar metal surface is presented. An exact formula in terms of a form factor is derived within the point dipole approximation and non-retarded limit valid for shorter separation. The interaction potential is studied via SCIB model, and a substantial modification over its classical form is found at shorter distances. (author)

  14. 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.

  15. Analysis of deterministic swapping of photonic and atomic states through single-photon Raman interaction

    Science.gov (United States)

    Rosenblum, Serge; Borne, Adrien; Dayan, Barak

    2017-03-01

    The long-standing goal of deterministic quantum interactions between single photons and single atoms was recently realized in various experiments. Among these, an appealing demonstration relied on single-photon Raman interaction (SPRINT) in a three-level atom coupled to a single-mode waveguide. In essence, the interference-based process of SPRINT deterministically swaps the qubits encoded in a single photon and a single atom, without the need for additional control pulses. It can also be harnessed to construct passive entangling quantum gates, and can therefore form the basis for scalable quantum networks in which communication between the nodes is carried out only by single-photon pulses. Here we present an analytical and numerical study of SPRINT, characterizing its limitations and defining parameters for its optimal operation. Specifically, we study the effect of losses, imperfect polarization, and the presence of multiple excited states. In all cases we discuss strategies for restoring the operation of SPRINT.

  16. "Material interactions": from atoms & bits to entangled practices

    DEFF Research Database (Denmark)

    Vallgårda, Anna

    and intellectually stimulating panel moderated by Prof. Mikael Wiberg consisting of a number of scholars with a well-developed view on digital materialities to fuel a discussion on material interactions - from atoms & bits to entangled practices. These scholars include: Prof. Hiroshi Ishii, Prof. Paul Dourish...

  17. Dressed molecules in resonantly interacting ultracold atomic Fermi gases

    NARCIS (Netherlands)

    Falco, G.M.; Stoof, H.T.C.

    2007-01-01

    We present a detailed analysis of the two-channel atom-molecule effective Hamiltonian for an ultracold two-component homogeneous Fermi gas interacting near a Feshbach resonance. We particularly focus on the two-body and many-body properties of the dressed molecules in such a gas. An exact result

  18. Measurement of strong interaction effects in antiprotonic helium atoms

    International Nuclear Information System (INIS)

    Davies, J.D.; Gorringe, T.P.; Lowe, J.; Nelson, J.M.; Playfer, S.M.; Pyle, G.J.; Squier, G.T.A.

    1984-01-01

    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. (orig.)

  19. Reactive Collisions and Interactions of Ultracold Dipolar Atoms

    Science.gov (United States)

    2014-10-29

    Kotochigova Department of Physics, Temple University, Philadelphia, PA 19122-6082 I. COLLISIONAL INTERACTIONS OF RARE- EARTH MAGNETIC ATOMS The breakthroughs...technologies, it was not previously implemented, possibly owing to the misconception that molecular ions predominantly undergo charge-exchange reactions leading

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

    KAUST Repository

    Zhang, J.-Y.; Qian, Ying; Schwingenschlö gl, Udo; Yan, Z.-C.

    2013-01-01

    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

  1. Interaction of atomic hydrogen with ethylene adsorbed on nickel films

    International Nuclear Information System (INIS)

    Korchak, V.N.; Tret'yakov, I.I.; Kislyuk, M.U.

    1976-01-01

    The reactivity of ethylene adsorbed on the pure films of nickel at various temperatures was studied with respect to hydrogen atoms generated in the gaseous phase. The experiments were conducted in a glass vacuum apparatus enabling one to obtain the highest vacuum up to 2x20 -10 torr. The catalyst, nickel films, was produced by their deposition onto the walls of the glass reactor at a pressure of the residual gas of 10 -9 torr and a temperature of the walls of 25 deg C. Gas purity was analyzed by the mass spectrometric method. The ethylene adsorbed at the temperatures below 173 deg K reacted readily with the hydrogen atoms to yield ethane. The process ran without practically any activation energy involved and was limited by the attachment of the first hydrogen atom to the ethylene molecule. The efficiency of this interaction was 0.02 of the number of the hydrogen atoms collisions against the surface occupied by the ethylene. The adsorption of the ethylene at room and higher temperatures was accompanied by its disproportioning with the release of the hydrogen into the gaseous phase and a serious destruction of the ethylene molecules adsorbed to produce hydrogen residues interacting with neither molecular nor atomic hydrogen [ru

  2. Interaction of GaN epitaxial layers with atomic hydrogen

    Energy Technology Data Exchange (ETDEWEB)

    Losurdo, M.; Giangregorio, M.M.; Capezzuto, P.; Bruno, G.; Namkoong, G.; Doolittle, W.A.; Brown, A.S

    2004-08-15

    GaN surface passivation processes are still under development and among others hydrogen treatments are investigated. In this study, we use non-destructive optical and electrical probes such as spectroscopic ellipsometry (SE) and surface potential Kelvin probe microscopy (SP-KPM) in conjunction with non-contact atomic force microscopy (AFM) for the study of the different reactivity of Ga-polar and N-polar GaN epitaxial layers with atomic hydrogen. The GaN epitaxial layers are grown by molecular beam epitaxy on sapphire (0 0 0 1) substrates, and GaN and AlN buffer layers are used to grow N-polar and Ga-polar films, respectively. The atomic hydrogen is produced by a remote rf (13.56 MHz) H{sub 2} plasma in order to rule out any ion bombardment of the GaN surface and make the interaction chemical. It is found that the interaction of GaN surfaces with atomic hydrogen depends on polarity, with N-polar GaN exhibiting greater reactivity. Furthermore, it is found that atomic hydrogen is effective in the passivation of grain boundaries and surface defects states.

  3. Interaction of GaN epitaxial layers with atomic hydrogen

    International Nuclear Information System (INIS)

    Losurdo, M.; Giangregorio, M.M.; Capezzuto, P.; Bruno, G.; Namkoong, G.; Doolittle, W.A.; Brown, A.S.

    2004-01-01

    GaN surface passivation processes are still under development and among others hydrogen treatments are investigated. In this study, we use non-destructive optical and electrical probes such as spectroscopic ellipsometry (SE) and surface potential Kelvin probe microscopy (SP-KPM) in conjunction with non-contact atomic force microscopy (AFM) for the study of the different reactivity of Ga-polar and N-polar GaN epitaxial layers with atomic hydrogen. The GaN epitaxial layers are grown by molecular beam epitaxy on sapphire (0 0 0 1) substrates, and GaN and AlN buffer layers are used to grow N-polar and Ga-polar films, respectively. The atomic hydrogen is produced by a remote rf (13.56 MHz) H 2 plasma in order to rule out any ion bombardment of the GaN surface and make the interaction chemical. It is found that the interaction of GaN surfaces with atomic hydrogen depends on polarity, with N-polar GaN exhibiting greater reactivity. Furthermore, it is found that atomic hydrogen is effective in the passivation of grain boundaries and surface defects states

  4. Statistical physics of interacting neural networks

    Science.gov (United States)

    Kinzel, Wolfgang; Metzler, Richard; Kanter, Ido

    2001-12-01

    Recent results on the statistical physics of time series generation and prediction are presented. A neural network is trained on quasi-periodic and chaotic sequences and overlaps to the sequence generator as well as the prediction errors are calculated numerically. For each network there exists a sequence for which it completely fails to make predictions. Two interacting networks show a transition to perfect synchronization. A pool of interacting networks shows good coordination in the minority game-a model of competition in a closed market. Finally, as a demonstration, a perceptron predicts bit sequences produced by human beings.

  5. Many-Body Theory for Positronium-Atom Interactions

    Science.gov (United States)

    Green, D. G.; Swann, A. R.; Gribakin, G. F.

    2018-05-01

    A many-body-theory approach has been developed to study positronium-atom interactions. As first applications, we calculate the elastic scattering and momentum-transfer cross sections and the pickoff annihilation rate 1Zeff for Ps collisions with He and Ne. For He the cross section is in agreement with previous coupled-state calculations, while comparison with experiment for both atoms highlights discrepancies between various sets of measured data. In contrast, the calculated 1Zeff (0.13 and 0.26 for He and Ne, respectively) are in excellent agreement with the measured values.

  6. Noise in strong laser-atom interactions: Phase telegraph noise

    International Nuclear Information System (INIS)

    Eberly, J.H.; Wodkiewicz, K.; Shore, B.W.

    1984-01-01

    We discuss strong laser-atom interactions that are subjected to jump-type (random telegraph) random-phase noise. Physically, the jumps may arise from laser fluctuations, from collisions of various kinds, or from other external forces. Our discussion is carried out in two stages. First, direct and partially heuristic calculations determine the laser spectrum and also give a third-order differential equation for the average inversion of a two-level atom on resonance. At this stage a number of general features of the interaction are able to be studied easily. The optical analog of motional narrowing, for example, is clearly predicted. Second, we show that the theory of generalized Poisson processes allows laser-atom interactions in the presence of random telegraph noise of all kinds (not only phase noise) to be treated systematically, by means of a master equation first used in the context of quantum optics by Burshtein. We use the Burshtein equation to obtain an exact expression for the two-level atom's steady-state resonance fluorescence spectrum, when the exciting laser exhibits phase telegraph noise. Some comparisons are made with results obtained from other noise models. Detailed treatments of the effects ofmly jumps, or as a model of finite laser bandwidth effects, in which the laser frequency exhibits random jumps. We show that these two types of frequency noise can be distinguished in light-scattering spectra. We also discuss examples which demonstrate both temporal and spectral motional narrowing, nonexponential correlations, and non-Lorentzian spectra. Its exact solubility in finite terms makes the frequency-telegraph noise model an attractive alternative to the white-noise Ornstein-Uhlenbeck frequency noise model which has been previously applied to laser-atom interactions

  7. Interactions of circular Rydberg atoms with charged particles

    International Nuclear Information System (INIS)

    Wang, J.

    1994-01-01

    Recent progress in experimental cross-field techniques has made it possible to produce oriented Rydberg atoms of any angular momentum l within a given n manifold. The largest angular momentum state l max = n - 1 of a given n manifold is of particular interest because of its semiclassical properties for n much-gt 1. The corresponding classical Kepler orbit is circular with highly localized phase space distribution. The circular Rydberg atoms afford the opportunity to study various interactions in the semiclassical regime. The authors report electron capture from circular Rydberg atoms by protons and positrons at speeds comparable to the electron orbital speed. They find orientation dependent, novel peak structures for both protons and positrons in the angular scattering of the particles. The structures may be understood in terms of quasi Thomas double scattering mechanism for capture. Other related aspects including final state population and orientation indulged scattering asymmetry will also be discussed

  8. Atom-surface interaction: Zero-point energy formalism

    International Nuclear Information System (INIS)

    Paranjape, V.V.

    1985-01-01

    The interaction energy between an atom and a surface formed by a polar medium is derived with use of a new approach based on the zero-point energy formalism. It is shown that the energy depends on the separation Z between the atom and the surface. With increasing Z, the energy decreases according to 1/Z 3 , while with decreasing Z the energy saturates to a finite value. It is also shown that the energy is affected by the velocity of the atom, but this correction is small. Our result for large Z is consistent with the work of Manson and Ritchie [Phys. Rev. B 29, 1084 (1984)], who follow a more traditional approach to the problem

  9. Atom depth analysis delineates mechanisms of protein intermolecular interactions

    International Nuclear Information System (INIS)

    Alocci, Davide; Bernini, Andrea; Niccolai, Neri

    2013-01-01

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

  10. Calculation of parameters of the interaction potential between excited alkali atoms and mercury atoms: The Cs*, Pr*-Hg interaction

    International Nuclear Information System (INIS)

    Glushkov, A.V.

    1994-01-01

    Based on the method of effective potential involving the new polarization interaction potential calculated from polarization diagrams of the perturbation theory in the Thomas-Fermi approximation, the main parameters of the interatomic potentials (equilibrium distances, potential well depth) are evaluated for a system consisting of an alkali atom in the ground and excited states and of a mercury atom. The results of calculations of quasi-molecular terms for the A-Hg system, where A = Na, Cs, Fr, are reported, some of which are obtained for the first time. A comparison is made with available experimental and theoretical data. 29 refs., 2 figs., 1 tab

  11. Evolution of a protein domain interaction network

    International Nuclear Information System (INIS)

    Li-Feng, Gao; Jian-Jun, Shi; Shan, Guan

    2010-01-01

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

  12. 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.

  13. Weak Interaction Measurements with Optically Trapped Radioactive Atoms

    International Nuclear Information System (INIS)

    Vieira, D.J.; Crane, S.G.; Guckert, R.; Zhao, X.; Brice, S.J.; Goldschmidt, A.; Hime, A.; Tupa, D.

    1999-01-01

    This is the final report of a three-year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The goal of this project is to apply the latest in magneto-optical and pure magnetic trapping technology to concentrate, cool, confine, and polarize radioactive atoms for precise electroweak interaction measurements. In particular, the authors have concentrated their efforts on the trapping of 82 Rb for a parity-violating, beta-asymmetry measurement. Progress has been made in successfully trapping of up to 6 million 82 Rb(t 1/2 =75s) atoms in a magneto-optical trap coupled to a mass separator. This represents a two order of magnitude improvement in the number trapped radioactive atoms over all previous work. They have also measured the atomic hyperfine structure of 82 Rb and demonstrated the MOT-to-MOT transfer and accumulation of atoms in a second trap. Finally, they have constructed and tested a time-orbiting-potential magnetic trap that will serve as a rotating beacon of spin-polarized nuclei and a beta-telescope detection system. Prototype experiments are now underway with the initial goal of making a 1% measurements of the beta-asymmetry parameter A which would match the world's best measurements

  14. Rayleigh scattering under light-atom coherent interaction

    OpenAIRE

    Takamizawa, Akifumi; Shimoda, Koichi

    2012-01-01

    Semi-classical calculation of an oscillating dipole induced in a two-level atom indicates that spherical radiation from the dipole under coherent interaction, i.e., Rayleigh scattering, has a power level comparable to that of spontaneous emission resulting from an incoherent process. Whereas spontaneous emission is nearly isotropic and has random polarization generally, Rayleigh scattering is strongly anisotropic and polarized in association with incident light. In the case where Rabi frequen...

  15. Atomic interactions in precision interferometry using Bose-Einstein condensates

    International Nuclear Information System (INIS)

    Jamison, Alan O.; Gupta, Subhadeep; Kutz, J. Nathan

    2011-01-01

    We present theoretical tools for predicting and reducing the effects of atomic interactions in Bose-Einstein condensate (BEC) interferometry experiments. To address mean-field shifts during free propagation, we derive a robust scaling solution that reduces the three-dimensional Gross-Pitaevskii equation to a set of three simple differential equations valid for any interaction strength. To model the other common components of a BEC interferometer--condensate splitting, manipulation, and recombination--we generalize the slowly varying envelope reduction, providing both analytic handles and dramatically improved simulations. Applying these tools to a BEC interferometer to measure the fine structure constant, α[S. Gupta, K. Dieckmann, Z. Hadzibabic, and D. E. Pritchard, Phys. Rev. Lett. 89, 140401 (2002)], we find agreement with the results of the original experiment and demonstrate that atomic interactions do not preclude measurement to better than part-per-billion accuracy, even for atomic species with relatively large scattering lengths. These tools help make BEC interferometry a viable choice for a broad class of precision measurements.

  16. Dipole-dipole interactions in a hot atomic vapor and in an ultracold gas of Rydberg atoms

    Science.gov (United States)

    Sautenkov, V. A.; Saakyan, S. A.; Bronin, S. Ya; Klyarfeld, A. B.; Zelener, B. B.; Zelener, B. V.

    2018-01-01

    In our paper ideal and non-ideal gas media of neutral atoms are analyzed. The first we discuss a dipole broadening of atomic transitions in excited dilute and dense metal vapors. Then the theoretical studies of the dipole-dipole interactions in dense ultracold gas of Rydberg atoms are considered. Possible future experiments on a base of our experimental arrangement are suggested.

  17. STATE NETWORK INTERNATIONAL POLITICAL INTERACTION

    Directory of Open Access Journals (Sweden)

    D. M. Feldman

    2011-01-01

    Full Text Available Abstract: The processes of fragmentation (regionalization and localization and globalization turn the state as the basic system forming element of the state-centric world political system into the component of the world political network. The political relations between actors of the world political network are ruled by the effectiveness and not by legitimacy (“victory rules”, what is different from the participatory principles of interstate relations (“participation rules” accepted by the Westphalian state system. The article argues that the post-Westphalian world political system will witness the clashes between victory rules and participation rules and their eventual coexistence since the very nature of the victory rules hinders its institutionalization, consolidation and legitimation. The article suggests that the new system of state relations regardless of the name will be not less Westphalian than the preceding one thus new participation rules will have to be formulated and codified.

  18. Unraveling spurious properties of interaction networks with tailored random networks.

    Directory of Open Access Journals (Sweden)

    Stephan Bialonski

    Full Text Available We investigate interaction networks that we derive from multivariate time series with methods frequently employed in diverse scientific fields such as biology, quantitative finance, physics, earth and climate sciences, and the neurosciences. Mimicking experimental situations, we generate time series with finite length and varying frequency content but from independent stochastic processes. Using the correlation coefficient and the maximum cross-correlation, we estimate interdependencies between these time series. With clustering coefficient and average shortest path length, we observe unweighted interaction networks, derived via thresholding the values of interdependence, to possess non-trivial topologies as compared to Erdös-Rényi networks, which would indicate small-world characteristics. These topologies reflect the mostly unavoidable finiteness of the data, which limits the reliability of typically used estimators of signal interdependence. We propose random networks that are tailored to the way interaction networks are derived from empirical data. Through an exemplary investigation of multichannel electroencephalographic recordings of epileptic seizures--known for their complex spatial and temporal dynamics--we show that such random networks help to distinguish network properties of interdependence structures related to seizure dynamics from those spuriously induced by the applied methods of analysis.

  19. Cavity-QED interactions of two correlated atoms

    Science.gov (United States)

    Esfandiarpour, Saeideh; Safari, Hassan; Bennett, Robert; Yoshi Buhmann, Stefan

    2018-05-01

    We consider the resonant van der Waals (vdW) interaction between two correlated identical two-level atoms (at least one of which being excited) within the framework of macroscopic cavity quantum electrodynamics in linear, dispersing and absorbing media. The interaction of both atoms with the body-assisted electromagnetic field of the cavity is assumed to be strong. Our time-independent evaluation is based on an extended Jaynes–Cummings model. For a system prepared in a superposition of its dressed states, we derive the general form of the vdW forces, using a Lorentzian single-mode approximation. We demonstrate the applicability of this approach by considering the case of a planar cavity and showing the position dependence of Rabi oscillations. We also show that in the limiting case of weak coupling, our results reproduce the perturbative ones for the case where the field is initially in vacuum state while the atomic state is in a superposition of two correlated states sharing one excitation.

  20. 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.

  1. 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.

  2. 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.

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

    International Nuclear Information System (INIS)

    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 μW c) intensity of a probe laser : 1/10 of that of a pump laser. EIT (Electromagnetically Induced Transparency) generated by coherent laser-atom interactions was investigated experimentally and analyzed theoretically. The absorption of a probe laser could be remarkably reduced more than 90 % due to EIT effect. The EIT spectrum as narrow as 6 MHz which is even narrower than the natural linewidth of an excited state could be obtained under proper conditions

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

    International Nuclear Information System (INIS)

    Hussein, M.S.; Vorov, O.K.

    2002-01-01

    Using the Perron-Frobenius theorem, we prove that the results by Wilkin, Gunn, and Smith [Phys. Rev. Lett. 80, 2265 (1998)] for the ground states at angular momentum L of N harmonically trapped Bose atoms, interacting via weak attractive δ 2 (r) forces, are valid for a broad class of predominantly attractive interactions V(r), not necessarily attractive for any r. This class is described by sufficient conditions on the two-body matrix elements of the potential V(r). It includes, in particular, the Gaussian attraction of arbitrary radius, -1/r-Coulomb and log(r)-Coulomb forces, as well as all the short-range interactions satisfying inequality ∫d 2 r-vectorV(r)<0. In the precollapse regime, the angular momentum L is concentrated in the collective 'center-of-mass' mode, and there is no condensation at high L

  5. IAEA activities on atomic, molecular and plasma-material interaction data for fusion

    Science.gov (United States)

    Braams, Bastiaan J.; Chung, Hyun-Kyung

    2013-09-01

    The IAEA Atomic and Molecular Data Unit (http://www-amdis.iaea.org/) aims to provide internationally evaluated and recommended data for atomic, molecular and plasma-material interaction (A+M+PMI) processes in fusion research. The Unit organizes technical meetings and coordinates an A+M Data Centre Network (DCN) and a Code Centre Network (CCN). In addition the Unit organizes Coordinated Research Projects (CRPs), for which the objectives are mixed between development of new data and evaluation and recommendation of existing data. In the area of A+M data we are placing new emphasis in our meeting schedule on data evaluation and especially on uncertainties in calculated cross section data and the propagation of uncertainties through structure data and fundamental cross sections to effective rate coefficients. Following a recent meeting of the CCN it is intended to use electron scattering on Be, Ne and N2 as exemplars for study of uncertainties and uncertainty propagation in calculated data; this will be discussed further at the presentation. Please see http://www-amdis.iaea.org/CRP/ for more on our active and planned CRPs, which are concerned with atomic processes in core and edge plasma and with plasma interaction with beryllium-based surfaces and with irradiated tungsten.

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

    International Nuclear Information System (INIS)

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

    1985-01-01

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

  7. Interaction of antihydrogen with ordinary atoms and solid surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Froelich, Piotr, E-mail: piotr.froelich@kvac.uu.se; Voronin, Alexei [P.N. Lebedev Physical Institute (Russian Federation)

    2012-12-15

    The characteristic features of cold atom-antiatom collisions and antiatom-surface interactions are discussed and illustrated by the results for hydrogen-antihydrogen scattering and for quantum reflection of ultracold antihydrogen from a metallic surface. We discuss in some detail the case of spin-exchange in ultracold H-bar - H collisions, exposing the interplay of Coulombic, strong and dispersive forces, and demonstrating the sensitivity of the spin-exchange cross sections to hypothetical violations of Charge-Parity-Time (CPT) symmetry.

  8. Attractive interaction between an atom and a surface

    International Nuclear Information System (INIS)

    Manson, J.R.; Ritchie, R.H.

    1983-01-01

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

  9. Construction of high-dimensional neural network potentials using environment-dependent atom pairs.

    Science.gov (United States)

    Jose, K V Jovan; Artrith, Nongnuch; Behler, Jörg

    2012-05-21

    An accurate determination of the potential energy is the crucial step in computer simulations of chemical processes, but using electronic structure methods on-the-fly in molecular dynamics (MD) is computationally too demanding for many systems. Constructing more efficient interatomic potentials becomes intricate with increasing dimensionality of the potential-energy surface (PES), and for numerous systems the accuracy that can be achieved is still not satisfying and far from the reliability of first-principles calculations. Feed-forward neural networks (NNs) have a very flexible functional form, and in recent years they have been shown to be an accurate tool to construct efficient PESs. High-dimensional NN potentials based on environment-dependent atomic energy contributions have been presented for a number of materials. Still, these potentials may be improved by a more detailed structural description, e.g., in form of atom pairs, which directly reflect the atomic interactions and take the chemical environment into account. We present an implementation of an NN method based on atom pairs, and its accuracy and performance are compared to the atom-based NN approach using two very different systems, the methanol molecule and metallic copper. We find that both types of NN potentials provide an excellent description of both PESs, with the pair-based method yielding a slightly higher accuracy making it a competitive alternative for addressing complex systems in MD simulations.

  10. Low-energy positron interactions with atoms and molecules

    International Nuclear Information System (INIS)

    Surko, C M; Gribakin, G F; Buckman, S J

    2005-01-01

    This paper is a review of low-energy positron interactions with atoms and molecules. Processes of interest include elastic scattering, electronic and vibrational excitation, ionization, positronium formation and annihilation. An overview is presented of the currently available theoretical and experimental techniques to study these phenomena, including the use of trap-based positron beam sources to study collision processes with improved energy resolution. State-resolved measurements of electronic and vibrational excitation cross sections and measurement of annihilation rates in atoms and molecules as a function of incident positron energy are discussed. Where data are available, comparisons are made with analogous electron scattering cross sections. Resonance phenomena, common in electron scattering, appear to be less common in positron scattering. Possible exceptions include the sharp onsets of positron-impact electronic and vibrational excitation of selected molecules. Recent energy-resolved studies of positron annihilation in hydrocarbons containing more than a few carbon atoms provide direct evidence that vibrational Feshbach resonances underpin the anomalously large annihilation rates observed for many polyatomic species. We discuss open questions regarding this process in larger molecules, as well as positron annihilation in smaller molecules where the theoretical picture is less clear. (topical review)

  11. Interaction of atomic hydrogen with charcoal at 77 K

    International Nuclear Information System (INIS)

    Gorodetsky, A.E.; Vnukov, S.P.; Zalavutdinov, R.Kh.; Zakharov, A.P.; Buryak, A.K.; Ulyanov, A.V.; Federici, G.; Day, Chr.

    2005-01-01

    Charcoal is a working material of sorption cryopumps in the ITER project. The interaction of thermal hydrogen molecules and atoms with charcoal has been analyzed by TDS (77-300 K) and sorption measurements at 77 K. A stream quartz reactor with an H 2 RF discharge was used for the production of H atoms. The ratio of H and H 2 in the gas mixture in the afterglow zone was ∼10 -4 , hydrogen flow and inlet pressure were 6.9 sccm and 30 Pa, respectively. After exposure in the H/H 2 mixture during 1 hour the marked change in the shape of the TD spectra and decrease of the charcoal sorption capacity for hydrogen and nitrogen were detected. A wide spectrum of hydrocarbon fragments formed at 77 K was registered by mass-spectrometry at charcoal heating up to 700 K. The specific adsorption volume of charcoal, which was measured by N 2 adsorption at 77 K, decreased directly as amount of H atoms passed through the section with charcoal. (author)

  12. 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.

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

    International Nuclear Information System (INIS)

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

    2015-01-01

    Effective oscillator strength distributions are systematically generated and tabulated for the alkali atoms, the alkaline-earth atoms, the alkaline-earth ions, the rare gases and some miscellaneous atoms. These effective distributions are used to compute the dipole, quadrupole and octupole static polarizabilities, and are then applied to the calculation of the dynamic polarizabilities at imaginary frequencies. These polarizabilities can be used to determine the long-range C 6 , C 8 and C 10 atom–atom interactions for the dimers formed from any of these atoms and ions, and we present tables covering all of these combinations

  14. Cold atoms at unitarity and inverse square interaction

    Energy Technology Data Exchange (ETDEWEB)

    Bhaduri, R K [Department of Physics and Astronomy, McMaster University, Hamilton L8S 4M1 (Canada); Murthy, M V N [The Institute of Mathematical Sciences, Chennai 600113 (India); Srivastava, M K [Department of Physics, Indian Institute of Technology, Roorkee 247667 (India)

    2009-12-14

    Consider two identical atoms in a spherical harmonic oscillator interacting with a zero-range interaction which is tuned to produce an s-wave zero-energy bound state. The quantum spectrum of the system is known to be exactly solvable. We note that the same partial wave quantum spectrum is obtained by the one-dimensional scale-invariant inverse square potential. Long known as the Calogero-Sutherland-Moser (CSM) model, it leads to the fractional exclusion statistics (FES) of Haldane and Wu. The statistical parameter is deduced from the analytically calculated second virial coefficient. When FES is applied to a Fermi gas at unitarity, it gives good agreement with experimental data without the use of any free parameter.

  15. Atom-scale molecular interactions in lipid raft mixtures

    DEFF Research Database (Denmark)

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

    2009-01-01

    We review the relationship between molecular interactions and the properties of lipid environments. A specific focus is given on bilayers which contain sphingomyelin (SM) and sterols due to their essential role for the formation of lipid rafts. The discussion is based on recent atom-scale molecular...... dynamics simulations, complemented by extensive comparison to experimental data. The discussion is divided into four sections. The first part investigates the properties of one-component SM bilayers and compares them to bilayers with phosphatidylcholine (PC), the focus being on a detailed analysis...... examples of this issue. The third part concentrates on the specificity of intermolecular interactions in three-component mixtures of SM, PC and cholesterol (CHOL) under conditions where the concentrations of SM and CHOL are dilute with respect to that of PC. The results show how SM and CHOL favor one...

  16. Near-atomic model of microtubule-tau interactions.

    Science.gov (United States)

    Kellogg, Elizabeth H; Hejab, Nisreen M A; Poepsel, Simon; Downing, Kenneth H; DiMaio, Frank; Nogales, Eva

    2018-06-15

    Tau is a developmentally regulated axonal protein that stabilizes and bundles microtubules (MTs). Its hyperphosphorylation is thought to cause detachment from MTs and subsequent aggregation into fibrils implicated in Alzheimer's disease. It is unclear which tau residues are crucial for tau-MT interactions, where tau binds on MTs, and how it stabilizes them. We used cryo-electron microscopy to visualize different tau constructs on MTs and computational approaches to generate atomic models of tau-tubulin interactions. The conserved tubulin-binding repeats within tau adopt similar extended structures along the crest of the protofilament, stabilizing the interface between tubulin dimers. Our structures explain the effect of phosphorylation on MT affinity and lead to a model of tau repeats binding in tandem along protofilaments, tethering together tubulin dimers and stabilizing polymerization interfaces. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  17. Revealing the fast atomic motion of network glasses.

    Science.gov (United States)

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

    2014-05-19

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

  18. Study of Adhesion Interaction Using Atomic Force Microscopy

    Science.gov (United States)

    Grybos, J.; Pyka-Fosciak, G.; Lebed, K.; Lekka, M.; Stachura, Z.; Styczeñ, J.

    2003-05-01

    An atomic force microscope is a useful tool to study the interaction forces at molecular level. In particular the atomic force microscope can measure an unbinding force needed to separate the two single molecule complexes. Recent studies have shown that such unbinding force depends linearly on the logarithm of the applied loading rate, defined as a product of scanning velocity and the spring constant characterizing the investigated system (cantilever vs. surface). This dependence can be used to study the energy landscape shape of a molecular complex by the estimation of energy barrier locations and the related dissociation rates. In the present work the complex consisting of ethylene(di)aminetetraacetic acid and the bovine serum albumin was measured. The dependence between the unbinding force and the logarithm of the loading rate was linear. Using the Bell model describing the dissociation of the above molecules caused by the action of the external bond breaking force, two parameters were estimated: the dissociation rate and the position of the energy barrier needed to overcome during a transition from a bound to unbound state. The obtained results are similar to those obtained for a typical ligand--receptor interaction.

  19. Analytical local electron-electron interaction model potentials for atoms

    International Nuclear Information System (INIS)

    Neugebauer, Johannes; Reiher, Markus; Hinze, Juergen

    2002-01-01

    Analytical local potentials for modeling the electron-electron interaction in an atom reduce significantly the computational effort in electronic structure calculations. The development of such potentials has a long history, but some promising ideas have not yet been taken into account for further improvements. We determine a local electron-electron interaction potential akin to those suggested by Green et al. [Phys. Rev. 184, 1 (1969)], which are widely used in atom-ion scattering calculations, electron-capture processes, and electronic structure calculations. Generalized Yukawa-type model potentials are introduced. This leads, however, to shell-dependent local potentials, because the origin behavior of such potentials is different for different shells as has been explicated analytically [J. Neugebauer, M. Reiher, and J. Hinze, Phys. Rev. A 65, 032518 (2002)]. It is found that the parameters that characterize these local potentials can be interpolated and extrapolated reliably for different nuclear charges and different numbers of electrons. The analytical behavior of the corresponding localized Hartree-Fock potentials at the origin and at long distances is utilized in order to reduce the number of fit parameters. It turns out that the shell-dependent form of Green's potential, which we also derive, yields results of comparable accuracy using only one shell-dependent parameter

  20. Synchronization in networks with multiple interaction layers

    Science.gov (United States)

    del Genio, Charo I.; Gómez-Gardeñes, Jesús; 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 multilayered structure of connections affects the synchronization properties of dynamical systems evolving on top of it is a highly relevant endeavor in mathematics and physics and has potential applications in several socially relevant topics, such as power grid engineering and neural dynamics. We propose a general framework to assess the 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 by applying it to a network of Rössler oscillators with a double layer of interactions and show that highly rich phenomenology emerges from this. This includes cases where the stability of synchronization can be induced even if both layers would have individually induced unstable synchrony, an effect genuinely arising from the true multilayer structure of the interactions among the units in the network. PMID:28138540

  1. Structure of the human chromosome interaction network.

    Directory of Open Access Journals (Sweden)

    Sergio Sarnataro

    Full Text Available New Hi-C technologies have revealed that chromosomes have a complex network of spatial contacts in the cell nucleus of higher organisms, whose organisation is only partially understood. Here, we investigate the structure of such a network in human GM12878 cells, to derive a large scale picture of nuclear architecture. We find that the intensity of intra-chromosomal interactions is power-law distributed. Inter-chromosomal interactions are two orders of magnitude weaker and exponentially distributed, yet they are not randomly arranged along the genomic sequence. Intra-chromosomal contacts broadly occur between epigenomically homologous regions, whereas inter-chromosomal contacts are especially associated with regions rich in highly expressed genes. Overall, genomic contacts in the nucleus appear to be structured as a network of networks where a set of strongly individual chromosomal units, as envisaged in the 'chromosomal territory' scenario derived from microscopy, interact with each other via on average weaker, yet far from random and functionally important interactions.

  2. Designing Networked Adaptive Interactive Hybrid Systems

    NARCIS (Netherlands)

    Kester, L.J.H.M.

    2008-01-01

    Advances in network technologies enable distributed systems, operating in complex physical environments, to coordinate their activities over larger areas within shorter time intervals. In these systems humans and intelligent machines will, in close interaction, be able to reach their goals under

  3. Dynamics of moving interacting atoms in a laser radiation field and optical size resonances

    International Nuclear Information System (INIS)

    Gadomskii, O.N.; Glukhov, A.G.

    2005-01-01

    The forces acting on interacting moving atoms exposed to resonant laser radiation are calculated. It is shown that the forces acting on the atoms include the radiation pressure forces as well as the external and internal bias forces. The dependences of the forces on the atomic spacing, polarization, and laser radiation frequency are given. It is found that the internal bias force associated with the interaction of atomic dipoles via the reemitted field may play an important role in the dynamics of dense atomic ensembles in a light field. It is shown that optical size resonances appear in the system of interacting atoms at frequencies differing substantially from transition frequencies in the spectrum of atoms. It is noted that optical size resonances as well as the Doppler frequency shift in the spectrum of interacting atoms play a significant role in the processes of laser-radiation-controlled motion of the atoms

  4. Network Compression as a Quality Measure for Protein Interaction Networks

    Science.gov (United States)

    Royer, Loic; Reimann, Matthias; Stewart, A. Francis; Schroeder, Michael

    2012-01-01

    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. PMID:22719828

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

    International Nuclear Information System (INIS)

    1993-01-01

    The International Atomic Energy Agency, through its Atomic and Molecular Data Unit, coordinates a wide spectrum of programmes for the compilation, evaluation, and generation of atomic, molecular, and plasma-wall interaction data for fusion research. The present volume is exclusively devoted to cross sections for collisions of hydrogen atoms with electron, protons and multiply charged ions

  6. Rabi Oscillations between Ground and Rydberg States with Dipole-Dipole Atomic Interactions

    International Nuclear Information System (INIS)

    Johnson, T. A.; Urban, E.; Henage, T.; Isenhower, L.; Yavuz, D. D.; Walker, T. G.; Saffman, M.

    2008-01-01

    We demonstrate Rabi oscillations of small numbers of 87 Rb atoms between ground and Rydberg states with n≤43. Coherent population oscillations are observed for single atoms, while the presence of two or more atoms decoheres the oscillations. We show that these observations are consistent with van der Waals interactions of Rydberg atoms

  7. Network Interactions in the Great Altai Region

    Directory of Open Access Journals (Sweden)

    Lev Aleksandrovich Korshunov

    2017-12-01

    Full Text Available To improve the efficiency and competitiveness of the regional economy, an effective interaction between educational institutions in the Great Altai region is needed. The innovation growth can enhancing this interaction. The article explores the state of network structures in the economy and higher education in the border territories of the countries of Great Altai. The authors propose an updated approach to the three-level classification of network interaction. We analyze growing influence of the countries with emerging economies. We define the factors that impede the more stable and multifaceted regional development of these countries. Further, the authors determine indicators of the higher education systems and cooperation systems at the university level between the Shanghai Cooperation Organization countries (SCO and BRICS countries, showing the international rankings of the universities in these countries. The teaching language is important to overcome the obstacles in the interregional cooperation. The authors specify the problems of the development of the universities of the SCO and BRICS countries as global educational networks. The research applies basic scientific logical methods of analysis and synthesis, induction and deduction, as well as the SWOT analysis method. We have indentified and analyzed the existing economic and educational relations. To promote the economic innovation development of the border territories of the Great Altai, we propose a model of regional network university. Modern universities function in a new economic environment. Thus, in a great extent, they form the technological and social aspects of this environment. Innovative network structures contribute to the formation of a new network institutional environment of the regional economy, which impacts the macro- and microeconomic performance of the region as a whole. The results of the research can help to optimize the regional economies of the border

  8. Models of the atomic nucleus. With interactive software

    International Nuclear Information System (INIS)

    Cook, N.D.

    2006-01-01

    This book-and-CD-software package supplies users with an interactive experience for nuclear visualization via a computer-graphical interface, similar in principle to the molecular visualizations already available in chemistry. Models of the Atomic Nucleus, a largely non-technical introduction to nuclear theory, explains the nucleus in a way that makes nuclear physics as comprehensible as chemistry or cell biology. The book/software supplements virtually any of the current textbooks in nuclear physics by providing a means for 3D visual display of the diverse models of nuclear structure. For the first time, an easy-to-master software for scientific visualization of the nucleus makes this notoriously ''non-visual'' field become immediately 'visible.' After a review of the basics, the book explores and compares the competing models, and addresses how the lattice model best resolves remaining controversies. The appendix explains how to obtain the most from the software provided on the accompanying CD. (orig.)

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

    Science.gov (United States)

    Santos, Sergio; Barcons, Victor; Font, Josep; Verdaguer, Albert

    2014-01-01

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

  10. 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.

  11. The Global Alzheimer's Association Interactive Network.

    Science.gov (United States)

    Toga, Arthur W; Neu, Scott C; Bhatt, Priya; Crawford, Karen L; Ashish, Naveen

    2016-01-01

    The Global Alzheimer's Association Interactive Network (GAAIN) is consolidating the efforts of independent Alzheimer's disease data repositories around the world with the goals of revealing more insights into the causes of Alzheimer's disease, improving treatments, and designing preventative measures that delay the onset of physical symptoms. We developed a system for federating these repositories that is reliant on the tenets that (1) its participants require incentives to join, (2) joining the network is not disruptive to existing repository systems, and (3) the data ownership rights of its members are protected. We are currently in various phases of recruitment with over 55 data repositories in North America, Europe, Asia, and Australia and can presently query >250,000 subjects using GAAIN's search interfaces. GAAIN's data sharing philosophy, which guided our architectural choices, is conducive to motivating membership in a voluntary data sharing network. Copyright © 2016 The Alzheimer's Association. Published by Elsevier Inc. All rights reserved.

  12. 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

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

    International Nuclear Information System (INIS)

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

    2006-01-01

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

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

    International Nuclear Information System (INIS)

    Jiang Jun; Cheng Yongjun; Mitroy, J

    2013-01-01

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

  15. 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

  16. Temporal stability in human interaction networks

    Science.gov (United States)

    Fabbri, Renato; Fabbri, Ricardo; Antunes, Deborah Christina; Pisani, Marilia Mello; de Oliveira, Osvaldo Novais

    2017-11-01

    This paper reports on stable (or invariant) properties of human interaction networks, with benchmarks derived from public email lists. Activity, recognized through messages sent, along time and topology were observed in snapshots in a timeline, and at different scales. Our analysis shows that activity is practically the same for all networks across timescales ranging from seconds to months. The principal components of the participants in the topological metrics space remain practically unchanged as different sets of messages are considered. The activity of participants follows the expected scale-free trace, thus yielding the hub, intermediary and peripheral classes of vertices by comparison against the Erdös-Rényi model. The relative sizes of these three sectors are essentially the same for all email lists and the same along time. Typically, 45% are peripheral vertices. Similar results for the distribution of participants in the three sectors and for the relative importance of the topological metrics were obtained for 12 additional networks from Facebook, Twitter and ParticipaBR. These properties are consistent with the literature and may be general for human interaction networks, which has important implications for establishing a typology of participants based on quantitative criteria.

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

    Indian Academy of Sciences (India)

    2014-07-18

    Jul 18, 2014 ... 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 ...

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

    Directory of Open Access Journals (Sweden)

    Marton J.

    2014-01-01

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

  19. Controlling interactions between highly magnetic atoms with Feshbach resonances.

    Science.gov (United States)

    Kotochigova, Svetlana

    2014-09-01

    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)S3 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.

  20. Stimulated adiabatic passage in a dissipative ensemble of atoms with strong Rydberg-state interactions

    DEFF Research Database (Denmark)

    Petrosyan, David; Molmer, Klaus

    2013-01-01

    We study two-photon excitation of Rydberg states of atoms under stimulated adiabatic passage with delayed laser pulses. We find that the combination of strong interaction between the atoms in Rydberg state and the spontaneous decay of the intermediate exited atomic state leads to the Rydberg exci...... for deterministic creation and, possibly, extraction of Rydberg atoms or ions one at a time. The sympathetic monitoring via decay of ancilla particles may find wider applications for state preparation and probing of interactions in dissipative many-body systems.......We study two-photon excitation of Rydberg states of atoms under stimulated adiabatic passage with delayed laser pulses. We find that the combination of strong interaction between the atoms in Rydberg state and the spontaneous decay of the intermediate exited atomic state leads to the Rydberg...

  1. Interactions of C+(2PJ) with rare gas atoms: incipient chemical interactions, potentials and transport coefficients

    Science.gov (United States)

    Tuttle, William D.; Thorington, Rebecca L.; Viehland, Larry A.; Breckenridge, W. H.; Wright, Timothy G.

    2018-03-01

    Accurate interatomic potentials were calculated for the interaction of a singly charged carbon cation, C+, with a single rare gas atom, RG (RG = Ne-Xe). The RCCSD(T) method and basis sets of quadruple-ζ and quintuple-ζ quality were employed; each interaction energy was counterpoise corrected and extrapolated to the basis set limit. The lowest C+(2P) electronic term of the carbon cation was considered, and the interatomic potentials calculated for the diatomic terms that arise from these: 2Π and 2Σ+. Additionally, the interatomic potentials for the respective spin-orbit levels were calculated, and the effect on the spectroscopic parameters was examined. In doing this, anomalously large spin-orbit splittings for RG = Ar-Xe were found, and this was investigated using multi-reference configuration interaction calculations. The latter indicated a small amount of RG → C+ electron transfer and this was used to rationalize the observations. This is taken as evidence of an incipient chemical interaction, which was also examined via contour plots, Birge-Sponer plots and various population analyses across the C+-RG series (RG = He-Xe), with the latter showing unexpected results. Trends in several spectroscopic parameters were examined as a function of the increasing atomic number of the RG atom. Finally, each set of RCCSD(T) potentials was employed, including spin-orbit coupling to calculate the transport coefficients for C+ in RG, and the results were compared with the limited available data. This article is part of the theme issue `Modern theoretical chemistry'.

  2. Interaction mechanisms between ceramic particles and atomized metallic droplets

    Science.gov (United States)

    Wu, Yue; Lavernia, Enrique J.

    1992-10-01

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

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

    International Nuclear Information System (INIS)

    1992-01-01

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

  4. Repulsive interactions between two polyelectrolyte networks

    Science.gov (United States)

    Erbas, Aykut; Olvera de La Cruz, Monica; Olvera Group Collaboration

    Surfaces formed by charged polymeric species are highly_abundant in both synthetic and biological systems, for which maintaining_an optimum contact distance and a pressure balance is paramount. We investigate interactions between surfaces of two same-charged and_highly swollen polyelectrolyte gels, using extensive molecular dynamic_simulations and minimal analytical methods. The external-pressure_responses of the gels and the polymer-free ionic solvent layer separating_two surfaces are considered. Simulations confirmed that the surfaces are_held apart by osmotic pressure resulting from excess charges diffusing out_of the network. Both the solvent layer and pressure dependence are well_described by an analytical model based on the Poisson -Boltzmann solution for low and moderate electrostatic strengths. Our results can be of great importance for systems where charged gels or gel-like structures interact in various solvents, including systems encapsulated by gels and microgels in confinement.

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

    International Nuclear Information System (INIS)

    Mitroy, J.; Bromley, M. W. 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 ΔX 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

  6. Light absorption during alkali atom-noble gas atom interactions at thermal energies: a quantum dynamics treatment.

    Science.gov (United States)

    Pacheco, Alexander B; Reyes, Andrés; Micha, David A

    2006-10-21

    The absorption of light during atomic collisions is treated by coupling electronic excitations, treated quantum mechanically, to the motion of the nuclei described within a short de Broglie wavelength approximation, using a density matrix approach. The time-dependent electric dipole of the system provides the intensity of light absorption in a treatment valid for transient phenomena, and the Fourier transform of time-dependent intensities gives absorption spectra that are very sensitive to details of the interaction potentials of excited diatomic states. We consider several sets of atomic expansion functions and atomic pseudopotentials, and introduce new parametrizations to provide light absorption spectra in good agreement with experimentally measured and ab initio calculated spectra. To this end, we describe the electronic excitation of the valence electron of excited alkali atoms in collisions with noble gas atoms with a procedure that combines l-dependent atomic pseudopotentials, including two- and three-body polarization terms, and a treatment of the dynamics based on the eikonal approximation of atomic motions and time-dependent molecular orbitals. We present results for the collision induced absorption spectra in the Li-He system at 720 K, which display both atomic and molecular transition intensities.

  7. When hydroquinone meets methoxy radical: Hydrogen abstraction reaction from the viewpoint of interacting quantum atoms.

    Science.gov (United States)

    Petković, Milena; Nakarada, Đura; Etinski, Mihajlo

    2018-05-25

    Interacting Quantum Atoms methodology is used for a detailed analysis of hydrogen abstraction reaction from hydroquinone by methoxy radical. Two pathways are analyzed, which differ in the orientation of the reactants at the corresponding transition states. Although the discrepancy between the two barriers amounts to only 2 kJ/mol, which implies that the two pathways are of comparable probability, the extent of intra-atomic and inter-atomic energy changes differs considerably. We thus demonstrated that Interacting Quantum Atoms procedure can be applied to unravel distinct energy transfer routes in seemingly similar mechanisms. Identification of energy components with the greatest contribution to the variation of the overall energy (intra-atomic and inter-atomic terms that involve hydroquinone's oxygen and the carbon atom covalently bound to it, the transferring hydrogen and methoxy radical's oxygen), is performed using the Relative energy gradient method. Additionally, the Interacting Quantum Fragments approach shed light on the nature of dominant interactions among selected fragments: both Coulomb and exchange-correlation contributions are of comparable importance when considering interactions of the transferring hydrogen atom with all other atoms, whereas the exchange-correlation term dominates interaction between methoxy radical's methyl group and hydroquinone's aromatic ring. This study represents one of the first applications of Interacting Quantum Fragments approach on first order saddle points. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

  8. Interaction of Rydberg atoms with two contrapropagating ultrashort laser pulses

    International Nuclear Information System (INIS)

    Lugovskoy, A. V.; Bray, I.

    2006-01-01

    In this paper we investigate how Rydberg atoms respond to perturbation by two contrapropagating ultrashort laser pulses. We consider the case where the durations of both pulses τ 1 and τ 2 are shorter than the inverse of the initial-state energy ε i -1 . When acting alone such a pulse passes through the atom without noticeable alteration in the atomic state. The situation is different if two such pulses interfere in the region of atom localization. In this case the atomic response is significantly enhanced. This is due to the nonzero momentum transferred to the electron by the interplay of the electric field of one pulse and the magnetic field of the other. The sudden perturbation approximation is used to evaluate the transition probabilities. They are shown to depend on the atom position with respect to the pulse interference region. This dependence is determined by the relationship between the atomic diameter d i and the interference-region size l=c(τ 1 +τ 2 ) (c is the speed of light). If d i i >>l the transition probabilities are sensitive to the electron density distribution along the propagation direction. The probabilities of the initial-state destruction and atom ionization drop as l/d i irrespective of the characteristics of the pulses

  9. 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.

  10. 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.

    2016-01-01

    Tailoring the interactions between quantum emitters and single photons constitutes one of the cornerstones of quantum optics. Coupling a quantum emitter to the band edge of a photonic crystal waveguide (PCW) provides a unique platform for tuning these interactions. In particular, the cross-over from propagating fields E(x)∝e±ikxx outside the bandgap to localized fields 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 D1 line of atomic cesium for N¯=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. PMID:27582467

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

    Science.gov (United States)

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

    2015-05-22

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

  12. Frequency shifts in spontaneous emission from two interacting atoms

    International Nuclear Information System (INIS)

    James, D.F.V.

    1993-01-01

    A model radiating system consisting of two atoms in close proximity is analyzed. This system demonstrates the influence of spatial coherence on the spectrum of the radiation field. Explicit expressions for the degree of coherence, the source spectrum, and the spectrum of the radiation field are derived. The results are discussed in terms of Wolf's work [Phys. Rev. Lett. 56, 1370 (1986)] on this effect, which can be considered in terms of a multiple-atom analog of the effects of radiation reaction on a single atom, i.e., spontaneous decay and the Lamb shift

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

    International Nuclear Information System (INIS)

    2006-01-01

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

  14. Information entropy properties of the atoms in the system of coupled Λ-type three-level atoms interacting with coherent field in Kerr medium

    International Nuclear Information System (INIS)

    Li Ke; Ling Weijun

    2011-01-01

    The information entropy properties of the atoms of coupled Λ-type three-level atoms interacting with coherent field are studied by means of quantum theory, and discussed the time evolutions of the information entropy of the atoms via the average photon number, initial state of the atoms, detuning, coupling constant between the atoms and the coefficient of Kerr medium. Numerical calculation results show that the time evolutions of the information entropy properties of the atoms strongly dependent on the initial state of the system and the average photon number. Detuning, coupling constant between the atoms and the Kerr coefficient still make influence on the information entropy of the atoms. (authors)

  15. Elastic interactions between hydrogen atoms in metals. II. Elastic interaction energies

    International Nuclear Information System (INIS)

    Shirley, A.I.; Hall, C.K.

    1986-01-01

    The fully harmonic lattice approximation derived in a previous paper is used to calculate the elastic interaction energies in the niobium-hydrogen system. The permanent-direct, permanent-indirect, induced-direct, and induced-indirect forces calculated previously each give rise to a corresponding elastic interaction between hydrogen atoms. The latter three interactions have three- and four-body terms in addition to the usual two-body terms. These quantities are calculated and compared with the corresponding two-body permanent elastic interactions obtained in the harmonic-approximation treatment of Horner and Wagner. The results show that the total induced elastic energy is approximately (1/3) the size of the total permanent elastic energy and opposite to it in sign. The total elastic energy due to three-body interactions is approximately (1/4) the size of the total two-body elastic energy, while the total four-body elastic energy is approximately 5% of the total two-body energy. These additional elastic energies are expected to have a profound effect on the thermodynamic and phase-change behavior of a metal hydride

  16. 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.

  17. Intershell interaction in excited atom and ion photoionization

    International Nuclear Information System (INIS)

    Amusia, M.Ya.; Avdonina, N.B.

    1989-01-01

    It is demonstrated, that the photoionization cross section of an excited electron in Cs atom isoelectronic sequence acquire additional structure if the virtual polarization of the core by the incident photon is taken into account. (orig.)

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

    KAUST Repository

    Zhang, J.-Y.; Babb, J. F.; Mitroy, J.; Sadeghpour, H. R.; Schwingenschlö gl, Udo; Yan, Z.-C.

    2013-01-01

    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.

  19. 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.

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

    Directory of Open Access Journals (Sweden)

    Finkelstein Alexei V

    2007-07-01

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

  1. Atoms

    International Nuclear Information System (INIS)

    Fuchs, Alain; Villani, Cedric; Guthleben, Denis; Leduc, Michele; Brenner, Anastasios; Pouthas, Joel; Perrin, Jean

    2014-01-01

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

  2. Atomic oxygen-MoS sub 2 chemical interactions

    Energy Technology Data Exchange (ETDEWEB)

    Cross, J.B.; Martin, J.A. (Los Alamos National Lab., NM (USA)); Pope, L.E. (Sandia National Labs., Albuquerque, NM (USA)); Koontz, S.L. (National Aeronautics and Space Administration, Johnson Space Center, Houston, TX (USA))

    1990-10-01

    The present study shows that an O-atom translation energy of 1.5 eV, SO{sub 2} is generated and outgases from an anhydrous MoS{sub 2} surface with an initial reactivity nearly 50% that of kapton. The reaction of atomic oxygen with MoS{sub 2} has little or no translational energy barrier, i.e. thermally generated atomic oxygen reacts as readily as that having 1.5 eV of translational energy. For MoS{sub 2} films sputter-deposited at 50-70deg C, friction measurements showed a high initial friction coefficient (up to 0.25) for MoS{sub 2} surfaces exposed to atomic oxygen, which dropped to the normal low values after several cycles of operation in air and ultrahigh vacuum. For MoS{sub 2} films deposited at 200deg C, the friction coefficient was not affected by the O-atom exposure. (orig.).

  3. Decoherence-Free Interaction between Giant Atoms in Waveguide Quantum Electrodynamics.

    Science.gov (United States)

    Kockum, Anton Frisk; Johansson, Göran; Nori, Franco

    2018-04-06

    In quantum-optics experiments with both natural and artificial atoms, the atoms are usually small enough that they can be approximated as pointlike compared to the wavelength of the electromagnetic radiation with which they interact. However, superconducting qubits coupled to a meandering transmission line, or to surface acoustic waves, can realize "giant artificial atoms" that couple to a bosonic field at several points which are wavelengths apart. Here, we study setups with multiple giant atoms coupled at multiple points to a one-dimensional (1D) waveguide. We show that the giant atoms can be protected from decohering through the waveguide, but still have exchange interactions mediated by the waveguide. Unlike in decoherence-free subspaces, here the entire multiatom Hilbert space (2^{N} states for N atoms) is protected from decoherence. This is not possible with "small" atoms. We further show how this decoherence-free interaction can be designed in setups with multiple atoms to implement, e.g., a 1D chain of atoms with nearest-neighbor couplings or a collection of atoms with all-to-all connectivity. This may have important applications in quantum simulation and quantum computing.

  4. Decoherence-Free Interaction between Giant Atoms in Waveguide Quantum Electrodynamics

    Science.gov (United States)

    Kockum, Anton Frisk; Johansson, Göran; Nori, Franco

    2018-04-01

    In quantum-optics experiments with both natural and artificial atoms, the atoms are usually small enough that they can be approximated as pointlike compared to the wavelength of the electromagnetic radiation with which they interact. However, superconducting qubits coupled to a meandering transmission line, or to surface acoustic waves, can realize "giant artificial atoms" that couple to a bosonic field at several points which are wavelengths apart. Here, we study setups with multiple giant atoms coupled at multiple points to a one-dimensional (1D) waveguide. We show that the giant atoms can be protected from decohering through the waveguide, but still have exchange interactions mediated by the waveguide. Unlike in decoherence-free subspaces, here the entire multiatom Hilbert space (2N states for N atoms) is protected from decoherence. This is not possible with "small" atoms. We further show how this decoherence-free interaction can be designed in setups with multiple atoms to implement, e.g., a 1D chain of atoms with nearest-neighbor couplings or a collection of atoms with all-to-all connectivity. This may have important applications in quantum simulation and quantum computing.

  5. A Waveguide Platform for Collective Light-Atom Interaction

    DEFF Research Database (Denmark)

    Sørensen, Heidi Lundgaard

    is compared against a prediction derived from a numerical model build upon an easy experimental calibration of the viscosity profile within the heater. Very good agreement between the modeled and measured fiber shape is found. We next study the coherent back-scattering off atoms confined as two one......-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...

  6. 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

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

    International Nuclear Information System (INIS)

    1991-01-01

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

  8. 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.

  9. Dark Entangled Steady States of Interacting Rydberg Atoms

    DEFF Research Database (Denmark)

    Dasari, Durga; Mølmer, Klaus

    2013-01-01

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

  10. Inelastic Processes in the Interaction of an Atom with an Ultrashort Electromagnetic Pulse

    International Nuclear Information System (INIS)

    Matveev, V.I.; Gusarevich, E.S.; Pashev, I.N.

    2005-01-01

    Electron transitions occurring during the interaction of a heavy relativistic atom with a spatially inhomogeneous ultrashort electromagnetic pulse are considered by solving the Dirac equation. The corresponding transition probabilities are expressed in terms of known inelastic atomic form factors, which are widely used in the theory of relativistic collisions between charged particles and atoms. By way of example, the inelastic processes accompanying the interaction of ultrashort pulses with hydrogen-like atoms are considered. The probabilities of ionization and production of a bound-free electron-positron pair on a bare nucleus, which are accompanied by the formation of a hydrogen-like atom in the final state and a positron in the continuum, are calculated. The developed technique makes it possible to take into account exactly not only the spatial inhomogeneity of an ultrashort electromagnetic pulse, but also the magnetic interaction

  11. 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.

  12. Enhancing the Functional Content of Eukaryotic Protein Interaction Networks

    Science.gov (United States)

    Pandey, Gaurav; Arora, Sonali; Manocha, Sahil; Whalen, Sean

    2014-01-01

    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 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 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. PMID:25275489

  13. Online networks, social interaction and segregation: An evolutionary approach

    OpenAIRE

    Antoci, Angelo; Sabatini, Fabio

    2018-01-01

    There is growing evidence that face-to-face interaction is declining in many countries, exacerbating the phenomenon of social isolation. On the other hand, social interaction through online networking sites is steeply rising. To analyze these societal dynamics, we have built an evolutionary game model in which agents can choose between three strategies of social participation: 1) interaction via both online social networks and face-to-face encounters; 2) interaction by exclusive means of face...

  14. Discerning molecular interactions: A comprehensive review on biomolecular interaction databases and network analysis tools.

    Science.gov (United States)

    Miryala, Sravan Kumar; Anbarasu, Anand; Ramaiah, Sudha

    2018-02-05

    Computational analysis of biomolecular interaction networks is now gaining a lot of importance to understand the functions of novel genes/proteins. Gene interaction (GI) network analysis and protein-protein interaction (PPI) network analysis play a major role in predicting the functionality of interacting genes or proteins and gives an insight into the functional relationships and evolutionary conservation of interactions among the genes. An interaction network is a graphical representation of gene/protein interactome, where each gene/protein is a node, and interaction between gene/protein is an edge. In this review, we discuss the popular open source databases that serve as data repositories to search and collect protein/gene interaction data, and also tools available for the generation of interaction network, visualization and network analysis. Also, various network analysis approaches like topological approach and clustering approach to study the network properties and functional enrichment server which illustrates the functions and pathway of the genes and proteins has been discussed. Hence the distinctive attribute mentioned in this review is not only to provide an overview of tools and web servers for gene and protein-protein interaction (PPI) network analysis but also to extract useful and meaningful information from the interaction networks. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. 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...

  16. 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…

  17. A model for the interaction between F centers and H atoms in ionic crystals

    International Nuclear Information System (INIS)

    Dumke, V.R.; Souza, M. de

    1975-01-01

    The interaction between an F center and neutral hydrogen atoms, the most simple paramagnetic defects in ionic crystals, is described in terms of a perturbation theory of two square potential wells. The good agreement with experimental data indicates that lattice distortion due to the presence of the hydrogen atoms is negligible [pt

  18. Dynamic evolution of double Λ five-level atom interacting with one ...

    Indian Academy of Sciences (India)

    Home; Journals; Pramana – Journal of Physics; Volume 89; Issue 6. Dynamic evolution ... Five-level atom; squeezing; collapse revivals. Abstract. In this paper, the model describing a double Λ five-level atom interacting with a single mode electromagnetic cavity field in the (off) non-resonate case is studied. We obtained the ...

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

    Science.gov (United States)

    You, Y.; Yan, M. F.

    2013-05-01

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

  20. Cluster Approach to Network Interaction in Pedagogical University

    Science.gov (United States)

    Chekaleva, Nadezhda V.; Makarova, Natalia S.; Drobotenko, Yulia B.

    2016-01-01

    The study presented in the article is devoted to the analysis of theory and practice of network interaction within the framework of education clusters. Education clusters are considered to be a novel form of network interaction in pedagogical education in Russia. The aim of the article is to show the advantages and disadvantages of the cluster…

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

    International Nuclear Information System (INIS)

    Zhang, J.-Y.; Mitroy, J.

    2007-01-01

    A general procedure for systematically evaluating the long-range dispersion interaction between two heteronuclear atoms in arbitrary states is outlined. The C 6 dispersion parameter can always be written in terms of sum rules involving oscillator strengths only and formulas for a number of symmetry cases are given. The dispersion coefficients for excited alkali-metal atoms interacting with the ground-state H and He are tabulated

  2. Entropy for the Quantized Field in the Atom-Field Interaction: Initial Thermal Distribution

    Directory of Open Access Journals (Sweden)

    Luis Amilca Andrade-Morales

    2016-09-01

    Full Text Available We study the entropy of a quantized field in interaction with a two-level atom (in a pure state when the field is initially in a mixture of two number states. We then generalise the result for a thermal state; i.e., an (infinite statistical mixture of number states. We show that for some specific interaction times, the atom passes its purity to the field and therefore the field entropy decreases from its initial value.

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

    KAUST Repository

    Zhang, J.-Y.; Schwingenschlö gl, Udo; Shi, T.-Y.; Tang, L.-Y.; Yan, Z.-C.

    2012-01-01

    –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

  4. Entanglement of two atoms interacting with a dissipative coherent cavity field without rotating wave approximation

    International Nuclear Information System (INIS)

    Kang Guo-Dong; Fang Mao-Fa; Ouyang Xi-Cheng; Deng Xiao-Juan

    2010-01-01

    Considering two identical two-level atoms interacting with a single-model dissipative coherent cavity field without rotating wave approximation, we explore the entanglement dynamics of the two atoms prepared in different states using concurrence. Interestingly, our results show that the entanglement between the two atoms that initially disentangled will come up to a large constant rapidly, and then keeps steady in the following time or always has its maximum when prepared in some special Bell states. The model considered in this study is a good candidate for quantum information processing especially for quantum computation as steady high-degree atomic entanglement resource obtained in dissipative cavity

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

    International Nuclear Information System (INIS)

    1995-01-01

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

  6. Spin-rotation interaction of alkali-metal endash He-atom pairs

    International Nuclear Information System (INIS)

    Walker, T.G.; Thywissen, J.H.; Happer, W.

    1997-01-01

    A treatment of the spin-rotation coupling between alkali-metal atoms and He atoms is presented. Rotational distortions are accounted for in the wave function using a Coriolis interaction in the rotating frame. The expectation value of the spin-orbit interaction gives values of the spin-rotation coupling that explain previous experimental results. For spin-exchange optical pumping, the results suggest that lighter alkali-metal atoms would be preferred spin-exchange partners, other factors being equal. copyright 1997 The American Physical Society

  7. Emission and electron transitions in an atom interacting with an ultrashort electromagnetic pulse

    International Nuclear Information System (INIS)

    Matveev, V.I.

    2003-01-01

    Electron transitions and emission of an atom interacting with a spatially inhomogeneous ultrashort electromagnetic pulse are considered. The excitation and ionization probabilities are obtained as well as the spectra and cross sections of the reemission of such a pulse by atoms. By way of an example, one- and two-electron inelastic processes accompanying the interaction of ultrashort pulses with hydrogen- and helium-like atoms are considered. The developed technique makes it possible to take into account exactly the spatial nonuniformity of the ultrashort pulse field and photon momenta in the course of reemission

  8. 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

  9. Estimation of atomic interaction parameters by quantum measurements

    DEFF Research Database (Denmark)

    Kiilerich, Alexander Holm; Mølmer, Klaus

    Quantum systems, ranging from atomic systems to field modes and mechanical devices are useful precision probes for a variety of physical properties and phenomena. Measurements by which we extract information about the evolution of single quantum systems yield random results and cause a back actio...... strategies, we address the Fisher information and the Cramér-Rao sensitivity bound. We investigate monitoring by photon counting, homodyne detection and frequent projective measurements respectively, and exemplify by Rabi frequency estimation in a driven two-level system....

  10. Dispersion interaction between an atom and linear molecule

    International Nuclear Information System (INIS)

    Carvalho, I.L. de

    1987-01-01

    The Jacobi-Csanak method is adapted to the calculation of the dipole-dipole, dipole-quadrupole, quadrupole-dipole, and quadrupole-quadrupole terms of the dispersion energy of an atom-linear molecule system. The angle-dependent parts of the Born amplitudes for the linear molecule are represented by real spherical harmonics. The dispersion energy is finite at all distances and reproduces the usual expression in the asymptotic region (R≥4.7 (angstrom)). In the intermediary region (2.4(angstrom) ≤ R [pt

  11. Coherence and fluctuations in the interaction between moving atoms and a quantum field

    International Nuclear Information System (INIS)

    Hu, B.L.; Raval, A.

    1998-01-01

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

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

    Science.gov (United States)

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

    2013-09-27

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

  13. Atom

    International Nuclear Information System (INIS)

    Auffray, J.P.

    1997-01-01

    The atom through centuries, has been imagined, described, explored, then accelerated, combined...But what happens truly inside the atom? And what are mechanisms who allow its stability? Physicist and historian of sciences, Jean-Paul Auffray explains that these questions are to the heart of the modern physics and it brings them a new lighting. (N.C.)

  14. Toward a Rigorous Definition of a Strength of Any Interaction Between Bader's Atomic Basins.

    Science.gov (United States)

    Ananyev, Ivan V; Karnoukhova, Valentina A; Dmitrienko, Artem O; Lyssenko, Konstantin A

    2017-06-15

    Strength of interaction between Bader's atomic basins, enclosed by zero-flux surfaces of electron distribution, was proposed to be a measure of elastic deformation of an interaction. The set containing 53 atomic aggregate and covering all range of interaction strength (from van der Waals interactions to triple covalent bonds) was calculated by DFT and perturbation theory methods. Further analysis was performed to seek correlations between various local quantities based on electron density and effective force constants of stretching diatomic vibrations. The linear trend between effective force constants and the potential energy density at the (3, -1) critical point of electron distribution was found. This correlation was improved by the integration of the potential energy density over an interbasin zero-flux surface of electron density. Simple mechanical explanation of established trends is presented. The correlations can be further used to at least semiquantitatively compare any pair of interactions between Bader's atomic basins.

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

    International Nuclear Information System (INIS)

    Li, Xiaowei; Wang, Aiying; Lee, Kwang-Ryeol

    2012-01-01

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

  16. Ion mobilities and ion-atom interaction potentials

    International Nuclear Information System (INIS)

    Gatland, I.R.

    1982-01-01

    The techniques for measuring the mobilities of ions in gases, relating interaction potentials to mobilities, and determining potentials from experimental mobilities are reviewed. Applications are presented for positive alkali ions and negative halogen ions in inert gases. (Auth.)

  17. Energetic Analysis of Conjugated Hydrocarbons Using the Interacting Quantum Atoms Method.

    Science.gov (United States)

    Jara-Cortés, Jesús; Hernández-Trujillo, Jesús

    2018-07-05

    A number of aromatic, antiaromatic, and nonaromatic organic molecules was analyzed in terms of the contributions to the electronic energy defined in the quantum theory of atoms in molecules and the interacting quantum atoms method. Regularities were found in the exchange and electrostatic interatomic energies showing trends that are closely related to those of the delocalization indices defined in the theory. In particular, the CC interaction energies between bonded atoms allow to rationalize the energetic stabilization associated with the bond length alternation in conjugated polyenes. This approach also provides support to Clar's sextet rules devised for aromatic systems. In addition, the H⋯H bonding found in some of the aromatic molecules studied was of an attractive nature, according to the stabilizing exchange interaction between the bonded H atoms. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  18. Inelastic processes in interaction of an atom with ultrashort pulse of an electromagnetic field

    International Nuclear Information System (INIS)

    Matveev, V.I.; Gusarevich, E.S.; Pashev, I.N.

    2005-01-01

    Electron transitions occurring when a heavy relativistic atom interacts with a spatially inhomogeneous ultrashort electromagnetic pulse are considered. Transition probabilities are expressed in terms of the known inelastic atomic form factors. By way of example, the inelastic processes accompanying the interaction of ultrashort pulses with hydrogen-like atoms are considered. The probabilities of ionization and production of a bound-free electron-positron pair on a bare nucleus, which are accompanied by the formation of a hydrogen-like atom in the final state and a positron in the continuum, are calculated. The developed technique makes it possible to take into exact account magnetic interaction besides spatial inhomogeneity of an ultrashort electromagnetic pulse [ru

  19. 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. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. Theoretical investigation of electron-positive ion/atom interactions

    International Nuclear Information System (INIS)

    Msezane, A.Z.

    1992-01-01

    Very brief summaries are given on three research topics. Electron impact elastic, excitation, and total cross sections for K were investigated by using elaborate Cl target wave functions in the close-coupling approximation. Photoionization cross sections from ground-state Na were calculated near the 2s 2 2p 5 3s and 2s2p 6 3s inner-shell thresholds; also, the photoionization cross sections of excited 3p 2 P o and 3d 2 D states were calculated with the R-matrix methodology near the 2s2p 6 3s thresholds. A numerical approach was developed to calculate the charge transfer matrix elements for ion-atom(ion) collisions; this was used for the proton-hydrogen collision problem as an illustration

  1. Coherence and decoherence in the interaction of light with atoms

    Science.gov (United States)

    Carmichael, H. J.

    1997-12-01

    Amplification without population inversion in a resonant V-type atomic medium is analyzed using the theory of quantum trajectories. A global view of the dynamics underlying the amplification is provided by a quantum stochastic process governing an interplay between coherence and decoherence. The quantum trajectories decompose into distinct ``gain cycles'' and ``loss cycles'' which determine, respectively, the emission and absorption spectra that might be calculated from perturbation theory. Two methods for calculating net gain are developed, motivated by complementary views of the exchange of energy between an atom and a probe field. One time averages the energy radiated continuously by the induced dipole, while the other determines probabilities for discontinuous energy exchange through the emission and absorption of individual quanta. In the latter case, the emission and absorption probabilities are evaluated as sums over probabilities for classical records that define the unobservable exchange of a quantum with the probe field in terms of observable scattering events. Quantum trajectories for a V-type medium driven by a coherent field are compared with those for a medium driven incoherently. Two relationships which connect amplification to population inversion in the latter case are shown to be lacking in the former; hence the possibility for amplification without population inversion arises from the following: (1) a decoupling of the rate of gain-cycle (loss-cycle) initiation from the time-averaged population in the initial state for gain (loss), and (2) loss of the symmetry that the final state for emission be the initial state for absorption and vice versa. The specific influences of these general observations vary from model to model. The details are worked out for the resonant V-type medium, where the quantum trajectory analysis sheds light on the meaning of ``without population inversion'' and ``cancellation of absorption by quantum interference.''

  2. Interaction of an atom subject to an intense laser field with its own radiation field and nonlocality of electromagnetic interaction

    International Nuclear Information System (INIS)

    Gainutdinov, R Kh; Mutygullina, A A

    2009-01-01

    We discuss the interaction of an atom subject to an intense driving laser field with its own radiation field. In contrast to the states of bare atoms, the energy difference between some dressed states with the same total angular momentum, its projection and parity may be very small. The self-interaction of a combined atom-laser system associated with nonradiative transitions between such states is effectively strong. We show that the contribution to the radiative shift of the sidebands of the Mollow spectrum, which comes from such processes, is very significant and may be much larger than the trivial Lamb shift, which is the simple redistribution of the Lamb shifts of the corresponding bare states. In the final part, we discuss the possibility that in the Mollow spectrum nonlocality of electromagnetic interaction, which in other cases is hidden in the regularization and renormalization procedures, can manifest itself explicitly.

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

    International Nuclear Information System (INIS)

    Humbert, D.

    2009-02-01

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

  4. Effects impeding the observation of weak neutral interaction between muons and nuclei in light mesic atoms

    International Nuclear Information System (INIS)

    Grechukhin, D.P.; Soldatov, A.A.

    1977-01-01

    The intensity of the satellite lines of the 2s1/2→1s1/2 radiative transition in a mesic atom due to configurational interaction between the meson and shell electrons of the mesic atom is estimated. The intensity of these satellite lines is shown to be about six orders of magnitude greater than the intensity of the emission in the 2s1/2→1s1/2 meson transition. Configurational interaction between the meson and conductivity band electrons in metals precludes the usage of a metal target for stopping the mesons in the experiment. Estimates show that for mesic atoms produced in a gas the Stark effect of the electric dipole field induced in collisions between atoms of the medium and a mesic atom (Z>=2) stripped of electrons significantly restricts the density of the medium from above such that the density is 14 at/cm 3 ; in the case of the Stark effect of the intra-atomic field and collisions between a μH atom and atoms of the medium the corresponding value is 11 at/cm 3

  5. Resonance interaction energy between two entangled atoms in a photonic bandgap environment.

    Science.gov (United States)

    Notararigo, Valentina; Passante, Roberto; Rizzuto, Lucia

    2018-03-26

    We consider the resonance interaction energy between two identical entangled atoms, where one is in the excited state and the other in the ground state. They interact with the quantum electromagnetic field in the vacuum state and are placed in a photonic-bandgap environment with a dispersion relation quadratic near the gap edge and linear for low frequencies, while the atomic transition frequency is assumed to be inside the photonic gap and near its lower edge. This problem is strictly related to the coherent resonant energy transfer between atoms in external environments. The analysis involves both an isotropic three-dimensional model and the one-dimensional case. The resonance interaction asymptotically decays faster with distance compared to the free-space case, specifically as 1/r 2 compared to the 1/r free-space dependence in the three-dimensional case, and as 1/r compared to the oscillatory dependence in free space for the one-dimensional case. Nonetheless, the interaction energy remains significant and much stronger than dispersion interactions between atoms. On the other hand, spontaneous emission is strongly suppressed by the environment and the correlated state is thus preserved by the spontaneous-decay decoherence effects. We conclude that our configuration is suitable for observing the elusive quantum resonance interaction between entangled atoms.

  6. Investigating physics learning with layered student interaction networks

    DEFF Research Database (Denmark)

    Bruun, Jesper; Traxler, Adrienne

    Centrality in student interaction networks (SINs) can be linked to variables like grades [1], persistence [2], and participation [3]. Recent efforts in the field of network science have been done to investigate layered - or multiplex - networks as mathematical objects [4]. These networks can be e......, this study investigates how target entropy [5,1] and pagerank [6,7] are affected when we take time and modes of interaction into account. We present our preliminary models and results and outline our future work in this area....

  7. Global patterns of interaction specialization in bird-flower networks

    DEFF Research Database (Denmark)

    Zanata, Thais B.; Dalsgaard, Bo; Passos, Fernando C.

    2017-01-01

    , such as plant species richness, asymmetry, latitude, insularity, topography, sampling methods and intensity. Results: Hummingbird–flower networks were more specialized than honeyeater–flower networks. Specifically, hummingbird–flower networks had a lower proportion of realized interactions (lower C), decreased...... in the interaction patterns with their floral resources. Location: Americas, Africa, Asia and Oceania/Australia. Methods: We compiled interaction networks between birds and floral resources for 79 hummingbird, nine sunbird and 33 honeyeater communities. Interaction specialization was quantified through connectance...... (C), complementary specialization (H2′), binary (QB) and weighted modularity (Q), with both observed and null-model corrected values. We compared interaction specialization among the three types of bird–flower communities, both independently and while controlling for potential confounding variables...

  8. Predicting and validating protein interactions using network structure.

    Directory of Open Access Journals (Sweden)

    Pao-Yang Chen

    2008-07-01

    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.

  9. Interaction of attosecond electromagnetic pulses with atoms: The exactly solvable model

    International Nuclear Information System (INIS)

    Popov, Yu. V.; Kouzakov, K. A.; Vinitsky, S. I.; Gusev, A. A.

    2007-01-01

    We consider the exactly solvable model of interaction of zero-duration electromagnetic pulses with an atom. The model has a number of peculiar properties which are outlined in the cases of a single pulse and two opposite pulses. In perspective, it can be useful in different fields of physics involving interaction of attosecond laser pulses with quantum systems

  10. Transport properties for some atom-ion interactions in air

    International Nuclear Information System (INIS)

    Biolsi, L.; Holland, P.M.; Procter and Gamble Co., Cincinnati, OH)

    1985-01-01

    The thermal conductivity and viscosity for the N-N(+) and O-O(+) interactions have been calculated, using the kinetic theory of gases, from 500 K-20,000 K. Accurate spectroscopically determined potentials have been used for the calculations. The results are compared with previous results obtained using less accurate potentials. 62 references

  11. Continuous atom laser with Bose-Einstein condensates involving three-body interactions

    Energy Technology Data Exchange (ETDEWEB)

    Carpentier, A V; Michinel, H; Novoa, D [Area de Optica, Facultade de Ciencias de Ourense, Universidade de Vigo, As Lagoas s/n, Ourense, ES-32004 (Spain); Olivieri, D N, E-mail: avcarpentier@uvigo.e [Area de Linguaxes e sistemas informaticos, Escola Superior de EnxenerIa Informatica, Universidade de Vigo, As Lagoas s/n, Ourense, ES-32004 (Spain)

    2010-05-28

    We demonstrate, through numerical simulations, the emission of a coherent continuous matter wave of constant amplitude from a Bose-Einstein condensate in a shallow optical dipole trap. The process is achieved by spatial control of the variations of the scattering length along the trapping axis, including elastic three-body interactions due to dipole interactions. In our approach, the outcoupling mechanism is atomic interactions, and thus, the trap remains unaltered. We calculate analytically the parameters for the experimental implementation of this continuous wave atom laser.

  12. Specific non-monotonous interactions increase persistence of ecological networks.

    Science.gov (United States)

    Yan, Chuan; Zhang, Zhibin

    2014-03-22

    The relationship between stability and biodiversity has long been debated in ecology due to opposing empirical observations and theoretical predictions. Species interaction strength is often assumed to be monotonically related to population density, but the effects on stability of ecological networks of non-monotonous interactions that change signs have not been investigated previously. We demonstrate that for four kinds of non-monotonous interactions, shifting signs to negative or neutral interactions at high population density increases persistence (a measure of stability) of ecological networks, while for the other two kinds of non-monotonous interactions shifting signs to positive interactions at high population density decreases persistence of networks. Our results reveal a novel mechanism of network stabilization caused by specific non-monotonous interaction types through either increasing stable equilibrium points or reducing unstable equilibrium points (or both). These specific non-monotonous interactions may be important in maintaining stable and complex ecological networks, as well as other networks such as genes, neurons, the internet and human societies.

  13. Unfavorable regions in the ramachandran plot: Is it really steric hindrance? The interacting quantum atoms perspective.

    Science.gov (United States)

    Maxwell, Peter I; Popelier, Paul L A

    2017-11-05

    Accurate description of the intrinsic preferences of amino acids is important to consider when developing a biomolecular force field. In this study, we use a modern energy partitioning approach called Interacting Quantum Atoms to inspect the cause of the φ and ψ torsional preferences of three dipeptides (Gly, Val, and Ile). Repeating energy trends at each of the molecular, functional group, and atomic levels are observed across both (1) the three amino acids and (2) the φ/ψ scans in Ramachandran plots. At the molecular level, it is surprisingly electrostatic destabilization that causes the high-energy regions in the Ramachandran plot, not molecular steric hindrance (related to the intra-atomic energy). At the functional group and atomic levels, the importance of key peptide atoms (O i -1 , C i , N i , N i +1 ) and some sidechain hydrogen atoms (H γ ) are identified as responsible for the destabilization seen in the energetically disfavored Ramachandran regions. Consistently, the O i -1 atoms are particularly important for the explanation of dipeptide intrinsic behavior, where electrostatic and steric destabilization unusually complement one another. The findings suggest that, at least for these dipeptides, it is the peptide group atoms that dominate the intrinsic behavior, more so than the sidechain atoms. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

  14. 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].

  15. 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].

  16. Intersegmental interactions in supercoiled DNA: atomic force microscope study

    Energy Technology Data Exchange (ETDEWEB)

    Shlyakhtenko, Luda S.; Miloseska, Lela; Potaman, Vladimir N.; Sinden, Richard R.; Lyubchenko, Yuri L

    2003-10-15

    Intersegmental interactions in DNA facilitated by the neutralization of electrostatic repulsion was studied as a function of salt concentration and DNA supercoiling. DNA samples with defined superhelical densities were deposited onto aminopropyl mica at different ionic conditions and imaged in air after drying of the samples. Similar to hydrodynamic data, we did not observe a collapse of supercoiled DNA, as proposed earlier by cryo-EM studies. Instead, the formation of the contacts between DNA helices within supercoiled loops with no visible space between the duplexes was observed. The length of such close contacts increased upon increasing NaCl concentration. DNA supercoiling was a critical factor for the stabilization of intersegmental contacts. Implications of the observed effect for understanding DNA compaction in the cell and for regulation DNA transactions via interaction of distantly separated DNA regions are discussed.

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

    International Nuclear Information System (INIS)

    Villette, J.

    2000-10-01

    Grazing collisions ( + , Ne + , Ne 0 , Na + on LiF (001) single crystal, an ionic insulator, are investigated by a time of flight technique. The incident beam is chopped and the scattered particles are collected on a position sensitive detector providing differential cross section while the time of flight gives the energy loss. Deflection plates allow the charge state analysis. Secondary electrons are detected in coincidence allowing direct measurements of electron emission yield, angular and energetic distribution through time of flight measurements. The target electronic structure characterized by a large band gap, governs the collisional processes: charge exchange, electronic excitations and electron emission. In particular, these studies show that the population of local target excitations surface excitons is the major contribution to the kinetic energy transfer (stopping power). Auger neutralization of Ne + and He + ions reveals the population of quasi-molecular excitons, an exciton bound on two holes. Referenced in the literature as trion. A direct energy balance determines the binding energy associated with these excited states of the surface. Besides these electronic energy loss processes, two nuclear energy loss mechanisms are characterized. These processes imply momentum transfer to individual target atoms during close binary collisions or, if the projectile is charged, to collective mode of optical phonons induced by the projectile coulomb field. The effect of the temperature on the scattering profile, the contribution of topological surface defects to the energy loss profile and to skipping motion on the surface are analyzed in view of classical trajectory simulations. (author)

  18. Ion-atom interactions probed by photofragment spectroscopy

    International Nuclear Information System (INIS)

    Helm, H.

    1984-01-01

    Photofragment spectroscopy studies energetic and dynamical properties of molecular states interacting with dissociation continuum. So far, data for eighteen diatomic molecular ions have been gathered by this technique. This paper is a review of these investigations, introduced by a discussion of the experimental methods used. The wealth of information accessible by ion photofragment spectroscopy challenges the experimentalist in the application of innovative techniques and the theoretician for less approximate accounts of the Hamiltonian. (Auth.)

  19. Influences of brain development and ageing on cortical interactive networks.

    Science.gov (United States)

    Zhu, Chengyu; Guo, Xiaoli; Jin, Zheng; Sun, Junfeng; Qiu, Yihong; Zhu, Yisheng; Tong, Shanbao

    2011-02-01

    To study the effect of brain development and ageing on the pattern of cortical interactive networks. By causality analysis of multichannel electroencephalograph (EEG) with partial directed coherence (PDC), we investigated the different neural networks involved in the whole cortex as well as the anterior and posterior areas in three age groups, i.e., children (0-10 years), mid-aged adults (26-38 years) and the elderly (56-80 years). By comparing the cortical interactive networks in different age groups, the following findings were concluded: (1) the cortical interactive network in the right hemisphere develops earlier than its left counterpart in the development stage; (2) the cortical interactive network of anterior cortex, especially at C3 and F3, is demonstrated to undergo far more extensive changes, compared with the posterior area during brain development and ageing; (3) the asymmetry of the cortical interactive networks declines during ageing with more loss of connectivity in the left frontal and central areas. The age-related variation of cortical interactive networks from resting EEG provides new insights into brain development and ageing. Our findings demonstrated that the PDC analysis of EEG is a powerful approach for characterizing the cortical functional connectivity during brain development and ageing. Copyright © 2010 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

  20. Mean field interaction in biochemical reaction networks

    KAUST Repository

    Tembine, Hamidou; Tempone, Raul; Vilanova, Pedro

    2011-01-01

    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

  1. 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.

  2. 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.

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

    Science.gov (United States)

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

    2016-01-07

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

  4. 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.

  5. Empirical evaluation of neutral interactions in host-parasite networks.

    Science.gov (United States)

    Canard, E F; Mouquet, N; Mouillot, D; Stanko, M; Miklisova, D; Gravel, D

    2014-04-01

    While niche-based processes have been invoked extensively to explain the structure of interaction networks, recent studies propose that neutrality could also be of great importance. Under the neutral hypothesis, network structure would simply emerge from random encounters between individuals and thus would be directly linked to species abundance. We investigated the impact of species abundance distributions on qualitative and quantitative metrics of 113 host-parasite networks. We analyzed the concordance between neutral expectations and empirical observations at interaction, species, and network levels. We found that species abundance accurately predicts network metrics at all levels. Despite host-parasite systems being constrained by physiology and immunology, our results suggest that neutrality could also explain, at least partially, their structure. We hypothesize that trait matching would determine potential interactions between species, while abundance would determine their realization.

  6. Position and Momentum Entanglement of Dipole-Dipole Interacting Atoms in Optical Lattices

    Science.gov (United States)

    Opatrný, T.; Kolář, M.; Kurizki, G.

    We consider a possible realization of the position- and momentum-correlated atomic pairs that are confined to adjacent sites of two mutually shifted optical lattices and are entangled via laser-induced dipole-dipole interactions. The Einstein-Podolsky-Rosen (EPR) "paradox" [Einstein 1935] with translational variables is then modified by lattice-diffraction effects. We study a possible mechanism of creating such diatom entangled states by varying the effective mass of the atoms.

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

    International Nuclear Information System (INIS)

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

    2012-01-01

    Inelastic processes occuring in thermal-velocity metastable atoms and molecules passing at a mean distance (1–100 nm) are investigated. These processes are caused by the quadrupolar part of the van der Waals interaction: fine-structure transitions in atoms (Ar ∗ , Kr ∗ ), rovibrational transitions in N 2 ∗ ( 3 Σ u + ), transitions among magnetic sub-levels in the presence of a magnetic field.

  8. Mechanism and kinetics of Fe, Cr, Mo and Mn atom interaction with molecular oxygen

    International Nuclear Information System (INIS)

    Akhmadov, U.S.; Zaslonko, I.S.; Smirnov, V.N.

    1988-01-01

    Rate constants of atomic interaction of some transition metals (Fe, Cr, Mo, Mn) with molecular oxygen are measured in shock waves using the resonance atomic-absorption method. A new method for determination of the parameter γ in the modified Lambert-Beer law D=ε(lN)γ is suggested and applied. Bond strength in CrO and MoO molecules is estimated

  9. Correlated wave functions for three-particle systems with Coulomb interaction - The muonic helium atom

    Science.gov (United States)

    Huang, K.-N.

    1977-01-01

    A computational procedure for calculating correlated wave functions is proposed for three-particle systems interacting through Coulomb forces. Calculations are carried out for the muonic helium atom. Variational wave functions which explicitly contain interparticle coordinates are presented for the ground and excited states. General Hylleraas-type trial functions are used as the basis for the correlated wave functions. Excited-state energies of the muonic helium atom computed from 1- and 35-term wave functions are listed for four states.

  10. Interaction Networks: Generating High Level Hints Based on Network Community Clustering

    Science.gov (United States)

    Eagle, Michael; Johnson, Matthew; Barnes, Tiffany

    2012-01-01

    We introduce a novel data structure, the Interaction Network, for representing interaction-data from open problem solving environment tutors. We show how using network community detecting techniques are used to identify sub-goals in problems in a logic tutor. We then use those community structures to generate high level hints between sub-goals.…

  11. Default network modulation and large-scale network interactivity in healthy young and old adults.

    Science.gov (United States)

    Spreng, R Nathan; Schacter, Daniel L

    2012-11-01

    We investigated age-related changes in default, attention, and control network activity and their interactions in young and old adults. Brain activity during autobiographical and visuospatial planning was assessed using multivariate analysis and with intrinsic connectivity networks as regions of interest. In both groups, autobiographical planning engaged the default network while visuospatial planning engaged the attention network, consistent with a competition between the domains of internalized and externalized cognition. The control network was engaged for both planning tasks. In young subjects, the control network coupled with the default network during autobiographical planning and with the attention network during visuospatial planning. In old subjects, default-to-control network coupling was observed during both planning tasks, and old adults failed to deactivate the default network during visuospatial planning. This failure is not indicative of default network dysfunction per se, evidenced by default network engagement during autobiographical planning. Rather, a failure to modulate the default network in old adults is indicative of a lower degree of flexible network interactivity and reduced dynamic range of network modulation to changing task demands.

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

    International Nuclear Information System (INIS)

    Pashchenko, A.B.; Wienke, H.

    1998-01-01

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

  13. DFT Modeling of Cross-Linked Polyethylene: Role of Gold Atoms and Dispersion Interactions.

    Science.gov (United States)

    Blaško, Martin; Mach, Pavel; Antušek, Andrej; Urban, Miroslav

    2018-02-08

    Using DFT modeling, we analyze the concerted action of gold atoms and dispersion interactions in cross-linked polyethylene. Our model consists of two oligomer chains (PEn) with 7, 11, 15, 19, or 23 carbon atoms in each oligomer cross-linked with one to three Au atoms through C-Au-C bonds. In structures with a single gold atom the C-Au-C bond is located in the central position of the oligomer. Binding energies (BEs) with respect to two oligomer radical fragments and Au are as high as 362-489 kJ/mol depending on the length of the oligomer chain. When the dispersion contribution in PEn-Au-PEn oligomers is omitted, BE is almost independent of the number of carbon atoms, lying between 293 and 296 kJ/mol. The dispersion energy contributions to BEs in PEn-Au-PEn rise nearly linearly with the number of carbon atoms in the PEn chain. The carbon-carbon distance in the C-Au-C moiety is around 4.1 Å, similar to the bond distance between saturated closed shell chains in the polyethylene crystal. BEs of pure saturated closed shell PEn-PEn oligomers are 51-187 kJ/mol. Both Au atoms and dispersion interactions contribute considerably to the creation of nearly parallel chains of oligomers with reasonably high binding energies.

  14. Interacting Social Processes on Interconnected Networks.

    Directory of Open Access Journals (Sweden)

    Lucila G Alvarez-Zuzek

    Full Text Available 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*.

  15. Personal Profiles: Enhancing Social Interaction in Learning Networks

    NARCIS (Netherlands)

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

    2009-01-01

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

  16. Defaunation leads to interaction deficits, not interaction compensation, in an island seed dispersal network.

    Science.gov (United States)

    Fricke, Evan C; Tewksbury, Joshua J; Rogers, Haldre S

    2018-01-01

    Following defaunation, the loss of interactions with mutualists such as pollinators or seed dispersers may be compensated through increased interactions with remaining mutualists, ameliorating the negative cascading impacts on biodiversity. Alternatively, remaining mutualists may respond to altered competition by reducing the breadth or intensity of their interactions, exacerbating negative impacts on biodiversity. Despite the importance of these responses for our understanding of the dynamics of mutualistic networks and their response to global change, the mechanism and magnitude of interaction compensation within real mutualistic networks remains largely unknown. We examined differences in mutualistic interactions between frugivores and fruiting plants in two island ecosystems possessing an intact or disrupted seed dispersal network. We determined how changes in the abundance and behavior of remaining seed dispersers either increased mutualistic interactions (contributing to "interaction compensation") or decreased interactions (causing an "interaction deficit") in the disrupted network. We found a "rich-get-richer" response in the disrupted network, where remaining frugivores favored the plant species with highest interaction frequency, a dynamic that worsened the interaction deficit among plant species with low interaction frequency. Only one of five plant species experienced compensation and the other four had significant interaction deficits, with interaction frequencies 56-95% lower in the disrupted network. These results do not provide support for the strong compensating mechanisms assumed in theoretical network models, suggesting that existing network models underestimate the prevalence of cascading mutualism disruption after defaunation. This work supports a mutualist biodiversity-ecosystem functioning relationship, highlighting the importance of mutualist diversity for sustaining diverse and resilient ecosystems. © 2017 John Wiley & Sons Ltd.

  17. 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),…

  18. Global Diffusion of Interactive Networks. The Impact of Culture

    OpenAIRE

    Maitland, Carleen

    1998-01-01

    The Internet and other interactive networks are diffusing across the globe at rates that vary from country to country. Typically, economic and market structure variables are used to explain these differences. The addition of culture to these variables will provide a more robust understanding of the differences in Internet and interactive network diffusion. Existing analyses that identify culture as a predictor of diffusion do not adequately specificy the dimensions of culture and their imp...

  19. Functional Interaction Network Construction and Analysis for Disease Discovery.

    Science.gov (United States)

    Wu, Guanming; Haw, Robin

    2017-01-01

    Network-based approaches project seemingly unrelated genes or proteins onto a large-scale network context, therefore providing a holistic visualization and analysis platform for genomic data generated from high-throughput experiments, reducing the dimensionality of data via using network modules and increasing the statistic analysis power. Based on the Reactome database, the most popular and comprehensive open-source biological pathway knowledgebase, we have developed a highly reliable protein functional interaction network covering around 60 % of total human genes and an app called ReactomeFIViz for Cytoscape, the most popular biological network visualization and analysis platform. In this chapter, we describe the detailed procedures on how this functional interaction network is constructed by integrating multiple external data sources, extracting functional interactions from human curated pathway databases, building a machine learning classifier called a Naïve Bayesian Classifier, predicting interactions based on the trained Naïve Bayesian Classifier, and finally constructing the functional interaction database. We also provide an example on how to use ReactomeFIViz for performing network-based data analysis for a list of genes.

  20. Unveiling protein functions through the dynamics of the interaction network.

    Directory of Open Access Journals (Sweden)

    Irene Sendiña-Nadal

    Full Text Available Protein interaction networks have become a tool to study biological processes, either for predicting molecular functions or for designing proper new drugs to regulate the main biological interactions. Furthermore, such networks are known to be organized in sub-networks of proteins contributing to the same cellular function. However, the protein function prediction is not accurate and each protein has traditionally been assigned to only one function by the network formalism. By considering the network of the physical interactions between proteins of the yeast together with a manual and single functional classification scheme, we introduce a method able to reveal important information on protein function, at both micro- and macro-scale. In particular, the inspection of the properties of oscillatory dynamics on top of the protein interaction network leads to the identification of misclassification problems in protein function assignments, as well as to unveil correct identification of protein functions. We also demonstrate that our approach can give a network representation of the meta-organization of biological processes by unraveling the interactions between different functional classes.

  1. Evidence for the additions of clustered interacting nodes during the evolution of protein interaction networks from network motifs

    Directory of Open Access Journals (Sweden)

    Guo Hao

    2011-05-01

    Full Text Available Abstract Background High-throughput screens have revealed large-scale protein interaction networks defining most cellular functions. How the proteins were added to the protein interaction network during its growth is a basic and important issue. Network motifs represent the simplest building blocks of cellular machines and are of biological significance. Results Here we study the evolution of protein interaction networks from the perspective of network motifs. We find that in current protein interaction networks, proteins of the same age class tend to form motifs and such co-origins of motif constituents are affected by their topologies and biological functions. Further, we find that the proteins within motifs whose constituents are of the same age class tend to be densely interconnected, co-evolve and share the same biological functions, and these motifs tend to be within protein complexes. Conclusions Our findings provide novel evidence for the hypothesis of the additions of clustered interacting nodes and point out network motifs, especially the motifs with the dense topology and specific function may play important roles during this process. Our results suggest functional constraints may be the underlying driving force for such additions of clustered interacting nodes.

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

    International Nuclear Information System (INIS)

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

    2016-01-01

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

  3. Functional modules by relating protein interaction networks and gene expression.

    Science.gov (United States)

    Tornow, Sabine; Mewes, H W

    2003-11-01

    Genes and proteins are organized on the basis of their particular mutual relations or according to their interactions in cellular and genetic networks. These include metabolic or signaling pathways and protein interaction, regulatory or co-expression networks. Integrating the information from the different types of networks may lead to the notion of a functional network and functional modules. To find these modules, we propose a new technique which is based on collective, multi-body correlations in a genetic network. We calculated the correlation strength of a group of genes (e.g. in the co-expression network) which were identified as members of a module in a different network (e.g. in the protein interaction network) and estimated the probability that this correlation strength was found by chance. Groups of genes with a significant correlation strength in different networks have a high probability that they perform the same function. Here, we propose evaluating the multi-body correlations by applying the superparamagnetic approach. We compare our method to the presently applied mean Pearson correlations and show that our method is more sensitive in revealing functional relationships.

  4. Spin-spin interactions of electrons and also of nucleons create atomic molecular and nuclear structures

    International Nuclear Information System (INIS)

    Kaliambos, L.A.

    2008-01-01

    Fundamental interactions of spinning electrons at an interelectron separation less than 578.8 fm yield attractive electromagnetic forces with S = 0 creating vibrations under a motional emf. They explain the indistinguishability of electrons and give a vibration energy able for calculating the ground-state energies of many-electron atoms without using any perturbative approximation. Such forces create two-electron orbitals able to account for the exclusion principal and the mechanism of covalent bonds. In the outer subshells of atoms the penetrating orbitals interact also as pair-pair systems and deform drastically the probability densities of the quantum mechanical electron clouds. Such a dynamics of deformation removes the degeneracy and leads to the deviation from the shell scheme. However in the interior of atoms the large nuclear charge leads to a spherically symmetric potential with non-interacting pairs for creating shells of degenerate states giving an accurate explanation of the X-ray lines. On the other hand, considerable charge distributions in nucleons as multiples of 2e/3 and - e/3 determined by the magnetic moments, interact for creating the nuclear structure with p-n bonds. Such spin-spin interactions show that the dominant concept of the untisymmetric wave function for fermions is inapplicable not only in the simple p-n, p-p, and n-n systems but also in the LS coupling of atoms in which the electrons interact from different quantum states giving either S = 0 or S = l. (author)

  5. Atom-field interaction in the single-quantum limit in a two dimensional travelling-wave cavity

    International Nuclear Information System (INIS)

    Youn, Sun Hyun; Chough, Young Tak; An, Kyung Won

    2003-01-01

    We analyze the interaction of an atom with two dimensional travelling-wave cavity modes in the strong coupling region, with the quantized atomic center of mass motion taken into account. Analytic and numerical calculation shows that the atom in two independent pairs of travelling wave modes can be made to interact only with a particular travelling mode by matching the initial momentum and the detuning of the cavities. We also numerically investigate the atomic momentum deflection in the cavities

  6. 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.

  7. Building a glaucoma interaction network using a text mining approach.

    Science.gov (United States)

    Soliman, Maha; Nasraoui, Olfa; Cooper, Nigel G F

    2016-01-01

    The volume of biomedical literature and its underlying knowledge base is rapidly expanding, making it beyond the ability of a single human being to read through all the literature. Several automated methods have been developed to help make sense of this dilemma. The present study reports on the results of a text mining approach to extract gene interactions from the data warehouse of published experimental results which are then used to benchmark an interaction network associated with glaucoma. To the best of our knowledge, there is, as yet, no glaucoma interaction network derived solely from text mining approaches. The presence of such a network could provide a useful summative knowledge base to complement other forms of clinical information related to this disease. A glaucoma corpus was constructed from PubMed Central and a text mining approach was applied to extract genes and their relations from this corpus. The extracted relations between genes were checked using reference interaction databases and classified generally as known or new relations. The extracted genes and relations were then used to construct a glaucoma interaction network. Analysis of the resulting network indicated that it bears the characteristics of a small world interaction network. Our analysis showed the presence of seven glaucoma linked genes that defined the network modularity. A web-based system for browsing and visualizing the extracted glaucoma related interaction networks is made available at http://neurogene.spd.louisville.edu/GlaucomaINViewer/Form1.aspx. This study has reported the first version of a glaucoma interaction network using a text mining approach. The power of such an approach is in its ability to cover a wide range of glaucoma related studies published over many years. Hence, a bigger picture of the disease can be established. To the best of our knowledge, this is the first glaucoma interaction network to summarize the known literature. The major findings were a set of

  8. Unified Alignment of Protein-Protein Interaction Networks.

    Science.gov (United States)

    Malod-Dognin, Noël; Ban, Kristina; Pržulj, Nataša

    2017-04-19

    Paralleling the increasing availability of protein-protein interaction (PPI) network data, several network alignment methods have been proposed. Network alignments have been used to uncover functionally conserved network parts and to transfer annotations. However, due to the computational intractability of the network alignment problem, aligners are heuristics providing divergent solutions and no consensus exists on a gold standard, or which scoring scheme should be used to evaluate them. We comprehensively evaluate the alignment scoring schemes and global network aligners on large scale PPI data and observe that three methods, HUBALIGN, L-GRAAL and NATALIE, regularly produce the most topologically and biologically coherent alignments. We study the collective behaviour of network aligners and observe that PPI networks are almost entirely aligned with a handful of aligners that we unify into a new tool, Ulign. Ulign enables complete alignment of two networks, which traditional global and local aligners fail to do. Also, multiple mappings of Ulign define biologically relevant soft clusterings of proteins in PPI networks, which may be used for refining the transfer of annotations across networks. Hence, PPI networks are already well investigated by current aligners, so to gain additional biological insights, a paradigm shift is needed. We propose such a shift come from aligning all available data types collectively rather than any particular data type in isolation from others.

  9. 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.

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

    DEFF Research Database (Denmark)

    Ruban, Andrei; Skriver, Hans Lomholt

    2002-01-01

    We have used the locally self-consistent Green's-function (LSGF) method in supercell calculations to establish the distribution of the net charges assigned to the atomic spheres of the alloy components in metallic alloys with different compositions and degrees of order. This allows us to determine......-site local interaction zone. We demonstrate that the basic mechanism that governs the charge distribution is the screening of the net charges of the alloy components that makes the direct Coulomb interactions short ranged. In the atomic-sphere approximation, this screening appears to be almost independent...

  11. Atomic and Plasma-Material Interaction Data for Fusion. V. 16

    International Nuclear Information System (INIS)

    Braams, B.J.; Chung, H.-K.

    2014-03-01

    A wide variety of atomic, molecular, radiative and plasma-wall interaction processes involving a mixture of atoms, ions and molecules occur in the plasmas produced in nuclear fusion experiments. In the low temperature divertor and near wall region, molecules and molecular ions are formed. The plasma particles react with electrons and with each other. Plasma modelling requires cross-sections and rate coefficients for all these processes, and in addition spectral signatures to support interpretation of data from fusion experiments. The mission of the International Atomic Energy Agency Nuclear Data Section (IAEA/NDS) in the area of atomic and molecular data is to enhance the competencies of Member States in their research into nuclear fusion through the provision of internationally recommended atomic, molecular, plasma-material interaction and material properties databases. One mechanism by which the IAEA pursues this mission is the Coordinated Research Project (CRP). The present volume of Atomic and Plasma-Material Interaction Data for Fusion contains contributions from participants in the CRP 'Atomic and Molecular Data for Plasma Modelling' (2004-2008). This CRP was concerned with data for processes in the near wall and divertor plasma and plasma-wall interaction in fusion experiments, with focus on cross-sections for molecular reactions. Participants in the CRP came from 14 different institutes, many with strong ties to fusion plasma modelling and experiment. D. Humbert of the Nuclear Data Section was scientific secretary of the CRP. Participants' contributions for this volume were collected and refereed after the conclusion of the CRP

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

    Directory of Open Access Journals (Sweden)

    Jonathan Sargent

    2013-03-01

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

  13. Structural stability of interaction networks against negative external fields

    Science.gov (United States)

    Yoon, S.; Goltsev, A. V.; Mendes, J. F. F.

    2018-04-01

    We explore structural stability of weighted and unweighted networks of positively interacting agents against a negative external field. We study how the agents support the activity of each other to confront the negative field, which suppresses the activity of agents and can lead to collapse of the whole network. The competition between the interactions and the field shape the structure of stable states of the system. In unweighted networks (uniform interactions) the stable states have the structure of k -cores of the interaction network. The interplay between the topology and the distribution of weights (heterogeneous interactions) impacts strongly the structural stability against a negative field, especially in the case of fat-tailed distributions of weights. We show that apart from critical slowing down there is also a critical change in the system structure that precedes the network collapse. The change can serve as an early warning of the critical transition. To characterize changes of network structure we develop a method based on statistical analysis of the k -core organization and so-called "corona" clusters belonging to the k -cores.

  14. 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

  15. 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…

  16. Evidence of probabilistic behaviour in protein interaction networks

    Directory of Open Access Journals (Sweden)

    Reifman Jaques

    2008-01-01

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

  17. Tensorial analysis of the long-range interaction between metastable alkaline-earth-metal atoms

    International Nuclear Information System (INIS)

    Santra, Robin; Greene, Chris H.

    2003-01-01

    Alkaline-earth-metal atoms in their lowest (nsnp) 3 P 2 state are exceptionally long lived and can be trapped magnetically. The nonspherical atomic structure leads to anisotropic long-range interactions between two metastable alkaline-earth-metal atoms. The anisotropy affects the rotational motion of the diatomic system and couples states of different rotational quantum numbers. This paper develops a tensorial decomposition of the most important long-range interaction operators, and a systematic inclusion of molecular rotations, in the presence of an external magnetic field. This analysis illuminates the nature of the coupling between the various degrees of freedom. The consequences are illustrated by application to a system of practical interest: metastable 88 Sr. Using atomic parameters determined in a nearly ab initio calculation, we compute adiabatic potential-energy curves. The anisotropic interatomic interaction, in combination with the applied magnetic field, is demonstrated to induce the formation of a long-range molecular potential well. This curve correlates to two fully polarized, low-field seeking atoms in a rotational s-wave state. The coupling among molecular rotational states controls the existence of the potential well, and its properties vary as a function of magnetic-field strength, thus allowing the scattering length in this state to be tuned. The scattering length of metastable 88 Sr displays a resonance at a field of 339 G

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

    Science.gov (United States)

    Friedlein, R; Van Bui, H; Wiggers, F B; Yamada-Takamura, Y; Kovalgin, A Y; de Jong, M P

    2014-05-28

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

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

    International Nuclear Information System (INIS)

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

    2015-01-01

    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. (paper)

  20. Network traffic intelligence using a low interaction honeypot

    Science.gov (United States)

    Nyamugudza, Tendai; Rajasekar, Venkatesh; Sen, Prasad; Nirmala, M.; Madhu Viswanatham, V.

    2017-11-01

    Advancements in networking technology have seen more and more devices becoming connected day by day. This has given organizations capacity to extend their networks beyond their boundaries to remote offices and remote employees. However as the network grows security becomes a major challenge since the attack surface also increases. There is need to guard the network against different types of attacks like intrusion and malware through using different tools at different networking levels. This paper describes how network intelligence can be acquired through implementing a low-interaction honeypot which detects and track network intrusion. Honeypot allows an organization to interact and gather information about an attack earlier before it compromises the network. This process is important because it allows the organization to learn about future attacks of the same nature and allows them to develop counter measures. The paper further shows how honeypot-honey net based model for interruption detection system (IDS) can be used to get the best valuable information about the attacker and prevent unexpected harm to the network.

  1. 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...

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

    International Nuclear Information System (INIS)

    1992-01-01

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

  3. Nonlinear Jaynes–Cummings model for two interacting two-level atoms

    International Nuclear Information System (INIS)

    Santos-Sánchez, O de los; González-Gutiérrez, C; Récamier, J

    2016-01-01

    In this work we examine a nonlinear version of the Jaynes–Cummings model for two identical two-level atoms allowing for Ising-like and dipole–dipole interplays between them. The model is said to be nonlinear in the sense that it can incorporate both a general intensity-dependent interaction between the atomic system and the cavity field and/or the presence of a nonlinear medium inside the cavity. As an example, we consider a particular type of atom-field coupling based upon the so-called Buck–Sukumar model and a lossless Kerr-like cavity. We describe the possible effects of such features on the evolution of some quantities of current interest, such as atomic excitation, purity, concurrence, the entropy of the field and the evolution of the latter in phase space. (paper)

  4. Towards passive and active laser stabilization using cavity-enhanced atomic interaction

    DEFF Research Database (Denmark)

    Schäffer, Stefan Alaric; Christensen, Bjarke Takashi Røjle; Rathmann, Stefan Mossor

    2017-01-01

    Ultra stable frequency references such as the ones used in optical atomic clocks and for quantum metrology may be obtained by stabilizing a laser to an optical cavity that is stable over time. State-of-the-art frequency references are constructed in this way, but their stabilities are currently...... experimental efforts derived from these proposals, to use cavity-enhanced interaction with atomic 88Sr samples as a frequency reference for laser stabilization. Such systems can be realized using both passive and active approaches where either the atomic phase response is used as an error signal, or the narrow...... atomic transition itself is used as a source for a spectrally pure laser. Both approaches shows the promise of being able to compete with the current state of the art in stable lasers and have similar limitations on their ultimately achievable linewidths [1, 2]....

  5. A Global Protein Kinase and Phosphatase Interaction Network in Yeast

    Science.gov (United States)

    Breitkreutz, Ashton; Choi, Hyungwon; Sharom, Jeffrey R.; Boucher, Lorrie; Neduva, Victor; Larsen, Brett; Lin, Zhen-Yuan; Breitkreutz, Bobby-Joe; Stark, Chris; Liu, Guomin; Ahn, Jessica; Dewar-Darch, Danielle; Reguly, Teresa; Tang, Xiaojing; Almeida, Ricardo; Qin, Zhaohui Steve; Pawson, Tony; Gingras, Anne-Claude; Nesvizhskii, Alexey I.; Tyers, Mike

    2011-01-01

    The interactions of protein kinases and phosphatases with their regulatory subunits and substrates underpin cellular regulation. We identified a kinase and phosphatase interaction (KPI) network of 1844 interactions in budding yeast by mass spectrometric analysis of protein complexes. The KPI network contained many dense local regions of interactions that suggested new functions. Notably, the cell cycle phosphatase Cdc14 associated with multiple kinases that revealed roles for Cdc14 in mitogen-activated protein kinase signaling, the DNA damage response, and metabolism, whereas interactions of the target of rapamycin complex 1 (TORC1) uncovered new effector kinases in nitrogen and carbon metabolism. An extensive backbone of kinase-kinase interactions cross-connects the proteome and may serve to coordinate diverse cellular responses. PMID:20489023

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

    Energy Technology Data Exchange (ETDEWEB)

    Gil, D.M. [Instituto de Química Física, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, San Lorenzo 456, T4000CAN San Miguel de Tucumán (Argentina); Osiry, H. [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional, México (Mexico); Pomiro, F.; Varetti, E.L. [CEQUINOR (CONICET-UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, 47 and 115, 1900, La Plata (Argentina); Carbonio, R.E. [INFIQC – CONICET, Departamento de Físico Química, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre esq, Medina Allende, Ciudad Universitaria, X5000HUA Córdoba (Argentina); Alejandro, R.R. [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional, México (Mexico); Ben Altabef, A. [INQUINOA-UNT-CONICET, Instituto de Química Física, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, San Lorenzo 456, T4000CAN San Miguel de Tucumán (Argentina); and others

    2016-07-15

    The hydrogen bond and π-π stacking are two non-covalent interactions able to support cooperative magnetic ordering between paramagnetic centers. This contribution reports the crystal structure and related magnetic properties for VO[Fe(CN){sub 5}NO]·2H{sub 2}O, which has a layered structure. This solid crystallizes with an orthorhombic unit cell, in the Pna2{sub 1} space group, with cell parameters a=14.1804(2), b=10.4935(1), c=7.1722(8) Å and four molecules per unit cell (Z=4). Its crystal structure was solved and refined from powder X-ray diffraction data. Neighboring layers remain linked through a network of hydrogen bonds involving a water molecule coordinated to the axial position for the V atom and the unbridged axial NO and CN ligands. An uncoordinated water molecule is found forming a triple bridge between these last two ligands and the coordinated water molecule. The magnetic measurements, recorded down to 2 K, shows a ferromagnetic interaction between V atoms located at neighboring layers, with a Curie-Weiss constant of 3.14 K. Such ferromagnetic behavior was interpreted as resulting from a superexchange interaction through the network of strong OH····O{sub H2O}, OH····N{sub CN}, and OH····O{sub NO} hydrogen bonds that connects neighboring layers. The interaction within the layer must be of antiferromagnetic nature and it was detected close to 2 K. - Graphical abstract: Coordination environment for the metals in vanadyl (II) nitroprusside dihydrate. Display Omitted - Highlights: • Crystal structure of vanadyl nitroprusside dehydrate. • Network of hydrogen bonds. • Magnetic interactions through a network of hydrogen bonds. • Layered transition metal nitroprussides.

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

    International Nuclear Information System (INIS)

    Benisti, D.

    2011-01-01

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

  8. Matrix elements and transition probabilities of interaction of electromagnetic field with a hydrogen-like atom

    International Nuclear Information System (INIS)

    Rajput, B.S.

    1977-01-01

    Using the reduced expansions of second quantized electromagnetic vector potential operator in terms of irreducible representations of Pioncare group in the interaction Hamiltonian, the exact matrix elements of interaction of electromagnetic field with a hydrogenic atom have been derived and the contributions of transitions for different combinations of angular momentum quantum numbers to the transition probabilities of various lines in Lyman-, Balmer-, and Paschen-series have been computed. (author)

  9. Specificity and evolvability in eukaryotic protein interaction networks.

    Directory of Open Access Journals (Sweden)

    Pedro Beltrao

    2007-02-01

    Full Text Available Progress in uncovering the protein interaction networks of several species has led to questions of what underlying principles might govern their organization. Few studies have tried to determine the impact of protein interaction network evolution on the observed physiological differences between species. Using comparative genomics and structural information, we show here that eukaryotic species have rewired their interactomes at a fast rate of approximately 10(-5 interactions changed per protein pair, per million years of divergence. For Homo sapiens this corresponds to 10(3 interactions changed per million years. Additionally we find that the specificity of binding strongly determines the interaction turnover and that different biological processes show significantly different link dynamics. In particular, human proteins involved in immune response, transport, and establishment of localization show signs of positive selection for change of interactions. Our analysis suggests that a small degree of molecular divergence can give rise to important changes at the network level. We propose that the power law distribution observed in protein interaction networks could be partly explained by the cell's requirement for different degrees of protein binding specificity.

  10. Interactively Evolving Compositional Sound Synthesis Networks

    DEFF Research Database (Denmark)

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

    2015-01-01

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

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

    Indian Academy of Sciences (India)

    The excitement to study dynamics of dipole–dipole interaction stems from the fact that ... As the detailed results for the two-atom case are published in [13], only .... state are |gee〉, |ege〉 and |eeg〉 and are denoted as |5〉, |6〉 and |7〉. Finally, the ...

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

    International Nuclear Information System (INIS)

    Mitroy, J.; Zhang, J.-Y.

    2007-01-01

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

  13. Parity violation in atoms and implications for unified models of weak and electromagnetic interactions

    International Nuclear Information System (INIS)

    Jarlskog, C.

    1976-07-01

    Parity violation experiments in atoms are probing structure of the weak neutral current couplings of the electrons and the quarks in the same range as the neutrino interactions are measuring couplings of neutrinos and quarks. In addition, leptonic neutral currents determine couplings of neutrinos and electrons. Therefore the three type of experiments give complete information and impose strong restrictions on theoretical possibilities. (BJ) [de

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

    International Nuclear Information System (INIS)

    Barbaro, Jacques

    1971-01-01

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

  15. Random model of two-level atoms interacting with electromagnetic field

    International Nuclear Information System (INIS)

    Kireev, A.N.; Meleshko, A.N.

    1983-12-01

    A phase transition has been studied in a random system of two-level atoms interacting with an electromagnetic field. It is shown that superradiation can arise when there is short-range order in a spin-subsystem. The existence of long-range order is irrelevant for this phase transition

  16. Tunneling couplings in discrete lattices, single-particle band structure, and eigenstates of interacting atom pairs

    International Nuclear Information System (INIS)

    Piil, Rune; Moelmer, Klaus

    2007-01-01

    By adjusting the tunneling couplings over longer than nearest-neighbor distances, it is possible in discrete lattice models to reproduce the properties of the lowest energy band of a real, continuous periodic potential. We propose to include such terms in problems with interacting particles, and we show that they have significant consequences for scattering and bound states of atom pairs in periodic potentials

  17. Atom Core Interactive Electronic Book to Develop Self Efficacy and Critical Thinking Skills

    Science.gov (United States)

    Pradina, Luthfia Puspa; Suyatna, Agus

    2018-01-01

    The purpose of this research is to develop interactive atomic electronic school book (IESB) to cultivate critical thinking skills and confidence of students grade 12. The method used in this research was the ADDIE (Analyze Design Development Implementation Evaluation) development procedure which is limited to the test phase of product design…

  18. 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

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

    Energy Technology Data Exchange (ETDEWEB)

    Li, Jun; Jiang, Bin; Guo, Hua, E-mail: hguo@unm.edu [Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131 (United States)

    2013-11-28

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

  20. Dynamic Interactions for Network Visualization and Simulation

    Science.gov (United States)

    2009-03-01

    projects.htm, Site accessed January 5, 2009. 12. John S. Weir, Major, USAF, Mediated User-Simulator Interactive Command with Visualization ( MUSIC -V). Master’s...Computing Sciences in Colleges, December 2005). 14. Enrique Campos -Nanez, “nscript user manual,” Department of System Engineer- ing University of

  1. Protein interaction networks by proteome peptide scanning.

    Directory of Open Access Journals (Sweden)

    Christiane Landgraf

    2004-01-01

    Full Text Available A substantial proportion of protein interactions relies on small domains binding to short peptides in the partner proteins. Many of these interactions are relatively low affinity and transient, and they impact on signal transduction. However, neither the number of potential interactions mediated by each domain nor the degree of promiscuity at a whole proteome level has been investigated. We have used a combination of phage display and SPOT synthesis to discover all the peptides in the yeast proteome that have the potential to bind to eight SH3 domains. We first identified the peptides that match a relaxed consensus, as deduced from peptides selected by phage display experiments. Next, we synthesized all the matching peptides at high density on a cellulose membrane, and we probed them directly with the SH3 domains. The domains that we have studied were grouped by this approach into five classes with partially overlapping specificity. Within the classes, however, the domains display a high promiscuity and bind to a large number of common targets with comparable affinity. We estimate that the yeast proteome contains as few as six peptides that bind to the Abp1 SH3 domain with a dissociation constant lower than 100 microM, while it contains as many as 50-80 peptides with corresponding affinity for the SH3 domain of Yfr024c. All the targets of the Abp1 SH3 domain, identified by this approach, bind to the native protein in vivo, as shown by coimmunoprecipitation experiments. Finally, we demonstrate that this strategy can be extended to the analysis of the entire human proteome. We have developed an approach, named WISE (whole interactome scanning experiment, that permits rapid and reliable identification of the partners of any peptide recognition module by peptide scanning of a proteome. Since the SPOT synthesis approach is semiquantitative and provides an approximation of the dissociation constants of the several thousands of interactions that are

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

    International Nuclear Information System (INIS)

    Humbert, D.; Braams, B.J.

    2010-01-01

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

  3. Detecting Friendship Within Dynamic Online Interaction Networks

    OpenAIRE

    Merritt, Sears; Jacobs, Abigail Z.; Mason, Winter; Clauset, Aaron

    2013-01-01

    In many complex social systems, the timing and frequency of interactions between individuals are observable but friendship ties are hidden. Recovering these hidden ties, particularly for casual users who are relatively less active, would enable a wide variety of friendship-aware applications in domains where labeled data are often unavailable, including online advertising and national security. Here, we investigate the accuracy of multiple statistical features, based either purely on temporal...

  4. 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

  5. Interacting epidemics and coinfection on contact networks.

    Science.gov (United States)

    Newman, M E J; Ferrario, Carrie R

    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.

  6. 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.

  7. Concerning the theory of radiation cascades of atomic collisions in a solid with an arbitrary interatomic interaction potential

    International Nuclear Information System (INIS)

    Ryazanov, A.I.; Metelkin, E.V.

    1980-01-01

    Cascades of atomic collisions created by high energy particles as a result of irradiation of solids by them are considered. The solution of the problem is based on the investigation of the Boltzmann stationary kinetic equation for moving atoms. For this equation a model scattering indicatrix is constructed with an arbitrary form of the potential of interaction of moving atoms with lattice atoms. The choice of the model scattering indicatrix of atoms is determined by the normalization, the average energy loss in a single collision and by the deviation of the energy losses really occurring in the collision from the mean value, as well as by the initial kinetic equation for moving atoms. The energy distribution of moving atoms for arbitrary interatomic interaction potentials has been obtained using the constructed model scattering indicatrix. On the basis of the theory constructed a cascade is calculated with an interatomic interaction potential in the form of the Thomas-Fermi potential and the power potential. (author)

  8. Models of the Dynamics of Spatially Separated Broadband Electromagnetic Fields Interacting with Resonant Atoms

    Science.gov (United States)

    Basharov, A. M.

    2018-03-01

    The Markov model of spontaneous emission of an atom localized in a spatial region with a broadband electromagnetic field with zero photon density is considered in the conditions of coupling of the electromagnetic field with the broadband field of a neighboring space. The evolution operator of the system and the kinetic equation for the atom are obtained. It is shown that the field coupling constant affects the rate of spontaneous emission of the atom, but is not manifested in the atomic frequency shift. The analytic expression for the radiative decay constant for the atom is found to be analogous in a certain sense to the expression for the decay constant for a singly excited localized ensemble of identical atoms in the conditions when the effect of stabilization of its excited state by the Stark interaction with the vacuum broadband electromagnetic field is manifested. The model is formulated based on quantum stochastic differential equations of the non- Wiener type and the generalized algebra of the Ito differential of quantum random processes.

  9. Speech networks at rest and in action: interactions between functional brain networks controlling speech production

    Science.gov (United States)

    Fuertinger, Stefan

    2015-01-01

    Speech production is one of the most complex human behaviors. Although brain activation during speaking has been well investigated, our understanding of interactions between the brain regions and neural networks remains scarce. We combined seed-based interregional correlation analysis with graph theoretical analysis of functional MRI data during the resting state and sentence production in healthy subjects to investigate the interface and topology of functional networks originating from the key brain regions controlling speech, i.e., the laryngeal/orofacial motor cortex, inferior frontal and superior temporal gyri, supplementary motor area, cingulate cortex, putamen, and thalamus. During both resting and speaking, the interactions between these networks were bilaterally distributed and centered on the sensorimotor brain regions. However, speech production preferentially recruited the inferior parietal lobule (IPL) and cerebellum into the large-scale network, suggesting the importance of these regions in facilitation of the transition from the resting state to speaking. Furthermore, the cerebellum (lobule VI) was the most prominent region showing functional influences on speech-network integration and segregation. Although networks were bilaterally distributed, interregional connectivity during speaking was stronger in the left vs. right hemisphere, which may have underlined a more homogeneous overlap between the examined networks in the left hemisphere. Among these, the laryngeal motor cortex (LMC) established a core network that fully overlapped with all other speech-related networks, determining the extent of network interactions. Our data demonstrate complex interactions of large-scale brain networks controlling speech production and point to the critical role of the LMC, IPL, and cerebellum in the formation of speech production network. PMID:25673742

  10. Speech networks at rest and in action: interactions between functional brain networks controlling speech production.

    Science.gov (United States)

    Simonyan, Kristina; Fuertinger, Stefan

    2015-04-01

    Speech production is one of the most complex human behaviors. Although brain activation during speaking has been well investigated, our understanding of interactions between the brain regions and neural networks remains scarce. We combined seed-based interregional correlation analysis with graph theoretical analysis of functional MRI data during the resting state and sentence production in healthy subjects to investigate the interface and topology of functional networks originating from the key brain regions controlling speech, i.e., the laryngeal/orofacial motor cortex, inferior frontal and superior temporal gyri, supplementary motor area, cingulate cortex, putamen, and thalamus. During both resting and speaking, the interactions between these networks were bilaterally distributed and centered on the sensorimotor brain regions. However, speech production preferentially recruited the inferior parietal lobule (IPL) and cerebellum into the large-scale network, suggesting the importance of these regions in facilitation of the transition from the resting state to speaking. Furthermore, the cerebellum (lobule VI) was the most prominent region showing functional influences on speech-network integration and segregation. Although networks were bilaterally distributed, interregional connectivity during speaking was stronger in the left vs. right hemisphere, which may have underlined a more homogeneous overlap between the examined networks in the left hemisphere. Among these, the laryngeal motor cortex (LMC) established a core network that fully overlapped with all other speech-related networks, determining the extent of network interactions. Our data demonstrate complex interactions of large-scale brain networks controlling speech production and point to the critical role of the LMC, IPL, and cerebellum in the formation of speech production network. Copyright © 2015 the American Physiological Society.

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

    International Nuclear Information System (INIS)

    Siebert, Xavier; Navaza, Jorge

    2009-01-01

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

  12. Tunable-Range, Photon-Mediated Atomic Interactions in Multimode Cavity QED

    Directory of Open Access Journals (Sweden)

    Varun D. Vaidya

    2018-01-01

    Full Text Available Optical cavity QED provides a platform with which to explore quantum many-body physics in driven-dissipative systems. Single-mode cavities provide strong, infinite-range photon-mediated interactions among intracavity atoms. However, these global all-to-all couplings are limiting from the perspective of exploring quantum many-body physics beyond the mean-field approximation. The present work demonstrates that local couplings can be created using multimode cavity QED. This is established through measurements of the threshold of a superradiant, self-organization phase transition versus atomic position. Specifically, we experimentally show that the interference of near-degenerate cavity modes leads to both a strong and tunable-range interaction between Bose-Einstein condensates (BECs trapped within the cavity. We exploit the symmetry of a confocal cavity to measure the interaction between real BECs and their virtual images without unwanted contributions arising from the merger of real BECs. Atom-atom coupling may be tuned from short range to long range. This capability paves the way toward future explorations of exotic, strongly correlated systems such as quantum liquid crystals and driven-dissipative spin glasses.

  13. Atomic wavefunctions probed through strong-field light-matter interaction

    Energy Technology Data Exchange (ETDEWEB)

    Mairesse, Y; Villeneuve, D M; Corkum, P B; Dudovich, N [Natl Res Council Canada, Ottawa, ON K1A 0R6 (Canada); Shafir, D; Dudovich, N [Weizmann Inst Sci, Dept Phys Complex Syst, IL-76100 Rehovot, (Israel); Mairesse, Y [Univ Bordeaux 1, CELIA, CNRS, UMR 5107, CEA, F-33405 Talence (France)

    2009-07-01

    Strong-field light-matter interactions can encode the spatial properties of the electronic wavefunctions that contribute to the process. In particular, the broadband harmonic spectra, measured for a series of molecular alignments, can be used to create a tomographic reconstruction of molecular orbitals. Here, we present an extension of the tomography approach to systems that cannot be naturally aligned. We demonstrate this ability by probing the two-dimensional properties of atomic wavefunctions. By manipulating an electron-ion re-collision process, we are able to resolve the symmetry of the atomic wavefunction with high contrast. (authors)

  14. 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)

  15. Engaging the Terminal: Promoting Halogen Bonding Interactions with Uranyl Oxo Atoms.

    Science.gov (United States)

    Carter, Korey P; Kalaj, Mark; Surbella, Robert G; Ducati, Lucas C; Autschbach, Jochen; Cahill, Christopher L

    2017-11-02

    Engaging the nominally terminal oxo atoms of the linear uranyl (UO 2 2+ ) cation in non-covalent interactions represents both a significant challenge and opportunity within the field of actinide hybrid materials. An approach has been developed for promoting oxo atom participation in a range of non-covalent interactions, through judicious choice of electron donating equatorial ligands and appropriately polarizable halogen-donor atoms. As such, a family of uranyl hybrid materials was generated based on a combination of 2,5-dihalobenzoic acid and aromatic, chelating N-donor ligands. Delineation of criteria for oxo participation in halogen bonding interactions has been achieved by preparing materials containing 2,5-dichloro- (25diClBA) and 2,5-dibromobenzoic acid (25diBrBA) coupled with 2,2'-bipyridine (bipy) (1 and 2), 1,10-phenanthroline (phen) (3-5), 2,2':6',2''-terpyridine (terpy) (6-8), or 4'-chloro-2,2':6',2''-terpyridine (Cl-terpy) (9-10), which have been characterized through single crystal X-ray diffraction, Raman, Infrared (IR), and luminescence spectroscopy, as well as through density functional calculations of electrostatic potentials. Looking comprehensively, these results are compared with recently published analogues featuring 2,5-diiodobenzoic acid which indicate that although inclusion of a capping ligand in the uranyl first coordination sphere is important, it is the polarizability of the selected halogen atom that ultimately drives halogen bonding interactions with the uranyl oxo atoms. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Integrated multimedia information system on interactive CATV network

    Science.gov (United States)

    Lee, Meng-Huang; Chang, Shin-Hung

    1998-10-01

    In the current CATV system architectures, they provide one- way delivery of a common menu of entertainment to all the homes through the cable network. Through the technologies evolution, the interactive services (or two-way services) can be provided in the cable TV systems. They can supply customers with individualized programming and support real- time two-way communications. With a view to the service type changed from the one-way delivery systems to the two-way interactive systems, `on demand services' is a distinct feature of multimedia systems. In this paper, we present our work of building up an integrated multimedia system on interactive CATV network in Shih Chien University. Besides providing the traditional analog TV programming from the cable operator, we filter some channels to reserve them as our campus information channels. In addition to the analog broadcasting channel, the system also provides the interactive digital multimedia services, e.g. Video-On- Demand (VOD), Virtual Reality, BBS, World-Wide-Web, and Internet Radio Station. These two kinds of services are integrated in a CATV network by the separation of frequency allocation for the analog broadcasting service and the digital interactive services. Our ongoing work is to port our previous work of building up a VOD system conformed to DAVIC standard (for inter-operability concern) on Ethernet network into the current system.

  17. 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

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

    International Nuclear Information System (INIS)

    O'Kane, T.J.; Scholten, R.E.; Walkiewicz, M.R.; Farrell, P.M.

    1998-01-01

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

  19. Entanglement for a Bimodal Cavity Field Interacting with a Two-Level Atom

    International Nuclear Information System (INIS)

    Liu Jia; Chen Ziyu; Bu Shenping; Zhang Guofeng

    2009-01-01

    Negativity has been adopted to investigate the entanglement in a system composed of a two-level atom and a two-mode cavity field. Effects of Kerr-like medium and the number of photon inside the cavity on the entanglement are studied. Our results show that atomic initial state must be superposed, so that the two cavity field modes can be entangled. Moreover, we also conclude that the number of photon in the two cavity mode should be equal. The interaction between modes, namely, the Kerr effect, has a significant negative contribution. Note that the atom frequency and the cavity frequency have an indistinguishable effect, so a corresponding approximation has been made in this article. These results may be useful for quantum information in optics systems.

  20. Transport and interaction blockade of cold bosonic atoms in a triple-well potential

    International Nuclear Information System (INIS)

    Schlagheck, P; Malet, F; Cremon, J C; Reimann, S M

    2010-01-01

    We theoretically investigate the transport properties of cold bosonic atoms in a quasi-one-dimensional (1D) triple-well potential that consists of two large outer wells, which act as microscopic source and drain reservoirs, and a small inner well, which represents a quantum-dot-like scattering region. Bias and gate 'voltages' introduce a time-dependent tilt of the triple-well configuration, and are used to shift the energetic level of the inner well with respect to the outer ones. By means of exact diagonalization considering a total number of six atoms in the triple-well potential, we find diamond-like structures for the occurrence of single-atom transport in the parameter space spanned by the bias and gate voltages. We discuss the analogy with Coulomb blockade in electronic quantum dots, and point out how one can infer the interaction energy in the central well from the distance between the diamonds.

  1. Interaction-induced decay of a heteronuclear two-atom system

    Science.gov (United States)

    Xu, Peng; Yang, Jiaheng; Liu, Min; He, Xiaodong; Zeng, Yong; Wang, Kunpeng; Wang, Jin; Papoular, D. J.; Shlyapnikov, G. V.; Zhan, Mingsheng

    2015-01-01

    Two-atom systems in small traps are of fundamental interest for understanding the role of interactions in degenerate cold gases and for the creation of quantum gates in quantum information processing with single-atom traps. One of the key quantities is the inelastic relaxation (decay) time when one of the atoms or both are in a higher hyperfine state. Here we measure this quantity in a heteronuclear system of 87Rb and 85Rb in a micro optical trap and demonstrate experimentally and theoretically the presence of both fast and slow relaxation processes, depending on the choice of the initial hyperfine states. This experimental method allows us to single out a particular relaxation process thus provides an extremely clean platform for collisional physics studies. Our results have also implications for engineering of quantum states via controlled collisions and creation of two-qubit quantum gates. PMID:26199051

  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. Elastic interaction of hydrogen atoms on graphene: A multiscale approach from first principles to continuum elasticity

    Science.gov (United States)

    Branicio, Paulo S.; Vastola, Guglielmo; Jhon, Mark H.; Sullivan, Michael B.; Shenoy, Vivek B.; Srolovitz, David J.

    2016-10-01

    The deformation of graphene due to the chemisorption of hydrogen atoms on its surface and the long-range elastic interaction between hydrogen atoms induced by these deformations are investigated using a multiscale approach based on first principles, empirical interactions, and continuum modeling. Focus is given to the intrinsic low-temperature structure and interactions. Therefore, all calculations are performed at T =0 , neglecting possible temperature or thermal fluctuation effects. Results from different methods agree well and consistently describe the local deformation of graphene on multiple length scales reaching 500 Å . The results indicate that the elastic interaction mediated by this deformation is significant and depends on the deformation of the graphene sheet both in and out of plane. Surprisingly, despite the isotropic elasticity of graphene, within the linear elastic regime, atoms elastically attract or repel each other depending on (i) the specific site they are chemisorbed; (ii) the relative position of the sites; (iii) and if they are on the same or on opposite surface sides. The interaction energy sign and power-law decay calculated from molecular statics agree well with theoretical predictions from linear elasticity theory, considering in-plane or out-of-plane deformations as a superposition or in a coupled nonlinear approach. Deviations on the exact power law between molecular statics and the linear elastic analysis are evidence of the importance of nonlinear effects on the elasticity of monolayer graphene. These results have implications for the understanding of the generation of clusters and regular formations of hydrogen and other chemisorbed atoms on graphene.

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

    OpenAIRE

    Starnini, Michele; Baronchelli, Andrea; 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 ...

  5. Molecular dynamics study of the interactions of incident N or Ti atoms with the TiN(001) surface

    International Nuclear Information System (INIS)

    Xu, Zhenhai; Zeng, Quanren; Yuan, Lin; Qin, Yi; Chen, Mingjun; Shan, Debin

    2016-01-01

    Graphical abstract: - Highlights: • Interactions of incident N or Ti atoms with TiN(001) surface are studied by CMD. • The impact position of incident N on the surface determines the interaction modes. • Adsorption could occur due to the atomic exchange process. • Resputtering and reflection may simultaneously occur. • The initial sticking coefficient of N on TiN(001) is much smaller than that of Ti. - Abstract: The interaction processes between incident N or Ti atoms and the TiN(001) surface are simulated by classical molecular dynamics based on the second nearest-neighbor modified embedded-atom method potentials. The simulations are carried out for substrate temperatures between 300 and 700 K and kinetic energies of the incident atoms within the range of 0.5–10 eV. When N atoms impact against the surface, adsorption, resputtering and reflection of particles are observed; several unique atomic mechanisms are identified to account for these interactions, in which the adsorption could occur due to the atomic exchange process while the resputtering and reflection may simultaneously occur. The impact position of incident N atoms on the surface plays an important role in determining the interaction modes. Their occurrence probabilities are dependent on the kinetic energy of incident N atoms but independent on the substrate temperature. When Ti atoms are the incident particles, adsorption is the predominant interaction mode between particles and the surface. This results in the much smaller initial sticking coefficient of N atoms on the TiN(001) surface compared with that of Ti atoms. Stoichiometric TiN is promoted by N/Ti flux ratios larger than one.

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

    Science.gov (United States)

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

    2011-09-01

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

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

    Science.gov (United States)

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

    2011-09-01

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

  8. Model analysis of molecular conformations in terms of weak interactions between non bonded atoms

    International Nuclear Information System (INIS)

    Lombardi, E.

    1988-01-01

    The aim of the present paper is to establish a reliable basis for the evaluation of stable conformations and rotational barriers for molecules, with possible applications to systems of biological interest. It is proceeded in two steps: first, the effect of chemical environment on orbitals of a given atom is studied for diatomic units, adopting a valence-bond approach and considering, as prototypes, the two simplest series of diatomic molecules with one valence electron each, i.e. the alkali diatomics and the alkali hydrides. In the model, the orbital of the hydrogen atom by a simple (''1S'') gaussian function, the valence orbital of an alkali atom by a function (r 2 -a 2 ) times a simple gaussian (''2S'' gaussian). Dissociation energies D e and equilibrium distances R e are calculated using a scanning procedure. Agreement with experiment is quantitative for the alkali diatomics. For alkali hydrides, good agreement is obtained only if validity of a rule β e R e =constant, for the two atoms separately, is postulated; β e is the characteristic parameter of a ''1S'' gaussian (hydrogen) or a ''2S'' gaussian (alkali atom) function. In a second step, the authors assume validity of the same rule in conformational analysis for any single bonded A-B molecule with A=C, O, N, P, Si, Ge and B=H, or a halogen atom. Gauge β e values for H, F and C are obtained by fitting experimental rotational barriers in C 2 H 6 , C 2 F 6 and C 3 H 8 . Stable conformation of, and barriers to rotation in, ethane-like rotors are determined, applying first-order exchange perturbation theory, in terms of two- and many-center exchange interactions in cluster of non-bonded atoms. Some 60 molecules are analyzed. Agreement with experiments is strikngly good except for a few systematic deviation. Reasons for such discrepancies are discussed

  9. Prediction of Protein-Protein Interactions Related to Protein Complexes Based on Protein Interaction Networks

    Directory of Open Access Journals (Sweden)

    Peng Liu

    2015-01-01

    Full Text Available A method for predicting protein-protein interactions based on detected protein complexes is proposed to repair deficient interactions derived from high-throughput biological experiments. Protein complexes are pruned and decomposed into small parts based on the adaptive k-cores method to predict protein-protein interactions associated with the complexes. The proposed method is adaptive to protein complexes with different structure, number, and size of nodes in a protein-protein interaction network. Based on different complex sets detected by various algorithms, we can obtain different prediction sets of protein-protein interactions. The reliability of the predicted interaction sets is proved by using estimations with statistical tests and direct confirmation of the biological data. In comparison with the approaches which predict the interactions based on the cliques, the overlap of the predictions is small. Similarly, the overlaps among the predicted sets of interactions derived from various complex sets are also small. Thus, every predicted set of interactions may complement and improve the quality of the original network data. Meanwhile, the predictions from the proposed method replenish protein-protein interactions associated with protein complexes using only the network topology.

  10. Entanglement Criteria of Two Two-Level Atoms Interacting with Two Coupled Modes

    Science.gov (United States)

    Baghshahi, Hamid Reza; Tavassoly, Mohammad Kazem; Faghihi, Mohammad Javad

    2015-08-01

    In this paper, we study the interaction between two two-level atoms and two coupled modes of a quantized radiation field in the form of parametric frequency converter injecting within an optical cavity enclosed by a medium with Kerr nonlinearity. It is demonstrated that, by applying the Bogoliubov-Valatin canonical transformation, the introduced model is reduced to a well-known form of the generalized Jaynes-Cummings model. Then, under particular initial conditions for the atoms (in a coherent superposition of its ground and upper states) and the fields (in a standard coherent state) which may be prepared, the time evolution of state vector of the entire system is analytically evaluated. In order to understand the degree of entanglement between subsystems (atom-field and atom-atom), the dynamics of entanglement through different measures, namely, von Neumann reduced entropy, concurrence and negativity is evaluated. In each case, the effects of Kerr nonlinearity and detuning parameter on the above measures are numerically analyzed, in detail. It is illustrated that the amount of entanglement can be tuned by choosing the evolved parameters, appropriately.

  11. Generalized atomic processes for interaction of intense femtosecond XUV- and X-ray radiation with solids

    International Nuclear Information System (INIS)

    Deschaud, B.; Peyrusse, O.; Rosmej, F.B.

    2014-01-01

    Generalized atomic processes are proposed to establish a consistent description from the free-atom approach to the heated and even up to the cold solid. It is based on a rigorous introduction of the Fermi-Dirac statistics, Pauli blocking factors and on the respect of the principle of detailed balance via the introduction of direct and inverse processes. A probability formalism driven by the degeneracy of the free electrons enables to establish a link of atomic rates valid from the heated atom up to the cold solid. This allows to describe photoionization processes in atomic population kinetics and subsequent solid matter heating on a femtosecond time scale. The Auger effect is linked to the 3-body recombination via a generalized 3-body recombination that is identified as a key mechanism, along with the collisional ionization, that follows energy deposition by photoionization of inner shells when short, intense and high-energy radiation interacts with matter. Detailed simulations are carried out for aluminum that highlight the importance of the generalized approach. (authors)

  12. Resonant atom-field interaction in large-size coupled-cavity arrays

    International Nuclear Information System (INIS)

    Ciccarello, Francesco

    2011-01-01

    We consider an array of coupled cavities with staggered intercavity couplings, where each cavity mode interacts with an atom. In contrast to large-size arrays with uniform hopping rates where the atomic dynamics is known to be frozen in the strong-hopping regime, we show that resonant atom-field dynamics with significant energy exchange can occur in the case of staggered hopping rates even in the thermodynamic limit. This effect arises from the joint emergence of an energy gap in the free photonic dispersion relation and a discrete frequency at the gap's center. The latter corresponds to a bound normal mode stemming solely from the finiteness of the array length. Depending on which cavity is excited, either the atomic dynamics is frozen or a Jaynes-Cummings-like energy exchange is triggered between the bound photonic mode and its atomic analog. As these phenomena are effective with any number of cavities, they are prone to be experimentally observed even in small-size arrays.

  13. Electronic spectral properties of surfaces and adsorbates and atom-adsorbate van der Waals interactions

    International Nuclear Information System (INIS)

    Lovric, D.; Gumhalter, B.

    1988-01-01

    The relevance of van der Waals interactions in the scattering of neutral atoms from adsorbates has been recently confirmed by highly sensitive molecular-beam techniques. The theoretical descriptions of the collision dynamics which followed the experimental studies have necessitated very careful qualitative and quantitative examinations and evaluations of the properties of atom-adsorbate van der Waals interactions for specific systems. In this work we present a microscopic calculation of the strengths and reference-plane positions for van der Waals potentials relevant for scattering of He atoms from CO adsorbed on various metallic substrates. In order to take into account the specificities of the polarization properties of real metals (noble and transition metals) and of chemisorbed CO, we first calculate the spectra of the electronic excitations characteristic of the respective electronic subsystems by using various data sources available and combine them with the existing theoretical models. The reliability of the calculated spectra is then verified in each particular case by universal sum rules which may be established for the electronic excitations of surfaces and adsorbates. The substrate and adsorbate polarization properties which derive from these calculations serve as input data for the evaluation of the strengths and reference-plane positions of van der Waals potentials whose computed values are tabulated for a number of real chemisorption systems. The implications of the obtained results are discussed in regard to the atom-adsorbate scattering cross sections pertinent to molecular-beam scattering experiments

  14. 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).

  15. Spatial Multiplexing of Atom-Photon Entanglement Sources using Feedforward Control and Switching Networks.

    Science.gov (United States)

    Tian, Long; Xu, Zhongxiao; Chen, Lirong; Ge, Wei; Yuan, Haoxiang; Wen, Yafei; Wang, Shengzhi; Li, Shujing; Wang, Hai

    2017-09-29

    The light-matter quantum interface that can create quantum correlations or entanglement between a photon and one atomic collective excitation is a fundamental building block for a quantum repeater. The intrinsic limit is that the probability of preparing such nonclassical atom-photon correlations has to be kept low in order to suppress multiexcitation. To enhance this probability without introducing multiexcitation errors, a promising scheme is to apply multimode memories to the interface. Significant progress has been made in temporal, spectral, and spatial multiplexing memories, but the enhanced probability for generating the entangled atom-photon pair has not been experimentally realized. Here, by using six spin-wave-photon entanglement sources, a switching network, and feedforward control, we build a multiplexed light-matter interface and then demonstrate a ∼sixfold (∼fourfold) probability increase in generating entangled atom-photon (photon-photon) pairs. The measured compositive Bell parameter for the multiplexed interface is 2.49±0.03 combined with a memory lifetime of up to ∼51  μs.

  16. Drug-domain interaction networks in myocardial infarction.

    Science.gov (United States)

    Wang, Haiying; Zheng, Huiru; Azuaje, Francisco; Zhao, Xing-Ming

    2013-09-01

    It has been well recognized that the pace of the development of new drugs and therapeutic interventions lags far behind biological knowledge discovery. Network-based approaches have emerged as a promising alternative to accelerate the discovery of new safe and effective drugs. Based on the integration of several biological resources including two recently published datasets i.e., Drug-target interactions in myocardial infarction (My-DTome) and drug-domain interaction network, this paper reports the association between drugs and protein domains in the context of myocardial infarction (MI). A MI drug-domain interaction network, My-DDome, was firstly constructed, followed by topological analysis and functional characterization of the network. The results show that My-DDome has a very clear modular structure, where drugs interacting with the same domain(s) within each module tend to have similar therapeutic effects. Moreover it has been found that drugs acting on blood and blood forming organs (ATC code B) and sensory organs (ATC code S) are significantly enriched in My-DDome (p drugs, their known targets, and seemingly unrelated proteins can be revealed.

  17. Robust collaborative process interactions under system crash and network failures

    NARCIS (Netherlands)

    Wang, Lei; Wombacher, Andreas; Ferreira Pires, Luis; van Sinderen, Marten J.; Chi, Chihung

    2013-01-01

    With the possibility of system crashes and network failures, the design of robust client/server interactions for collaborative process execution is a challenge. If a business process changes its state, it sends messages to the relevant processes to inform about this change. However, server crashes

  18. Characterizing interactions in online social networks during exceptional events

    Science.gov (United States)

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

    2015-08-01

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

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

    International Nuclear Information System (INIS)

    Lugo, J.O.; Vergara, L.I.; Bolcatto, P.G.; Goldberg, E.C.

    2002-01-01

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

  20. Translational-rotational interaction in dynamics and thermodynamics of 2D atomic crystal with molecular impurity

    International Nuclear Information System (INIS)

    Antsygina, T.N.; Poltavskaya, M.I.; Chishko, K.A.

    2003-01-01

    The interaction between the rotational degrees of freedom of a diatomic molecular impurity and the phonon excitations of a two-dimensional atomic matrix commensurate with a substrate is investigated theoretically. It is shown, that the translational-rotational interaction changes the form of the rotational kinetic energy operator as compared to the corresponding expression for a free rotator, and also renormalized the parameters of the crystal field without change in its initial form. The contribution of the impurity rotational degrees of freedom to the low-temperature heat capacity for a dilute solution of diatomic molecules in an atomic two-dimensional matrix is calculated. The possibility of experimental observation of the effects obtained is discussed

  1. Nanostructure van der Waals interaction between a quantum well and a quantum dot atom

    International Nuclear Information System (INIS)

    Horing, Norman J Morgenstern

    2006-01-01

    We examine the van der Waals interaction between mobile plasma electrons in a narrow quantum well nanostructure and a quantum dot atom. This formulation of the van der Waals interaction exhibits it to second order as the correlation energy (self-energy) of the dot-atom electrons mediated by the image potential arising from the dynamic, nonlocal and spatially inhomogeneous polarization of the quantum well plasma electrons. This image potential of the quantum-well plasma is, in turn, determined by the dynamic, nonlocal, inhomogeneous screening function of the quantum well, which involves the space-time matrix inversion of its spatially inhomogeneous, nonlocal and time-dependent dielectric function. The latter matrix inversion is carried out exactly, in closed form, and the van der Waals energy is evaluated in the electrostatic limit to dipole-dipole terms

  2. Quadripartite cluster and Greenberger–Horne–Zeilinger entangled light via cascade interactions with separated atomic ensembles

    International Nuclear Information System (INIS)

    Li Xing; Hu Xiangming

    2012-01-01

    It has been known that two-mode entangled light can possibly be generated by employing near-resonant interaction with an ensemble of two-level atoms. The responsible mechanism is the absorption of two photons from the strong driving field and the emission of two new photons into the cavity field. Here, we generalize such a mechanism to three separated atomic ensembles and establish cascade interactions for four nondegenerate fields. It is shown that the quadripartite cluster and Greenberger–Horne–Zeilinger entangled states occur for continuous variables. The advantage of the present scheme for the multipartite entanglement lies in that the coupling strengths are much larger due to the near resonances than for far-off-resonance-based parametric processes. (paper)

  3. Bayesian network model for identification of pathways by integrating protein interaction with genetic interaction data.

    Science.gov (United States)

    Fu, Changhe; Deng, Su; Jin, Guangxu; Wang, Xinxin; Yu, Zu-Guo

    2017-09-21

    Molecular interaction data at proteomic and genetic levels provide physical and functional insights into a molecular biosystem and are helpful for the construction of pathway structures complementarily. Despite advances in inferring biological pathways using genetic interaction data, there still exists weakness in developed models, such as, activity pathway networks (APN), when integrating the data from proteomic and genetic levels. It is necessary to develop new methods to infer pathway structure by both of interaction data. We utilized probabilistic graphical model to develop a new method that integrates genetic interaction and protein interaction data and infers exquisitely detailed pathway structure. We modeled the pathway network as Bayesian network and applied this model to infer pathways for the coherent subsets of the global genetic interaction profiles, and the available data set of endoplasmic reticulum genes. The protein interaction data were derived from the BioGRID database. Our method can accurately reconstruct known cellular pathway structures, including SWR complex, ER-Associated Degradation (ERAD) pathway, N-Glycan biosynthesis pathway, Elongator complex, Retromer complex, and Urmylation pathway. By comparing N-Glycan biosynthesis pathway and Urmylation pathway identified from our approach with that from APN, we found that our method is able to overcome its weakness (certain edges are inexplicable). According to underlying protein interaction network, we defined a simple scoring function that only adopts genetic interaction information to avoid the balance difficulty in the APN. Using the effective stochastic simulation algorithm, the performance of our proposed method is significantly high. We developed a new method based on Bayesian network to infer detailed pathway structures from interaction data at proteomic and genetic levels. The results indicate that the developed method performs better in predicting signaling pathways than previously

  4. Translational Entanglement of Dipole-Dipole Interacting Atoms in Optical Lattices

    OpenAIRE

    Opatrny, T.; Deb, B.; Kurizki, G.

    2003-01-01

    We propose and investigate a realization of the position- and momentum-correlated Einstein-Podolsky-Rosen (EPR) states [Phys. Rev. 47, 777 (1935)] that have hitherto eluded detection. The realization involves atom pairs that are confined to adjacent sites of two mutually shifted optical lattices and are entangled via laser-induced dipole-dipole interactions. The EPR "paradox" with translational variables is then modified by lattice-diffraction effects, and can be verified to a high degree of ...

  5. 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.

  6. Three-dimensional theory for interaction between atomic ensembles and free-space light

    International Nuclear Information System (INIS)

    Duan, L.-M.; Cirac, J.I.; Zoller, P.

    2002-01-01

    Atomic ensembles have shown to be a promising candidate for implementations of quantum information processing by many recently discovered schemes. All these schemes are based on the interaction between optical beams and atomic ensembles. For description of these interactions, one assumed either a cavity-QED model or a one-dimensional light propagation model, which is still inadequate for a full prediction and understanding of most of the current experimental efforts that are actually taken in the three-dimensional free space. Here, we propose a perturbative theory to describe the three-dimensional effects in interaction between atomic ensembles and free-space light with a level configuration important for several applications. The calculations reveal some significant effects that were not known before from the other approaches, such as the inherent mode-mismatching noise and the optimal mode-matching conditions. The three-dimensional theory confirms the collective enhancement of the signal-to-noise ratio which is believed to be one of the main advantages of the ensemble-based quantum information processing schemes, however, it also shows that this enhancement needs to be understood in a more subtle way with an appropriate mode-matching method

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

    Directory of Open Access Journals (Sweden)

    Xia Jiang

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

  8. 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.

  9. Exact tensor network ansatz for strongly interacting systems

    Science.gov (United States)

    Zaletel, Michael P.

    It appears that the tensor network ansatz, while not quite complete, is an efficient coordinate system for the tiny subset of a many-body Hilbert space which can be realized as a low energy state of a local Hamiltonian. However, we don't fully understand precisely which phases are captured by the tensor network ansatz, how to compute their physical observables (even numerically), or how to compute a tensor network representation for a ground state given a microscopic Hamiltonian. These questions are algorithmic in nature, but their resolution is intimately related to understanding the nature of quantum entanglement in many-body systems. For this reason it is useful to compute the tensor network representation of various `model' wavefunctions representative of different phases of matter; this allows us to understand how the entanglement properties of each phase are expressed in the tensor network ansatz, and can serve as test cases for algorithm development. Condensed matter physics has many illuminating model wavefunctions, such as Laughlin's celebrated wave function for the fractional quantum Hall effect, the Bardeen-Cooper-Schrieffer wave function for superconductivity, and Anderson's resonating valence bond ansatz for spin liquids. This thesis presents some results on exact tensor network representations of these model wavefunctions. In addition, a tensor network representation is given for the time evolution operator of a long-range one-dimensional Hamiltonian, which allows one to numerically simulate the time evolution of power-law interacting spin chains as well as two-dimensional strips and cylinders.

  10. 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.

  11. The Population Inversion and the Entropy of a Moving Two-Level Atom in Interaction with a Quantized Field

    Science.gov (United States)

    Abo-Kahla, D. A. M.; Abdel-Aty, M.; Farouk, A.

    2018-05-01

    An atom with only two energy eigenvalues is described by a two-dimensional state space spanned by the two energy eigenstates is called a two-level atom. We consider the interaction between a two-level atom system with a constant velocity. An analytic solution of the systems which interacts with a quantized field is provided. Furthermore, the significant effect of the temperature on the atomic inversion, the purity and the information entropy are discussed in case of the initial state either an exited state or a maximally mixed state. Additionally, the effect of the half wavelengths number of the field-mode is investigated.

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

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jingyu; Qian, Yong, E-mail: qianyong86@163.com; Deng, Yonghong; Liu, Di; Li, Hao; Qiu, Xueqing, E-mail: xueqingqiu66@163.com

    2016-12-30

    Graphical abstract: The interactions between lignin and inorganic oxides are quantitatively probed by atomic force microscopy, which is fundamental but beneficial for understanding and optimizing the absorption-dispersion and catalytic degradation processes of lignin. - Highlights: • The interactions between lignin and inorganic oxides are measured using AFM. • The adhesion forces between lignin and metal oxides are larger than that in nonmetal systems. • Hydrogen bond plays an important role in lignin-inorganic oxides system. - Abstract: 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 Al{sub 2}O{sub 3} or MgO is nearly two times bigger than that between AL and nonmetal oxide such as SiO{sub 2} 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 Al{sub 2}O{sub 3}, MgO and SiO{sub 2} 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. Interaction of primary cascades with different atomic grain boundaries in α-Zr: An atomic scale study

    Energy Technology Data Exchange (ETDEWEB)

    Hatami, F.; Feghhi, S.A.H., E-mail: a.feghhi@gmail.com; Arjhangmehr, A., E-mail: ms.arjangmehr@gmail.com; Esfandiarpour, A.

    2016-11-15

    In this paper, we investigate interaction of primary cascades with grain boundaries (GBs) in α-Zr using the atomistic-scale simulations, and intend to study the influence of different GB structures on production and evolution of defects on picosecond timescale. We observe that, contrary to the previous results in cubic metals, GBs in α-Zr are not necessarily biased toward interstitials, and can preferentially absorb vacancies. Further, in terms of energetic and kinetic behavior, we find that GBs act as defect sinks due to the substantial reduction of defect formation energies and migration barriers in close vicinity of the GB center, with either a preference toward interstitials or vacancies which depends on the atomic structure of the boundaries. Finally, using continuous ion bombardment, we investigate the stability of GBs in sever irradiation environment. The results indicate that the sink strength and efficiency of boundaries varies with increasing accumulated defects in GB region. - Highlights: • GBs in hcp Zr are not necessarily biased toward interstitials. • Defect content within bulk depends on PKA energy, PKA distance, and GB texture. • Defect formation energies and diffusion barriers decrease in close vicinity of GBs. • GBs become locally unstable due to absorption of excess defects in ion bombardment.

  14. Energy landscape of all-atom protein-protein interactions revealed by multiscale enhanced sampling.

    Directory of Open Access Journals (Sweden)

    Kei Moritsugu

    2014-10-01

    Full Text Available Protein-protein interactions are regulated by a subtle balance of complicated atomic interactions and solvation at the interface. To understand such an elusive phenomenon, it is necessary to thoroughly survey the large configurational space from the stable complex structure to the dissociated states using the all-atom model in explicit solvent and to delineate the energy landscape of protein-protein interactions. In this study, we carried out a multiscale enhanced sampling (MSES simulation of the formation of a barnase-barstar complex, which is a protein complex characterized by an extraordinary tight and fast binding, to determine the energy landscape of atomistic protein-protein interactions. The MSES adopts a multicopy and multiscale scheme to enable for the enhanced sampling of the all-atom model of large proteins including explicit solvent. During the 100-ns MSES simulation of the barnase-barstar system, we observed the association-dissociation processes of the atomistic protein complex in solution several times, which contained not only the native complex structure but also fully non-native configurations. The sampled distributions suggest that a large variety of non-native states went downhill to the stable complex structure, like a fast folding on a funnel-like potential. This funnel landscape is attributed to dominant configurations in the early stage of the association process characterized by near-native orientations, which will accelerate the native inter-molecular interactions. These configurations are guided mostly by the shape complementarity between barnase and barstar, and lead to the fast formation of the final complex structure along the downhill energy landscape.

  15. 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.

  16. Myths on Bi-direction Communication of Web 2.0 Based Social Networks: Is Social Network Truly Interactive?

    Science.gov (United States)

    2011-03-10

    more and more social interactions are happening on the on-line. Especially recent uptake of the social network sites (SNSs), such as Facebook (http...Smart phones • Live updates within social networks • Facebook & Twitters Solution: WebMon for Risk Management Need for New WebMon for Social Networks ...Title: Myths on bi-direction communication of Web 2.0 based social networks : Is social network truly interactive

  17. Interaction of K(nd) Rydberg atoms with an amorphous gold surface

    International Nuclear Information System (INIS)

    Gray, D.F.

    1988-01-01

    This thesis reports the first controlled study of the interactions of Rydberg atoms with a metal surface. In these experiments, a collimated beam of potassium Rydberg atoms is directed at a plane surface at near grazing incidence. Positive ions formed by surface ionization are attracted to the surface by their image charge, which is counterbalanced by an external electric field applied perpendicular to the surface. The ions are detected by a position-sensitive detector (PSD). At some critical value of the external field, the ion trajectories just miss the surface, suggesting that analysis of the dependence of the ion signals of external electric field can be used to determine the distance from the surface at which ionization occurs. This distance, and thus the corresponding critical electric field, is expected to be n-dependent. Experimentally, however, it was observed that the ion signal had a sudden n-independent onset when only a small positive perpendicular electric field was applied at the surface. This observation requires, surprisingly, that the ions produced by surface ionization can readily escape from the surface. The data do, however, show that Rydberg atoms are efficiently ionized in collisions with the surface. This process may provide a useful new detection technique for Rydberg atoms

  18. Self-organization of social hierarchy on interaction networks

    International Nuclear Information System (INIS)

    Fujie, Ryo; Odagaki, Takashi

    2011-01-01

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

  19. Attractive interaction between Mn atoms on the GaAs(110) surface observed by scanning tunneling microscopy.

    Science.gov (United States)

    Taninaka, Atsushi; Yoshida, Shoji; Kanazawa, Ken; Hayaki, Eiko; Takeuchi, Osamu; Shigekawa, Hidemi

    2016-06-16

    Scanning tunneling microscopy/spectroscopy (STM/STS) was carried out to investigate the structures of Mn atoms deposited on a GaAs(110) surface at room temperature to directly observe the characteristics of interactions between Mn atoms in GaAs. Mn atoms were paired with a probability higher than the random distribution, indicating an attractive interaction between them. In fact, re-pairing of unpaired Mn atoms was observed during STS measurement. The pair initially had a new structure, which was transformed during STS measurement into one of those formed by atom manipulation at 4 K. Mn atoms in pairs and trimers were aligned in the direction, which is theoretically predicted to produce a high Curie temperature.

  20. Shape-persistent two-component 2D networks with atomic-size tunability.

    Science.gov (United States)

    Liu, Jia; Zhang, Xu; Wang, Dong; Wang, Jie-Yu; Pei, Jian; Stang, Peter J; Wan, Li-Jun

    2011-09-05

    Over the past few years, two-dimensional (2D) nanoporous networks have attracted great interest as templates for the precise localization and confinement of guest building blocks, such as functional molecules or clusters on the solid surfaces. Herein, a series of two-component molecular networks with a 3-fold symmetry are constructed on graphite using a truxenone derivative and trimesic acid homologues with carboxylic-acid-terminated alkyl chains. The hydrogen-bonding partner-recognition-induced 2D crystallization of alkyl chains makes the flexible alkyl chains act as rigid spacers in the networks to continuously tune the pore size with an accuracy of one carbon atom per step. The two-component networks were found to accommodate and regulate the distribution and aggregation of guest molecules, such as COR and CuPc. This procedure provides a new pathway for the design and fabrication of molecular nanostructures on solid surfaces. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Study of Li atom diffusion in amorphous Li3PO4 with neural network potential

    Science.gov (United States)

    Li, Wenwen; Ando, Yasunobu; Minamitani, Emi; Watanabe, Satoshi

    2017-12-01

    To clarify atomic diffusion in amorphous materials, which is important in novel information and energy devices, theoretical methods having both reliability and computational speed are eagerly anticipated. In the present study, we applied neural network (NN) potentials, a recently developed machine learning technique, to the study of atom diffusion in amorphous materials, using Li3PO4 as a benchmark material. The NN potential was used together with the nudged elastic band, kinetic Monte Carlo, and molecular dynamics methods to characterize Li vacancy diffusion behavior in the amorphous Li3PO4 model. By comparing these results with corresponding DFT calculations, we found that the average error of the NN potential is 0.048 eV in calculating energy barriers of diffusion paths, and 0.041 eV in diffusion activation energy. Moreover, the diffusion coefficients obtained from molecular dynamics are always consistent with those from ab initio molecular dynamics simulation, while the computation speed of the NN potential is 3-4 orders of magnitude faster than DFT. Lastly, the structure of amorphous Li3PO4 and the ion transport properties in it were studied with the NN potential using a large supercell model containing more than 1000 atoms. The formation of P2O7 units was observed, which is consistent with the experimental characterization. The Li diffusion activation energy was estimated to be 0.55 eV, which agrees well with the experimental measurements.

  2. Effect of finite detection efficiency on the observation of the dipole-dipole interaction of a few Rydberg atoms

    International Nuclear Information System (INIS)

    Ryabtsev, I. I.; Tretyakov, D. B.; Beterov, I. I.; Entin, V. M.

    2007-01-01

    We have developed a simple analytical model describing multiatom signals that are measured in experiments on dipole-dipole interaction at resonant collisions of a few Rydberg atoms. It has been shown that finite efficiency of the selective field-ionization detector leads to the mixing up of the spectra of resonant collisions registered for various numbers of Rydberg atoms. The formulas which help to estimate an appropriate mean Rydberg atom number for a given detection efficiency are presented. We have found that a measurement of the relation between the amplitudes of collisional resonances observed in the one- and two-atom signals provides a straightforward determination of the absolute detection efficiency and mean Rydberg atom number. We also performed a testing experiment on resonant collisions in a small excitation volume of a sodium atomic beam. The resonances observed for 1-4 detected Rydberg atoms have been analyzed and compared with theory

  3. FENDL/E. Evaluated nuclear data library of neutron nuclear interaction cross-sections and photon production cross-sections and photon-atom interaction cross sections for fusion applications. Version 1.1 of November 1994

    International Nuclear Information System (INIS)

    Pashchenko, A.B.; Wienke, H.; Ganesan, S.; McLaughlin, P.K.

    1996-01-01

    This document presents the description of a physical tape containing the basic evaluated nuclear data library of neutron nuclear interaction cross-sections and photon production cross-sections and photon-atom interaction cross-sections for fusion applications. It is part of FENDL, the evaluated nuclear data library for fusion applications. The nuclear data are available cost-free for distribution to interested scientists upon request. The data can also be retrieved by the user via online access through international computer networks. (author). 11 refs, 1 tab

  4. 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.

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

    International Nuclear Information System (INIS)

    El-Bakry, M.Y.

    2003-01-01

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

  6. Auditing Medical Records Accesses via Healthcare Interaction Networks

    Science.gov (United States)

    Chen, You; Nyemba, Steve; Malin, Bradley

    2012-01-01

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

  7. Magnetic Interaction between Surface-Engineered Rare-Earth Atomic Spins

    Directory of Open Access Journals (Sweden)

    Chiung-Yuan Lin

    2012-06-01

    Full Text Available We report the ab-initio study of rare-earth adatoms (Gd on an insulating surface. This surface is of interest because of previous studies by scanning tunneling microscopy showing spin excitations of transition-metal adatoms. The present work is the first study of rare-earth spin-coupled adatoms, as well as the geometry effect of spin coupling and the underlying mechanism of ferromagnetic coupling. The exchange coupling between Gd atoms on the surface is calculated to be antiferromagnetic in a linear geometry and ferromagnetic in a diagonal geometry. We also find that the Gd dimers in these two geometries are similar to the nearest-neighbor and the next-nearest-neighbor Gd atoms in GdN bulk. We analyze how much direct exchange, superexchange, and Ruderman-Kittel-Kasuya-Yosida interactions contribute to the exchange coupling for both geometries by additional first-principles calculations of related model systems.

  8. Simultaneous multiphoton processes in the interaction of atoms with electromagnetic fields

    International Nuclear Information System (INIS)

    Levine, A.M.; Schreiber, W.M.; Weiszmann, A.N.

    1984-01-01

    It is impossible to obtain an exact description of multiphoton processes in the interaction of electromagnetic fields with atomic systems. Approximate approaches must be used to describe the physically different effects that can occur. One effect is the stepwise absorption/emission of many photons by a N-level system that evolves dynamically in between each absorption/emission. Another effect is described in the theories of Raman processes where the simultaneous absorption/emission of many photons is considered. In this paper, consideration is given to both processes allowing interference between the stepwise and simultaneous absorptions. An approximate Hamiltonian is obtained from the quantum mechanical multipole expansion. An exact solution of an atom-field system subject to this Hamiltonian will be presented. The extension of the method to multiple electromagnetic fields is discussed

  9. On the performance of atomic natural orbital basis sets: A full configuration interaction study

    International Nuclear Information System (INIS)

    Illas, F.; Ricart, J.M.; Rubio, J.; Bagus, P.S.

    1990-01-01

    The performance of atomic natural orbital (ANO) basis sets has been studied by comparing self-consistant field (SCF) and full configuration interaction (CI) results obtained for the first row atoms and hydrides. The ANO results have been compared with those obtained using a segmented basis set containing the same number of contracted basis functions. The total energies obtained with the ANO basis sets are always lower than the one obtained by using the segmented one. However, for the hydrides, differential electronic correlation energy obtained with the ANO basis set may be smaller than the one recovered with the segmented set. We relate this poorer differential correlation energy for the ANO basis set to the fact that only one contracted d function is used for the ANO and segmented basis sets

  10. Observation of the Borromean Three-Body Förster Resonances for Three Interacting Rb Rydberg Atoms.

    Science.gov (United States)

    Tretyakov, D B; Beterov, I I; Yakshina, E A; Entin, V M; Ryabtsev, I I; Cheinet, P; Pillet, P

    2017-10-27

    Three-body Förster resonances at long-range interactions of Rydberg atoms were first predicted and observed in Cs Rydberg atoms by Faoro et al. [Nat. Commun. 6, 8173 (2015)NCAOBW2041-172310.1038/ncomms9173]. In these resonances, one of the atoms carries away an energy excess preventing the two-body resonance, leading thus to a Borromean type of Förster energy transfer. But they were in fact observed as the average signal for the large number of atoms N≫1. In this Letter, we report on the first experimental observation of the three-body Förster resonances 3×nP_{3/2}(|M|)→nS_{1/2}+(n+1)S_{1/2}+nP_{3/2}(|M^{*}|) in a few Rb Rydberg atoms with n=36, 37. We have found here clear evidence that there is no signature of the three-body Förster resonance for exactly two interacting Rydberg atoms, while it is present for N=3-5 atoms. This demonstrates the assumption that three-body resonances can generalize to any Rydberg atom. As such resonance represents an effective three-body operator, it can be used to directly control the three-body interactions in quantum simulations and quantum information processing with Rydberg atoms.

  11. 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.

  12. Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces.

    Directory of Open Access Journals (Sweden)

    Ching-Tai Chen

    Full Text Available Protein-protein interactions are key to many biological processes. Computational methodologies devised to predict protein-protein interaction (PPI sites on protein surfaces are important tools in providing insights into the biological functions of proteins and in developing therapeutics targeting the protein-protein interaction sites. One of the general features of PPI sites is that the core regions from the two interacting protein surfaces are complementary to each other, similar to the interior of proteins in packing density and in the physicochemical nature of the amino acid composition. In this work, we simulated the physicochemical complementarities by constructing three-dimensional probability density maps of non-covalent interacting atoms on the protein surfaces. The interacting probabilities were derived from the interior of known structures. Machine learning algorithms were applied to learn the characteristic patterns of the probability density maps specific to the PPI sites. The trained predictors for PPI sites were cross-validated with the training cases (consisting of 432 proteins and were tested on an independent dataset (consisting of 142 proteins. The residue-based Matthews correlation coefficient for the independent test set was 0.423; the accuracy, precision, sensitivity, specificity were 0.753, 0.519, 0.677, and 0.779 respectively. The benchmark results indicate that the optimized machine learning models are among the best predictors in identifying PPI sites on protein surfaces. In particular, the PPI site prediction accuracy increases with increasing size of the PPI site and with increasing hydrophobicity in amino acid composition of the PPI interface; the core interface regions are more likely to be recognized with high prediction confidence. The results indicate that the physicochemical complementarity patterns on protein surfaces are important determinants in PPIs, and a substantial portion of the PPI sites can be predicted

  13. Protein-Protein Interaction Site Predictions with Three-Dimensional Probability Distributions of Interacting Atoms on Protein Surfaces

    Science.gov (United States)

    Chen, Ching-Tai; Peng, Hung-Pin; Jian, Jhih-Wei; Tsai, Keng-Chang; Chang, Jeng-Yih; Yang, Ei-Wen; Chen, Jun-Bo; Ho, Shinn-Ying; Hsu, Wen-Lian; Yang, An-Suei

    2012-01-01

    Protein-protein interactions are key to many biological processes. Computational methodologies devised to predict protein-protein interaction (PPI) sites on protein surfaces are important tools in providing insights into the biological functions of proteins and in developing therapeutics targeting the protein-protein interaction sites. One of the general features of PPI sites is that the core regions from the two interacting protein surfaces are complementary to each other, similar to the interior of proteins in packing density and in the physicochemical nature of the amino acid composition. In this work, we simulated the physicochemical complementarities by constructing three-dimensional probability density maps of non-covalent interacting atoms on the protein surfaces. The interacting probabilities were derived from the interior of known structures. Machine learning algorithms were applied to learn the characteristic patterns of the probability density maps specific to the PPI sites. The trained predictors for PPI sites were cross-validated with the training cases (consisting of 432 proteins) and were tested on an independent dataset (consisting of 142 proteins). The residue-based Matthews correlation coefficient for the independent test set was 0.423; the accuracy, precision, sensitivity, specificity were 0.753, 0.519, 0.677, and 0.779 respectively. The benchmark results indicate that the optimized machine learning models are among the best predictors in identifying PPI sites on protein surfaces. In particular, the PPI site prediction accuracy increases with increasing size of the PPI site and with increasing hydrophobicity in amino acid composition of the PPI interface; the core interface regions are more likely to be recognized with high prediction confidence. The results indicate that the physicochemical complementarity patterns on protein surfaces are important determinants in PPIs, and a substantial portion of the PPI sites can be predicted correctly with

  14. 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”...

  15. Protein Annotation from Protein Interaction Networks and Gene Ontology

    OpenAIRE

    Nguyen, Cao D.; Gardiner, Katheleen J.; Cios, Krzysztof J.

    2011-01-01

    We introduce a novel method for annotating protein function that combines Naïve Bayes and association rules, and takes advantage of the underlying topology in protein interaction networks and the structure of graphs in the Gene Ontology. We apply our method to proteins from the Human Protein Reference Database (HPRD) and show that, in comparison with other approaches, it predicts protein functions with significantly higher recall with no loss of precision. Specifically, it achieves 51% precis...

  16. Vacuum fluctuations and radiation reaction contributions to the resonance dipole-dipole interaction between two atoms near a reflecting boundary

    Science.gov (United States)

    Zhou, Wenting; Rizzuto, Lucia; Passante, Roberto

    2018-04-01

    We investigate the resonance dipole-dipole interaction energy between two identical atoms, one in the ground state and the other in the excited state, interacting with the electromagnetic field in the presence of a perfectly reflecting plane boundary. The atoms are prepared in a correlated (symmetric or antisymmetric) Bell-type state. Following a procedure due to Dalibard et al. [J. Dalibard et al., J. Phys. (Paris) 43, 1617 (1982);, 10.1051/jphys:0198200430110161700 J. Phys. (Paris) 45, 637 (1984), 10.1051/jphys:01984004504063700], we separate the contributions of vacuum fluctuations and radiation reaction (source) field to the resonance interaction energy between the two atoms and show that only the source field contributes to the interatomic interaction, while vacuum field fluctuations do not. By considering specific geometric configurations of the two-atom system with respect to the mirror and specific choices of dipole orientations, we show that the presence of the mirror significantly affects the resonance interaction energy and that different features appear with respect to the case of atoms in free space, for example, a change in the spatial dependence of the interaction. Our findings also suggest that the presence of a boundary can be exploited to tailor and control the resonance interaction between two atoms, as well as the related energy transfer process. The possibility of observing these phenomena is also discussed.

  17. Modeling of intracerebral interictal epileptic discharges: Evidence for network interactions.

    Science.gov (United States)

    Meesters, Stephan; Ossenblok, Pauly; Colon, Albert; Wagner, Louis; Schijns, Olaf; Boon, Paul; Florack, Luc; Fuster, Andrea

    2018-06-01

    The interictal epileptic discharges (IEDs) occurring in stereotactic EEG (SEEG) recordings are in general abundant compared to ictal discharges, but difficult to interpret due to complex underlying network interactions. A framework is developed to model these network interactions. To identify the synchronized neuronal activity underlying the IEDs, the variation in correlation over time of the SEEG signals is related to the occurrence of IEDs using the general linear model. The interdependency is assessed of the brain areas that reflect highly synchronized neural activity by applying independent component analysis, followed by cluster analysis of the spatial distributions of the independent components. The spatiotemporal interactions of the spike clusters reveal the leading or lagging of brain areas. The analysis framework was evaluated for five successfully operated patients, showing that the spike cluster that was related to the MRI-visible brain lesions coincided with the seizure onset zone. The additional value of the framework was demonstrated for two more patients, who were MRI-negative and for whom surgery was not successful. A network approach is promising in case of complex epilepsies. Analysis of IEDs is considered a valuable addition to routine review of SEEG recordings, with the potential to increase the success rate of epilepsy surgery. Copyright © 2018 International Federation of Clinical Neurophysiology. Published by Elsevier B.V. All rights reserved.

  18. Network characteristics emerging from agent interactions in balanced distributed system.

    Science.gov (United States)

    Salman, Mahdi Abed; Bertelle, Cyrille; Sanlaville, Eric

    2015-01-01

    A distributed computing system behaves like a complex network, the interactions between nodes being essential information exchanges and migrations of jobs or services to execute. These actions are performed by software agents, which behave like the members of social networks, cooperating and competing to obtain knowledge and services. The load balancing consists in distributing the load evenly between system nodes. It aims at enhancing the resource usage. A load balancing strategy specifies scenarios for the cooperation. Its efficiency depends on quantity, accuracy, and distribution of available information. Nevertheless, the distribution of information on the nodes, together with the initial network structure, may create different logical network structures. In this paper, different load balancing strategies are tested on different network structures using a simulation. The four tested strategies are able to distribute evenly the load so that the system reaches a steady state (the mean response time of the jobs is constant), but it is shown that a given strategy indeed behaves differently according to structural parameters and information spreading. Such a study, devoted to distributed computing systems (DCSs), can be useful to understand and drive the behavior of other complex systems.

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

    Directory of Open Access Journals (Sweden)

    Susan Grant

    2014-01-01

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

  20. Finite-field evaluation of the Lennard-Jones atom-wall interaction constant C3 for alkali-metal atoms

    International Nuclear Information System (INIS)

    Johnson, W.R.; Dzuba, V.A.; Safronova, U.I.; Safronova, M.S.

    2004-01-01

    A finite-field scaling method is applied to evaluate the Lennard-Jones interaction constant C 3 for alkali-metal atoms. The calculations are based on the relativistic single-double approximation in which single and double excitations of Dirac-Hartree-Fock wave functions are included to all orders in perturbation theory

  1. Proposal for Translational Entanglement of Dipole-Dipole Interacting Atoms in Optical Lattices

    Science.gov (United States)

    Opatrný, Tomáš; Deb, Bimalendu; Kurizki, Gershon

    2003-06-01

    We propose and investigate a realization of the position- and momentum-correlated Einstein-Podolsky-Rosen (EPR) states [Phys. Rev. 47, 777 (1935)] that have hitherto eluded detection. The realization involves atom pairs that are confined to adjacent sites of two mutually shifted optical lattices and are entangled via laser-induced dipole-dipole interactions. The EPR “paradox” with translational variables is then modified by lattice-diffraction effects and can be verified to a high degree of accuracy in this scheme.

  2. Entanglement manipulation via Coulomb interaction in an optomechanical cavity assisted by two-level cold atoms

    Science.gov (United States)

    Wang, Jing; Tian, Xue-Dong; Liu, Yi-Mou; Cui, Cui-Li; Wu, Jin-Hui

    2018-06-01

    We investigate the stationary entanglement properties in a hybrid system consisting of an optical cavity, a mechanical resonator, a charged object, and an atomic ensemble. Numerical results show that this hybrid system exhibits three kinds of controllable bipartite entanglements in an experimentally accessible parameter regime with the help of the charged object. More importantly, it is viable to enhance on demand each bipartite entanglement at the expense of reducing others by modulating the Coulomb coupling strength. Last but not least, these bipartite entanglements seem more robust against on the environmental temperature for the positive Coulomb interaction.

  3. px+ipy Superfluid from s-Wave Interactions of Fermionic Cold Atoms

    International Nuclear Information System (INIS)

    Zhang Chuanwei; Tewari, Sumanta; Lutchyn, Roman M.; Das Sarma, S.

    2008-01-01

    Two-dimensional (p x +ip y ) superfluids or superconductors offer a playground for studying intriguing physics such as quantum teleportation, non-Abelian statistics, and topological quantum computation. Creating such a superfluid in cold fermionic atom optical traps using p-wave Feshbach resonance is turning out to be challenging. Here we propose a method to create a p x +ip y superfluid directly from an s-wave interaction making use of a topological Berry phase, which can be artificially generated. We discuss ways to detect the spontaneous Hall mass current, which acts as a diagnostic for the chiral p-wave superfluid

  4. Collapse and Revival of an Atomic Beam Interacting with a Coherent State Light Field

    International Nuclear Information System (INIS)

    Ben, Li; Jing-Biao, Chen

    2009-01-01

    We report on the phenomena of the periodic spontaneous collapse and revival in the dynamics of an atomic beam interacting with a single-mode and coherent-state light field. Conventional collapse and revival by Eberly et al. [Phys. Rev. Lett. 44 (1980) 1323] are presented in the case of the evolution with time of the population inversion. Here, we study the evolution with coupling strength of population inversion. We define the collapse and revival coupling strengths as characteristic parameters to describe the above collapse and revival. Furthermore, we present the analytic formulas for the population inversion, the collapse and revival coupling strengths

  5. Electron, ion and atomic beams interaction with solid high-molecular dielectrics

    Energy Technology Data Exchange (ETDEWEB)

    Milyavskij, V V; Skvortsov, V A [Russian Academy of Sciences, Moscow (Russian Federation). High Energy Density Research Center

    1997-12-31

    A mathematical model was constructed and numerical investigation performed of the interaction between intense electron, ion and atomic beams and solid high-molecular dielectrics under various boundary conditions. The model is based on equations of the mechanics of continuum, electrodynamics and kinetics, describing the accumulation and relaxation of space charge and shock-wave processes, as well as the evolution of electric field in the sample. A semi-empirical procedure is proposed for the calculation of energy deposition by electron beam in a target in the presence of a non-uniform electric field. (author). 4 figs., 2 refs.

  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. Interactions between nitrogen molecules and barium atoms on Ru (0001) surface

    International Nuclear Information System (INIS)

    Zhao Xinxin; Mi Yiming; Xu Hongxia; Wang Lili; Ren Li; Tao Xiangming; Tan Mingqiu

    2011-01-01

    We had performed first principles calculations on interactions between nitrogen molecules and barium atoms on Ru (0001) surface using density function theory methods. It was shown that effects of barium atoms weakened the bond strength of nitrogen molecules. The bond length of nitrogen molecule increases from 0.113 nm on Ru (001)-N 2 to 0.120 nm on Ru (001)-N 2 /Ba surface. While stretch vibrational frequency of nitrogen molecule decreased from 2222 cm -1 and charge transfer toward nitrogen molecule increased from 0.3 e to 1.1 e. Charge was mainly translated from 6 s orbitals of barium atoms to 4 d orbitals of substrate, which enhanced the hybridization between 4 d and 2 π orbitals and increased the dipole moment of 5 σ and d π orbitals of nitrogen molecule. The molecular dipole moment of nitrogen molecule was increased by -0.136 e Anstrom. It was suggested that barium had some characters to be an electronic promoter on the process of activating nitrogen molecules on Ru (0001) surface. (authors)

  8. Van-der-Waals interaction of atoms in dipolar Rydberg states

    Science.gov (United States)

    Kamenski, Aleksandr A.; Mokhnenko, Sergey N.; Ovsiannikov, Vitaly D.

    2018-02-01

    An asymptotic expression for the van-der-Waals constant C 6( n) ≈ -0.03 n 12 K p ( x) is derived for the long-range interaction between two highly excited hydrogen atoms A and B in their extreme Stark states of equal principal quantum numbers n A = n B = n ≫ 1 and parabolic quantum numbers n 1(2) = n - 1, n 2(1) = m = 0 in the case of collinear orientation of the Stark-state dipolar electric moments and the interatomic axis. The cubic polynomial K 3( x) in powers of reciprocal values of the principal quantum number x = 1/ n and quadratic polynomial K 2( y) in powers of reciprocal values of the principal quantum number squared y = 1/ n 2 were determined on the basis of the standard curve fitting polynomial procedure from the calculated data for C 6( n). The transformation of attractive van-der-Waals force ( C 6 > 0) for low-energy states n < 23 into repulsive force ( C 6 < 0) for all higher-energy states of n ≥ 23, is observed from the results of numerical calculations based on the second-order perturbation theory for the operator of the long-range interaction between neutral atoms. This transformation is taken into account in the asymptotic formulas (in both cases of p = 2, 3) by polynomials K p tending to unity at n → ∞ ( K p (0) = 1). The transformation from low- n attractive van-der-Waals force into high- n repulsive force demonstrates the gradual increase of the negative contribution to C 6( n) from the lower-energy two-atomic states, of the A(B)-atom principal quantum numbers n'A(B) = n-Δ n (where Δ n = 1, 2, … is significantly smaller than n for the terms providing major contribution to the second-order series), which together with the states of n″B(A) = n+Δ n make the joint contribution proportional to n 12. So, the hydrogen-like manifold structure of the energy spectrum is responsible for the transformation of the power-11 asymptotic dependence C 6( n) ∝ n 11of the low-angular-momenta Rydberg states in many-electron atoms into the power

  9. Peptide microarrays to probe for competition for binding sites in a protein interaction network

    NARCIS (Netherlands)

    Sinzinger, M.D.S.; Ruttekolk, I.R.R.; Gloerich, J.; Wessels, H.; Chung, Y.D.; Adjobo-Hermans, M.J.W.; Brock, R.E.

    2013-01-01

    Cellular protein interaction networks are a result of the binding preferences of a particular protein and the entirety of interactors that mutually compete for binding sites. Therefore, the reconstruction of interaction networks by the accumulation of interaction networks for individual proteins

  10. [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.

  11. 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

  12. Exploring drug-target interaction networks of illicit drugs.

    Science.gov (United States)

    Atreya, Ravi V; Sun, Jingchun; Zhao, Zhongming

    2013-01-01

    Drug addiction is a complex and chronic mental disease, which places a large burden on the American healthcare system due to its negative effects on patients and their families. Recently, network pharmacology is emerging as a promising approach to drug discovery by integrating network biology and polypharmacology, allowing for a deeper understanding of molecular mechanisms of drug actions at the systems level. This study seeks to apply this approach for investigation of illicit drugs and their targets in order to elucidate their interaction patterns and potential secondary drugs that can aid future research and clinical care. In this study, we extracted 188 illicit substances and their related information from the DrugBank database. The data process revealed 86 illicit drugs targeting a total of 73 unique human genes, which forms an illicit drug-target network. Compared to the full drug-target network from DrugBank, illicit drugs and their target genes tend to cluster together and form four subnetworks, corresponding to four major medication categories: depressants, stimulants, analgesics, and steroids. External analysis of Anatomical Therapeutic Chemical (ATC) second sublevel classifications confirmed that the illicit drugs have neurological functions or act via mechanisms of stimulants, opioids, and steroids. To further explore other drugs potentially having associations with illicit drugs, we constructed an illicit-extended drug-target network by adding the drugs that have the same target(s) as illicit drugs to the illicit drug-target network. After analyzing the degree and betweenness of the network, we identified hubs and bridge nodes, which might play important roles in the development and treatment of drug addiction. Among them, 49 non-illicit drugs might have potential to be used to treat addiction or have addictive effects, including some results that are supported by previous studies. This study presents the first systematic review of the network

  13. Phase diagram of Rydberg atoms with repulsive van der Waals interaction

    International Nuclear Information System (INIS)

    Osychenko, O. N.; Astrakharchik, G. E.; Boronat, J.; Lutsyshyn, Y.; Lozovik, Yu. E.

    2011-01-01

    We report a quantum Monte Carlo calculation of the phase diagram of bosons interacting with a repulsive inverse sixth power pair potential, a model for assemblies of Rydberg atoms in the local van der Waals blockade regime. The model can be parametrized in terms of just two parameters, the reduced density and temperature. Solidification happens to the fcc phase. At zero temperature, the transition density is found with the diffusion Monte Carlo method at density ρ=3.9 ((ℎ/2π) 2 /mC 6 ) 3/4 , where C 6 is the strength of the interaction. The solidification curve at nonzero temperature is studied with the path-integral Monte Carlo approach and is compared with transitions in corresponding harmonic and classical crystals. Relaxation mechanisms are considered in relation to present experiments.

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

    Energy Technology Data Exchange (ETDEWEB)

    Zacate, M. O., E-mail: zacatem1@nku.edu [Northern Kentucky University, Department of Physics, Geology, and Engineering Technology (United States)

    2016-12-15

    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.

  15. 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}.

  16. Dislocation-stacking fault tetrahedron interaction: what can we learn from atomic-scale modelling

    International Nuclear Information System (INIS)

    Osetsky, Yu.N.; Stoller, R.E.; Matsukawa, Y.

    2004-01-01

    The high number density of stacking fault tetrahedra (SFTs) observed in irradiated fcc metals suggests that they should contribute to radiation-induced hardening and, therefore, taken into account when estimating mechanical properties changes of irradiated materials. The central issue is describing the individual interaction between a moving dislocation and an SFT, which is characterized by a very fine size scale, ∼100 nm. This scale is amenable to both in situ TEM experiments and large-scale atomic modelling. In this paper we present results of an atomistic simulation of dislocation-SFT interactions using molecular dynamics (MD). The results are compared with observations from in situ deformation experiments. It is demonstrated that in some cases the simulations and experimental observations are quite similar, suggesting a reasonable interpretation of experimental observations

  17. 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.

  18. First meeting of the atomic and molecular data centre network, Vienna, 9-13 May 1977. Summary report

    International Nuclear Information System (INIS)

    Lorenz, A.; Seamon, R.E.

    1977-08-01

    The general objective of the effort started at this meeting is the formation of an internationally coordinated network of centres and groups for the systematic world-wide compilation, evaluation, exchange and dissemination of bibliographic and numerical A+M data required by the fusion community. The specific accomplishments of this meeting were the establishment of agreements for the cooperation between existing A+M data centres and groups and the IAEA Nuclear Data Section/A+M Data Unit with regard to the Quarterly Bulletin on Atomic and Molecular Data for Fusion, the Bibliographic Index to Atomic Collision Data, and the exchange of evaluated atomic collision data

  19. Network of interactions between ciliates and phytoplankton during spring

    Directory of Open Access Journals (Sweden)

    Thomas ePosch

    2015-11-01

    Full Text Available The annually recurrent spring phytoplankton blooms in freshwater lakes initiate pronounced successions of planktonic ciliate species. Although there is considerable knowledge on the taxonomic diversity of these ciliates, their species-specific interactions with other microorganisms are still not well understood. Here we present the succession patterns of 20 morphotypes of ciliates during spring in Lake Zurich, Switzerland, and we relate their abundances to phytoplankton genera, flagellates, heterotrophic bacteria, and abiotic parameters. Interspecific relationships were analyzed by contemporaneous correlations and time-lagged co-occurrence and visualized as association networks. The contemporaneous network pointed to the pivotal role of distinct ciliate species (e.g., Balanion planctonicum, Rimostrombidium humile as primary consumers of cryptomonads, revealed a clear overclustering of mixotrophic / omnivorous species, and highlighted the role of Halteria / Pelagohalteria as important bacterivores. By contrast, time-lagged statistical approaches (like local similarity analyses, LSA proved to be inadequate for the evaluation of high-frequency sampling data. LSA led to a conspicuous inflation of significant associations, making it difficult to establish ecologically plausible interactions between ciliates and other microorganisms. Nevertheless, if adequate statistical procedures are selected, association networks can be powerful tools to formulate testable hypotheses about the autecology of only recently described ciliate species.

  20. Atomic Ensemble Effects and Non-Covalent Interactions at the Electrode–Electrolyte Interface

    Directory of Open Access Journals (Sweden)

    Angel Cuesta

    2016-09-01

    Full Text Available Cyanide-modified Pt(111 electrodes have been recently employed to study atomic ensemble effects in electrocatalysis. This work, which will be briefly reviewed, reveals that the smallest site required for methanol dehydrogenation and formic acid dehydration is composed of three contiguous Pt atoms. By blocking these trigonal sites, the specific adsorption of anions, such as sulfate and phosphate, can be inhibited, thus increasing the rate of oxygen reduction reaction by one order of magnitude or more. Moreover, alkali metal cations affect hydrogen adsorption on cyanide-modified Pt(111. This effect is attributed to the non-covalent interactions at the electrical double layer between specifically adsorbed anions or dipoles and the alkali metal cations. A systematic investigation is conducted on the effect of the concentration of alkali metal cations. Accordingly, a simple model that reproduces the experimental observations accurately and enables the understanding of the trends in the strength of the interaction between M+ and CNad when moving from Li+ to Cs+, as well as the deviations from the expected trends, is developed. This simple model can also explain the occurrence of super-Nernstian shifts of the equilibrium potential of interfacial proton-coupled electron transfers. Therefore, the model can be generally applied to explain quantitatively the effect of cations on the properties of the electrical double layer. The recently reported effects of alkali metal cations on several electrocatalytic reactions must be mediated by the interaction between these cations and chemisorbed species. As these interactions seem to be adequately and quantitatively described by our model, we expect the model to also be useful to describe, explain, and potentially exploit these effects.

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

    International Nuclear Information System (INIS)

    Siriratana Biramontri, Pantip Ampornrat

    2013-01-01

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

  2. Extended Bose Hubbard model of interacting bosonic atoms in optical lattices: From superfluidity to density waves

    International Nuclear Information System (INIS)

    Mazzarella, G.; Giampaolo, S. M.; Illuminati, F.

    2006-01-01

    For systems of interacting, ultracold spin-zero neutral bosonic atoms, harmonically trapped and subject to an optical lattice potential, we derive an Extended Bose Hubbard (EBH) model by developing a systematic expansion for the Hamiltonian of the system in powers of the lattice parameters and of a scale parameter, the lattice attenuation factor. We identify the dominant terms that need to be retained in realistic experimental conditions, up to nearest-neighbor interactions and nearest-neighbor hoppings conditioned by the on-site occupation numbers. In the mean field approximation, we determine the free energy of the system and study the phase diagram both at zero and at finite temperature. At variance with the standard on site Bose Hubbard model, the zero-temperature phase diagram of the EBH model possesses a dual structure in the Mott insulating regime. Namely, for specific ranges of the lattice parameters, a density wave phase characterizes the system at integer fillings, with domains of alternating mean occupation numbers that are the atomic counterparts of the domains of staggered magnetizations in an antiferromagnetic phase. We show as well that in the EBH model, a zero-temperature quantum phase transition to pair superfluidity is, in principle, possible, but completely suppressed at the lowest order in the lattice attenuation factor. Finally, we determine the possible occurrence of the different phases as a function of the experimentally controllable lattice parameters

  3. Elastic fields, dipole tensors, and interaction between self-interstitial atom defects in bcc transition metals

    Science.gov (United States)

    Dudarev, S. L.; Ma, Pui-Wai

    2018-03-01

    Density functional theory (DFT) calculations show that self-interstitial atom (SIA) defects in nonmagnetic body-centered-cubic (bcc) metals adopt strongly anisotropic configurations, elongated in the direction [S. Han et al., Phys. Rev. B 66, 220101 (2002), 10.1103/PhysRevB.66.220101; D. Nguyen-Manh et al., Phys. Rev. B 73, 020101 (2006), 10.1103/PhysRevB.73.020101; P. M. Derlet et al., Phys. Rev. B 76, 054107 (2007), 10.1103/PhysRevB.76.054107; S. L. Dudarev, Annu. Rev. Mater. Res. 43, 35 (2013), 10.1146/annurev-matsci-071312-121626]. Elastic distortions, associated with such anisotropic atomic structures, appear similar to distortions around small prismatic dislocation loops, although the extent of this similarity has never been quantified. We derive analytical formulas for the dipole tensors of SIA defects, which show that, in addition to the prismatic dislocation looplike character, the elastic field of a SIA defect also has a significant isotropic dilatation component. Using empirical potentials and DFT calculations, we parametrize dipole tensors of defects for all the nonmagnetic bcc transition metals. This enables a quantitative evaluation of the energy of elastic interaction between the defects, which also shows that in a periodic three-dimensional simple cubic arrangement of crowdions, long-range elastic interactions between a defect and all its images favor a orientation of the defect.

  4. Electron-electron interaction and transfer ionization in fast ion-atom collisions

    International Nuclear Information System (INIS)

    Voitkiv, A B

    2008-01-01

    Recently it was pointed out that electron capture occurring in fast ion-atom collisions can proceed via a mechanism which earlier was not considered. In the present paper we study this mechanism in more detail. Similarly as in radiative capture, where the electron transfer occurs due to the interaction with the radiation field and proceeds via emission of a photon, within this mechanism the electron capture is caused by the interaction with another atomic electron leading mainly to the emission of the latter. In contrast to the electron-electron Thomas capture, this electron-electron (E-E) mechanism is basically a first-order one having similarities to the kinematic and radiative capture channels. It also possesses important differences with the latter two. Leading to transfer ionization, this first-order capture mechanism results in the electron emission mainly in the direction opposite to the motion of the projectile ion. The same, although less pronounced, feature is also characteristic for the momenta of the target recoil ions produced via this mechanism. It is also shown that the action of the E-E mechanism is clearly seen in recent experimental data on the transfer ionization in fast proton-helium collisions.

  5. Interaction of light with planar lattices of atoms: Reflection, transmission, and cooperative magnetometry

    Science.gov (United States)

    Facchinetti, G.; Ruostekoski, J.

    2018-02-01

    We study strong, light-mediated, resonant dipole-dipole interactions in two-dimensional planar lattices of cold atoms. We provide a detailed analysis for the description of the dipolar point emitter lattice plane as a "superatom" whose response is similar to electromagnetically induced transparency but which exhibits an ultranarrow collective size-dependent subradiant resonance linewidth. The superatom model provides intuitively simple descriptions for the spectral response of the array, including the complete reflection, full transmission, narrow Fano resonances, and asymptotic expressions for the resonance linewidths of the collective eigenmodes. We propose a protocol to transfer almost the entire radiative excitation to a single correlated subradiant eigenmode in a lattice and show that the medium obtained by stacked lattice arrays can form a cooperative magnetometer. Such a magnetometer utilizes similar principles as magnetometers based on the electromagnetically induced transparency. The accuracy of the cooperative magnetometer, however, is not limited by the single-atom resonance linewidth but the much narrower collective linewidth that results from the strong dipole-dipole interactions.

  6. Visualising the Micro World of Chemical/Geochemical Interactions Using Atomic Force Microscopy (AFM)

    Energy Technology Data Exchange (ETDEWEB)

    Graham, G M; Sorbie, K S

    1997-12-31

    Scanning force microscopy, in particular AFM (Atomic Force Microscopy), provides a particular useful and interesting tool for the examination of surface structure at the near-atomic level. AFM is particularly well suited to the study of interactions at the surface in aqueous solutions using real time in-situ measurements. In this paper there is presented AFM images showing in situ crystal growth from supersaturated BaSO{sub 4} solutions onto the surface of barite. Growth structures in the form of spiral crystal growth features, presumably originating from screw dislocations, are illustrated. AFM images of novel scale crystal growth inhibition experiments are presented. Examination of the manner in which generically different species adsorb onto growth structures may help to explain mechanistic differences in the way which different inhibitor species perform against barium sulphate scale formation. Adsorption of polyacrylamide species onto mica surfaces have been viewed. The general utility of AFM to a number of other common surface interactions in oil field chemistry will be discussed. 17 refs., 3 figs.

  7. Systems pharmacology - Towards the modeling of network interactions.

    Science.gov (United States)

    Danhof, Meindert

    2016-10-30

    Mechanism-based pharmacokinetic and pharmacodynamics (PKPD) and disease system (DS) models have been introduced in drug discovery and development research, to predict in a quantitative manner the effect of drug treatment in vivo in health and disease. This requires consideration of several fundamental properties of biological systems behavior including: hysteresis, non-linearity, variability, interdependency, convergence, resilience, and multi-stationarity. Classical physiology-based PKPD models consider linear transduction pathways, connecting processes on the causal path between drug administration and effect, as the basis of drug action. Depending on the drug and its biological target, such models may contain expressions to characterize i) the disposition and the target site distribution kinetics of the drug under investigation, ii) the kinetics of target binding and activation and iii) the kinetics of transduction. When connected to physiology-based DS models, PKPD models can characterize the effect on disease progression in a mechanistic manner. These models have been found useful to characterize hysteresis and non-linearity, yet they fail to explain the effects of the other fundamental properties of biological systems behavior. Recently systems pharmacology has been introduced as novel approach to predict in vivo drug effects, in which biological networks rather than single transduction pathways are considered as the basis of drug action and disease progression. These models contain expressions to characterize the functional interactions within a biological network. Such interactions are relevant when drugs act at multiple targets in the network or when homeostatic feedback mechanisms are operative. As a result systems pharmacology models are particularly useful to describe complex patterns of drug action (i.e. synergy, oscillatory behavior) and disease progression (i.e. episodic disorders). In this contribution it is shown how physiology-based PKPD and

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

    Directory of Open Access Journals (Sweden)

    Brendan Chambers

    2016-08-01

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

  9. Quantum and semiclassical spin networks: from atomic and molecular physics to quantum computing and gravity

    Science.gov (United States)

    Aquilanti, Vincenzo; Bitencourt, Ana Carla P.; Ferreira, Cristiane da S.; Marzuoli, Annalisa; Ragni, Mirco

    2008-11-01

    The mathematical apparatus of quantum-mechanical angular momentum (re)coupling, developed originally to describe spectroscopic phenomena in atomic, molecular, optical and nuclear physics, is embedded in modern algebraic settings which emphasize the underlying combinatorial aspects. SU(2) recoupling theory, involving Wigner's 3nj symbols, as well as the related problems of their calculations, general properties, asymptotic limits for large entries, nowadays plays a prominent role also in quantum gravity and quantum computing applications. We refer to the ingredients of this theory—and of its extension to other Lie and quantum groups—by using the collective term of 'spin networks'. Recent progress is recorded about the already established connections with the mathematical theory of discrete orthogonal polynomials (the so-called Askey scheme), providing powerful tools based on asymptotic expansions, which correspond on the physical side to various levels of semi-classical limits. These results are useful not only in theoretical molecular physics but also in motivating algorithms for the computationally demanding problems of molecular dynamics and chemical reaction theory, where large angular momenta are typically involved. As for quantum chemistry, applications of these techniques include selection and classification of complete orthogonal basis sets in atomic and molecular problems, either in configuration space (Sturmian orbitals) or in momentum space. In this paper, we list and discuss some aspects of these developments—such as for instance the hyperquantization algorithm—as well as a few applications to quantum gravity and topology, thus providing evidence of a unifying background structure.

  10. Self-consistent collisional-radiative model for hydrogen atoms: Atom–atom interaction and radiation transport

    International Nuclear Information System (INIS)

    Colonna, G.; Pietanza, L.D.; D’Ammando, G.

    2012-01-01

    Graphical abstract: Self-consistent coupling between radiation, state-to-state kinetics, electron kinetics and fluid dynamics. Highlight: ► A CR model of shock-wave in hydrogen plasma has been presented. ► All equations have been coupled self-consistently. ► Non-equilibrium electron and level distributions are obtained. ► The results show non-local effects and non-equilibrium radiation. - Abstract: A collisional-radiative model for hydrogen atom, coupled self-consistently with the Boltzmann equation for free electrons, has been applied to model a shock tube. The kinetic model has been completed considering atom–atom collisions and the vibrational kinetics of the ground state of hydrogen molecules. The atomic level kinetics has been also coupled with a radiative transport equation to determine the effective adsorption and emission coefficients and non-local energy transfer.

  11. Precision Tests of the Electroweak Interaction using Trapped Atoms and Ions

    Energy Technology Data Exchange (ETDEWEB)

    Melconian, Daniel George [Texas A & M Univ., College Station, TX (United States)

    2017-06-21

    The objective of the proposed research is to study fundamental aspects of the electroweak interaction via precision measurements in beta decay to test our current understanding of fundamental particles and forces as contained in the so-called "Standard Model" of particle physics. By comparing elegant experiments to rigorous theoretical predictions, we will either confirm the Standard Model to a higher degree and rule out models which seek to extend it, or find evidence of new physics and help guide theorists in developing the New Standard Model. The use of ion and neutral atom traps at radioactive ion beam facilities has opened up a new vista in precision low-energy nuclear physics experiments. Traps provide an ideal source of decaying atoms: they can be extremely cold (~1 mK); they are compact (~1 mm^3); and perhaps most importantly, the daughter particles escape with negligible distortions to their momenta in a scattering-free, open environment. The project is taking advantage of these technologies and applying them to precision beta-decay studies at radioactive beam facilities. The program consists of two complementary efforts: 1) Ion traps are an extremely versatile tool for purifying, cooling and bunching low-energy beams of short-lived nuclei. A large-bore (210~mm) superconducting 7-Tesla solenoid is at the heart of a Penning trap system for which there is a dedicated beamline at T-REX, the upgraded radioactive beam facility at the Cyclotron Institute, Texas A&M University. In addition to providing a general-purpose decay station, the flagship program for this system is measuring the ft-values and beta-neutrino correlation parameters from isospin T=2 superallowed beta-delayed proton decays, complimenting and expanding the already strong program in fundamental interactions at the Institute. 2) A magneto-optical trap is being used at the TRIUMF Neutral Atom Trap facility to observe the (un)polarized angular distribution parameters of isotopes of potassium. We

  12. A Physical Interaction Network of Dengue Virus and Human Proteins*

    Science.gov (United States)

    Khadka, Sudip; Vangeloff, Abbey D.; Zhang, Chaoying; Siddavatam, Prasad; Heaton, Nicholas S.; Wang, Ling; Sengupta, Ranjan; Sahasrabudhe, Sudhir; Randall, Glenn; Gribskov, Michael; Kuhn, Richard J.; Perera, Rushika; LaCount, Douglas J.

    2011-01-01

    Dengue virus (DENV), an emerging mosquito-transmitted pathogen capable of causing severe disease in humans, interacts with host cell factors to create a more favorable environment for replication. However, few interactions between DENV and human proteins have been reported to date. To identify DENV-human protein interactions, we used high-throughput yeast two-hybrid assays to screen the 10 DENV proteins against a human liver activation domain library. From 45 DNA-binding domain clones containing either full-length viral genes or partially overlapping gene fragments, we identified 139 interactions between DENV and human proteins, the vast majority of which are novel. These interactions involved 105 human proteins, including six previously implicated in DENV infection and 45 linked to the replication of other viruses. Human proteins with functions related to the complement and coagulation cascade, the centrosome, and the cytoskeleton were enriched among the DENV interaction partners. To determine if the cellular proteins were required for DENV infection, we used small interfering RNAs to inhibit their expression. Six of 12 proteins targeted (CALR, DDX3X, ERC1, GOLGA2, TRIP11, and UBE2I) caused a significant decrease in the replication of a DENV replicon. We further showed that calreticulin colocalized with viral dsRNA and with the viral NS3 and NS5 proteins in DENV-infected cells, consistent with a direct role for calreticulin in DENV replication. Human proteins that interacted with DENV had significantly higher average degree and betweenness than expected by chance, which provides additional support for the hypothesis that viruses preferentially target cellular proteins that occupy central position in the human protein interaction network. This study provides a valuable starting point for additional investigations into the roles of human proteins in DENV infection. PMID:21911577

  13. A physical interaction network of dengue virus and human proteins.

    Science.gov (United States)

    Khadka, Sudip; Vangeloff, Abbey D; Zhang, Chaoying; Siddavatam, Prasad; Heaton, Nicholas S; Wang, Ling; Sengupta, Ranjan; Sahasrabudhe, Sudhir; Randall, Glenn; Gribskov, Michael; Kuhn, Richard J; Perera, Rushika; LaCount, Douglas J

    2011-12-01

    Dengue virus (DENV), an emerging mosquito-transmitted pathogen capable of causing severe disease in humans, interacts with host cell factors to create a more favorable environment for replication. However, few interactions between DENV and human proteins have been reported to date. To identify DENV-human protein interactions, we used high-throughput yeast two-hybrid assays to screen the 10 DENV proteins against a human liver activation domain library. From 45 DNA-binding domain clones containing either full-length viral genes or partially overlapping gene fragments, we identified 139 interactions between DENV and human proteins, the vast majority of which are novel. These interactions involved 105 human proteins, including six previously implicated in DENV infection and 45 linked to the replication of other viruses. Human proteins with functions related to the complement and coagulation cascade, the centrosome, and the cytoskeleton were enriched among the DENV interaction partners. To determine if the cellular proteins were required for DENV infection, we used small interfering RNAs to inhibit their expression. Six of 12 proteins targeted (CALR, DDX3X, ERC1, GOLGA2, TRIP11, and UBE2I) caused a significant decrease in the replication of a DENV replicon. We further showed that calreticulin colocalized with viral dsRNA and with the viral NS3 and NS5 proteins in DENV-infected cells, consistent with a direct role for calreticulin in DENV replication. Human proteins that interacted with DENV had significantly higher average degree and betweenness than expected by chance, which provides additional support for the hypothesis that viruses preferentially target cellular proteins that occupy central position in the human protein interaction network. This study provides a valuable starting point for additional investigations into the roles of human proteins in DENV infection.

  14. Interactive social contagions and co-infections on complex networks

    Science.gov (United States)

    Liu, Quan-Hui; Zhong, Lin-Feng; Wang, Wei; Zhou, Tao; Eugene Stanley, H.

    2018-01-01

    What we are learning about the ubiquitous interactions among multiple social contagion processes on complex networks challenges existing theoretical methods. We propose an interactive social behavior spreading model, in which two behaviors sequentially spread on a complex network, one following the other. Adopting the first behavior has either a synergistic or an inhibiting effect on the spread of the second behavior. We find that the inhibiting effect of the first behavior can cause the continuous phase transition of the second behavior spreading to become discontinuous. This discontinuous phase transition of the second behavior can also become a continuous one when the effect of adopting the first behavior becomes synergistic. This synergy allows the second behavior to be more easily adopted and enlarges the co-existence region of both behaviors. We establish an edge-based compartmental method, and our theoretical predictions match well with the simulation results. Our findings provide helpful insights into better understanding the spread of interactive social behavior in human society.

  15. 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.

  16. Atomic and plasma-material interaction data for fusion. Vol. 13

    International Nuclear Information System (INIS)

    Clark, R.E.H.

    2007-01-01

    of the A+M Subcommittee of the International Fusion Research Council in May 2000 to initiate a Coordinated Research Project (CRP) to address data needs in this area. The Atomic and Molecular Data of the International Atomic Energy Agency initiated the CRP on 'Atomic and Molecular Data for Fusion Plasma Diagnostics' in 2001. Results from this CRP will be incorporated into the A+M Data Unit databases and will be available through the worldwide-web for global access by researchers. These data will be of interest not only for direct fusion applications, but in other research plasma studies used in accelerators, environmental research and other fields. The work of the CRP was completed in 2005. During the course of the Coordinated Research Project, new data were generated for a variety of processes impacting on a number of diagnostic procedures for fusion plasmas: spectral observations near the strike zone and divertor (where alpha particles interact with molecules) require a variety of cross-section data that have been measured and calculated during the current work programme; helium beam diagnostics from fast to thermal require cross-section data for both electron and proton impact, that have been generated during the current work programme; data have been produced for use in the determination of species from light elements such as helium, boron and hydrocarbons, as well as heavy elements such as tungsten; large amounts of data on spectral properties were generated to assist in the spectral analysis of plasma emissions; X-ray emissions from impact on surfaces have been studied and quantified; data have been generated for use in hydrogen charge exchange spectroscopy for the determination of the flow and temperature of impurities in the divertor region. The CRP on 'Atomic and molecular data for plasma diagnosis' has been very successful in meeting all of the objectives established at the beginning of the project. The present volume of Atomic and Plasma

  17. Visualization of protein interaction networks: problems and solutions

    Directory of Open Access Journals (Sweden)

    Agapito Giuseppe

    2013-01-01

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

  18. A novel interaction fingerprint derived from per atom score contributions: exhaustive evaluation of interaction fingerprint performance in docking based virtual screening.

    Science.gov (United States)

    Jasper, Julia B; Humbeck, Lina; Brinkjost, Tobias; Koch, Oliver

    2018-03-16

    Protein ligand interaction fingerprints are a powerful approach for the analysis and assessment of docking poses to improve docking performance in virtual screening. In this study, a novel interaction fingerprint approach (PADIF, protein per atom score contributions derived interaction fingerprint) is presented which was specifically designed for utilising the GOLD scoring functions' atom contributions together with a specific scoring scheme. This allows the incorporation of known protein-ligand complex structures for a target-specific scoring. Unlike many other methods, this approach uses weighting factors reflecting the relative frequency of a specific interaction in the references and penalizes destabilizing interactions. In addition, and for the first time, an exhaustive validation study was performed that assesses the performance of PADIF and two other interaction fingerprints in virtual screening. Here, PADIF shows superior results, and some rules of thumb for a successful use of interaction fingerprints could be identified.

  19. Interacting loop-current model of superconducting networks

    International Nuclear Information System (INIS)

    Chi, C.C.; Santhanam, P.; Bloechl, P.E.

    1992-01-01

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

  20. Protein annotation from protein interaction networks and Gene Ontology.

    Science.gov (United States)

    Nguyen, Cao D; Gardiner, Katheleen J; Cios, Krzysztof J

    2011-10-01

    We introduce a novel method for annotating protein function that combines Naïve Bayes and association rules, and takes advantage of the underlying topology in protein interaction networks and the structure of graphs in the Gene Ontology. We apply our method to proteins from the Human Protein Reference Database (HPRD) and show that, in comparison with other approaches, it predicts protein functions with significantly higher recall with no loss of precision. Specifically, it achieves 51% precision and 60% recall versus 45% and 26% for Majority and 24% and 61% for χ²-statistics, respectively. Copyright © 2011 Elsevier Inc. All rights reserved.

  1. 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

  2. Dynamical assessment for evolutions of Atomic-Multinology (AM) in technology innovation using social network theory

    International Nuclear Information System (INIS)

    Woo, Taeho

    2012-01-01

    Highlights: ► The popularity of AM is analyzed by the social network theory. ► The graphical and colorful configurations are used for the meaning of the incident. ► The new industrial field is quantified by dynamical investigations. ► AM can be successfully used in nuclear industry for technology innovation. ► The method could be used for other industries. - Abstract: The technology evolution is investigated. The proposed Atomic Multinology (AM) is quantified by the dynamical method incorporated with Monte-Carlo method. There are three kinds of the technologies as the info-technology (IT), nano-technology (NT), and bio-technology (BT), which are applied to the nuclear technology. AM is initiated and modeled for the dynamic quantifications. The social network algorithm is used in the dynamical simulation for the management of the projects. The result shows that the successfulness of the AM increases, where the 60 years are the investigated period. The values of the dynamical simulation increase in later stage, which means that the technology is matured as time goes on.

  3. Reconstruction of the Tip-Surface Interaction Potential by Analysis of the Brownian Motion of an Atomic Force Microscope Tip

    NARCIS (Netherlands)

    Willemsen, O.H.; Kuipers, L.; van der Werf, Kees; de Grooth, B.G.; Greve, Jan

    2000-01-01

    The thermal movement of an atomic force microscope (AFM) tip is used to reconstruct the tip-surface interaction potential. If a tip is brought into the vicinity of a surface, its movement is governed by the sum of the harmonic cantilever potential and the tip-surface interaction potential. By

  4. 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

  5. Coevolution of Synchronization and Cooperation in Costly Networked Interactions

    Science.gov (United States)

    Antonioni, Alberto; Cardillo, Alessio

    2017-06-01

    Despite the large number of studies on synchronization, the hypothesis that interactions bear a cost for involved individuals has seldom been considered. The introduction of costly interactions leads, instead, to the formulation of a dichotomous scenario in which an individual may decide to cooperate and pay the cost in order to get synchronized with the rest of the population. Alternatively, the same individual can decide to free ride, without incurring any cost, waiting for others to get synchronized to his or her state. Thus, the emergence of synchronization may be seen as the byproduct of an evolutionary game in which individuals decide their behavior according to the benefit-to-cost ratio they accrued in the past. We study the onset of cooperation and synchronization in networked populations of Kuramoto oscillators and report how topology is essential in order for cooperation to thrive. We also display how different classes of topology foster synchronization differently both at microscopic and macroscopic levels.

  6. 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.

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

    Directory of Open Access Journals (Sweden)

    Omar Jehovani López Orozco

    2007-12-01

    Full Text Available 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.

  8. Chaos in generically coupled phase oscillator networks with nonpairwise interactions

    Energy Technology Data Exchange (ETDEWEB)

    Bick, Christian; Ashwin, Peter; Rodrigues, Ana [Centre for Systems, Dynamics and Control and Department of Mathematics, University of Exeter, Exeter EX4 4QF (United Kingdom)

    2016-09-15

    The Kuramoto–Sakaguchi system of coupled phase oscillators, where interaction between oscillators is determined by a single harmonic of phase differences of pairs of oscillators, has very simple emergent dynamics in the case of identical oscillators that are globally coupled: there is a variational structure that means the only attractors are full synchrony (in-phase) or splay phase (rotating wave/full asynchrony) oscillations and the bifurcation between these states is highly degenerate. Here we show that nonpairwise coupling—including three and four-way interactions of the oscillator phases—that appears generically at the next order in normal-form based calculations can give rise to complex emergent dynamics in symmetric phase oscillator networks. In particular, we show that chaos can appear in the smallest possible dimension of four coupled phase oscillators for a range of parameter values.

  9. Chaos in generically coupled phase oscillator networks with nonpairwise interactions.

    Science.gov (United States)

    Bick, Christian; Ashwin, Peter; Rodrigues, Ana

    2016-09-01

    The Kuramoto-Sakaguchi system of coupled phase oscillators, where interaction between oscillators is determined by a single harmonic of phase differences of pairs of oscillators, has very simple emergent dynamics in the case of identical oscillators that are globally coupled: there is a variational structure that means the only attractors are full synchrony (in-phase) or splay phase (rotating wave/full asynchrony) oscillations and the bifurcation between these states is highly degenerate. Here we show that nonpairwise coupling-including three and four-way interactions of the oscillator phases-that appears generically at the next order in normal-form based calculations can give rise to complex emergent dynamics in symmetric phase oscillator networks. In particular, we show that chaos can appear in the smallest possible dimension of four coupled phase oscillators for a range of parameter values.

  10. 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

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

    International Nuclear Information System (INIS)

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

    2015-01-01

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

  12. 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)

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

    NARCIS (Netherlands)

    Pickering, J.P.; Vancso, Gyula 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,

  14. Disease candidate gene identification and prioritization using protein interaction networks

    Directory of Open Access Journals (Sweden)

    Aronow Bruce J

    2009-02-01

    Full Text Available Abstract Background Although most of the current disease candidate gene identification and prioritization methods depend on functional annotations, the coverage of the gene functional annotations is a limiting factor. In the current study, we describe a candidate gene prioritization method that is entirely based on protein-protein interaction network (PPIN analyses. Results For the first time, extended versions of the PageRank and HITS algorithms, and the K-Step Markov method are applied to prioritize disease candidate genes in a training-test schema. Using a list of known disease-related genes from our earlier study as a training set ("seeds", and the rest of the known genes as a test list, we perform large-scale cross validation to rank the candidate genes and also evaluate and compare the performance of our approach. Under appropriate settings – for example, a back probability of 0.3 for PageRank with Priors and HITS with Priors, and step size 6 for K-Step Markov method – the three methods achieved a comparable AUC value, suggesting a similar performance. Conclusion Even though network-based methods are generally not as effective as integrated functional annotation-based methods for disease candidate gene prioritization, in a one-to-one comparison, PPIN-based candidate gene prioritization performs better than all other gene features or annotations. Additionally, we demonstrate that methods used for studying both social and Web networks can be successfully used for disease candidate gene prioritization.

  15. Sequence memory based on coherent spin-interaction neural networks.

    Science.gov (United States)

    Xia, Min; Wong, W K; Wang, Zhijie

    2014-12-01

    Sequence information processing, for instance, the sequence memory, plays an important role on many functions of brain. In the workings of the human brain, the steady-state period is alterable. However, in the existing sequence memory models using heteroassociations, the steady-state period cannot be changed in the sequence recall. In this work, a novel neural network model for sequence memory with controllable steady-state period based on coherent spininteraction is proposed. In the proposed model, neurons fire collectively in a phase-coherent manner, which lets a neuron group respond differently to different patterns and also lets different neuron groups respond differently to one pattern. The simulation results demonstrating the performance of the sequence memory are presented. By introducing a new coherent spin-interaction sequence memory model, the steady-state period can be controlled by dimension parameters and the overlap between the input pattern and the stored patterns. The sequence storage capacity is enlarged by coherent spin interaction compared with the existing sequence memory models. Furthermore, the sequence storage capacity has an exponential relationship to the dimension of the neural network.

  16. Graph theoretic analysis of protein interaction networks of eukaryotes

    Science.gov (United States)

    Goh, K.-I.; Kahng, B.; Kim, D.

    2005-11-01

    Owing to the recent progress in high-throughput experimental techniques, the datasets of large-scale protein interactions of prototypical multicellular species, the nematode worm Caenorhabditis elegans and the fruit fly Drosophila melanogaster, have been assayed. The datasets are obtained mainly by using the yeast hybrid method, which contains false-positive and false-negative simultaneously. Accordingly, while it is desirable to test such datasets through further wet experiments, here we invoke recent developed network theory to test such high-throughput datasets in a simple way. Based on the fact that the key biological processes indispensable to maintaining life are conserved across eukaryotic species, and the comparison of structural properties of the protein interaction networks (PINs) of the two species with those of the yeast PIN, we find that while the worm and yeast PIN datasets exhibit similar structural properties, the current fly dataset, though most comprehensively screened ever, does not reflect generic structural properties correctly as it is. The modularity is suppressed and the connectivity correlation is lacking. Addition of interologs to the current fly dataset increases the modularity and enhances the occurrence of triangular motifs as well. The connectivity correlation function of the fly, however, remains distinct under such interolog additions, for which we present a possible scenario through an in silico modeling.

  17. The paradox of caffeine-zolpidem interaction: a network analysis.

    Science.gov (United States)

    Myslobodsky, Michael

    2009-10-01

    A widely prescribed and potent short-acting hypnotic, zolpidem has become the mainstay for the treatment of middle-of-the-night sleeplessness. It is expected to be antagonized by caffeine. Paradoxically, in some cases caffeine appears to slightly enhance zolpidem sedation. The pharmacokinetic and pharmacodynamic nature of this odd effect remains unexplored. The purpose of this study is to reproduce a hypothetical molecular network recruited by caffeine when co-administered with zolpidem using Ingenuity Pathway Analysis. Thus generated, network drew attention to several possible contributors to caffeine sedation, such as tachykinin precursor 1, cannabinoid, and GABA receptors. The present overview is centered on the possibility that caffeine potentiation of zolpidem sedation does not involve a centralized interaction of specific neurotransmitters, but rather is contributed by its antioxidant capacity. It is proposed that by modifying the cellular redox state, caffeine ultimately reduces the pool of reactive oxygen species, thereby increasing the bioavailability of endogenous melatonin for interaction with zolpidem. This side effect of caffeine encourages further studies of multiple antioxidants as an attractive way to potentially increasing somnolence.

  18. 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.

  19. Protein-Protein Interaction Network and Gene Ontology

    Science.gov (United States)

    Choi, Yunkyu; Kim, Seok; Yi, Gwan-Su; Park, Jinah

    Evolution of computer technologies makes it possible to access a large amount and various kinds of biological data via internet such as DNA sequences, proteomics data and information discovered about them. It is expected that the combination of various data could help researchers find further knowledge about them. Roles of a visualization system are to invoke human abilities to integrate information and to recognize certain patterns in the data. Thus, when the various kinds of data are examined and analyzed manually, an effective visualization system is an essential part. One instance of these integrated visualizations can be combination of protein-protein interaction (PPI) data and Gene Ontology (GO) which could help enhance the analysis of PPI network. We introduce a simple but comprehensive visualization system that integrates GO and PPI data where GO and PPI graphs are visualized side-by-side and supports quick reference functions between them. Furthermore, the proposed system provides several interactive visualization methods for efficiently analyzing the PPI network and GO directedacyclic- graph such as context-based browsing and common ancestors finding.

  20. 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.

  1. Dynamics of a trapped two-level and three-level atom interacting with classical electromagnetic field

    International Nuclear Information System (INIS)

    Ray, Aditi

    2004-01-01

    The dynamics of a two-level atom driven by a single laser beam and three-level atom (Lambda configuration) irradiated by two laser beams are studied taking into account of the quantized center-of-mass motion of the atom. It is shown that the trapped atom system under appropriate resonance condition exhibits the large time-scale revivals when the index of the vibrational sideband responsible for the atomic electronic transition is greater than unity. The revival times are shown to be dependent on the initial number of vibrational excitations and the magnitude of the Lamb-Dicke parameter. The sub-Poissonian statistics in vibrational quantum number is observed at certain time intervals. The minimum time of interaction for which the squeezed states of motional quadrature are generated is found to be decreasing with the increase in the Lamb-Dicke parameter

  2. 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.

  3. Use of total cross sections for obtaining the anisotropic interaction potential in atom--diatom system

    International Nuclear Information System (INIS)

    Eccles, J.; Secrest, D.

    1977-01-01

    A study is made of the ''conservation of the total cross section'' and the ''equivalence of the total cross section'' rules for scattering from H 2 . It is shown that these rules are a better approximation than the random phase approximation would indicate. Cross section formulas are given for scattering atoms from m/sub j/ state selected molecules and it is shown that total cross sections for state selected molecules depend on the anisotropic part of the interaction potential, while the spin-averaged total cross section often depends only on the spherically symmetric part of the interaction potential. The total spin-averaged cross section is thus independent of the initial rotation state of the molecule and depends only on the relative collision energy. It is further demonstrated that isotopic substitution, which shifts the center of mass changing the symmetric part of the interaction potential, has too small an effect on the total cross section to be useful as a means of determining the anisotropy of the potential

  4. Near-threshold effects in ionization of atoms (post collision interaction)

    International Nuclear Information System (INIS)

    Amus'ya, M.Ya.; Kuchiev, M.Yu.; Shejnerman, S.A.

    1979-01-01

    The special class of phenomena of the post collision interaction PCI taking place in case of inelastic electron scattering on atoms, when the incident electron energy is close to the excitement threshold of an autoionization state, is studied. The quantitative quantum-mechanical theory of the PCI is developed. The theory is based only on the supposition that the change of the field in which a slow electron moves takes place in such a small time interval that the interaction of a fast and slow electron can be neglected. The possibility of carrying out calculations giving the direct comparison with the experimental results are shown in the concrete examples. All possible PCI effects such as the shift of the maximum in the energy distribution of fast (or slow) electrons, the asymmetry of the contour form and its broadening, the change of the angular distribution of slow electrons, have been practically illustrated. It is shown that the interaction of a slow electron and a vacancy in the final state essentially affects the process characteristics. Taking into account PCI in the concrete process calculations made it possible to get an acceptable agreement with the available experimental data

  5. First-principles calculations of the interaction between hydrogen and 3d alloying atom in nickel

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Wenguan, E-mail: liuwenguan@sinap.ac.cn [Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 (China); Key Laboratory of Nuclear Radiation and Nuclear Energy Technology, Chinese Academy of Sciences, Shanghai 201800 (China); Qian, Yuan; Zhang, Dongxun [Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 (China); Key Laboratory of Nuclear Radiation and Nuclear Energy Technology, Chinese Academy of Sciences, Shanghai 201800 (China); Liu, Wei, E-mail: liuwei@sinap.ac.cn [Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 (China); Key Laboratory of Nuclear Radiation and Nuclear Energy Technology, Chinese Academy of Sciences, Shanghai 201800 (China); Han, Han [Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 (China); Key Laboratory of Nuclear Radiation and Nuclear Energy Technology, Chinese Academy of Sciences, Shanghai 201800 (China)

    2015-10-15

    Knowledge of the behavior of hydrogen (H) in Ni-based alloy is essential for the prediction of Tritium behavior in Molten Salt Reactor. First-principles calculations were performed to investigate the interaction between H and 3d transition metal (TM) alloying atom in Ni-based alloy. H prefers the octahedral interstitial site to the tetrahedral interstitial site energetically. Most of the 3d TM elements (except Zn) attract H. The attraction to H in the Ni–TM–H system can be mainly attributed to the differences in electronegativity. With the large electronegativity, H and Ni gain electrons from the other TM elements, resulting in the enhanced Ni–H bonds which are the source of the attraction to H in the Ni–TM–H system. The obviously covalent-like Cr–H and Co–H bindings are also beneficial to the attraction to H. On the other hand, the repulsion to H in the Ni–Zn–H system is due to the stable electronic configuration of Zn. We mainly utilize the results calculated in 32-atom supercell which corresponds to the case of a relatively high concentration of hydrogen. Our results are in good agreement with the experimental ones.

  6. 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...

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

    Science.gov (United States)

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

    2016-01-01

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

  8. 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

  9. Atomic and plasma-material interaction data for fusion. V. 5

    International Nuclear Information System (INIS)

    1994-01-01

    Volume 5 of the supplements on ''atomic and plasma-material interaction data for fusion'' to the journal ''Nuclear Fusion'' is devoted to a critical assessment of the physical and thermo-mechanical properties of presently considered candidate plasma-facing and structural materials for next-generation thermonuclear fusion devices. It contains 9 papers. The subjects are: (i) requirements and selection criteria for plasma-facing materials and components in the ITER EDA (Engineering Design Activities) design; (ii) thermomechanical properties of Beryllium; (iii) material properties data for fusion reactor plasma-facing carbon-carbon composites; (iv) high-Z candidate plasma facing materials; (v) recommended property data for Molybdenum, Niobium and Vanadium alloys; (vi) copper alloys for high heat flux structure applications; (vii) erosion of plasma-facing materials during a tokamak disruption; (viii) runaway electron effects; and (ix) data bases for thermo-hydrodynamic coupling with coolants. Refs, figs, tabs

  10. Disentangling the co-structure of multilayer interaction networks: degree distribution and module composition in two-layer bipartite networks.

    Science.gov (United States)

    Astegiano, Julia; Altermatt, Florian; Massol, François

    2017-11-13

    Species establish different interactions (e.g. antagonistic, mutualistic) with multiple species, forming multilayer ecological networks. Disentangling network co-structure in multilayer networks is crucial to predict how biodiversity loss may affect the persistence of multispecies assemblages. Existing methods to analyse multilayer networks often fail to consider network co-structure. We present a new method to evaluate the modular co-structure of multilayer networks through the assessment of species degree co-distribution and network module composition. We focus on modular structure because of its high prevalence among ecological networks. We apply our method to two Lepidoptera-plant networks, one describing caterpillar-plant herbivory interactions and one representing adult Lepidoptera nectaring on flowers, thereby possibly pollinating them. More than 50% of the species established either herbivory or visitation interactions, but not both. These species were over-represented among plants and lepidopterans, and were present in most modules in both networks. Similarity in module composition between networks was high but not different from random expectations. Our method clearly delineates the importance of interpreting multilayer module composition similarity in the light of the constraints imposed by network structure to predict the potential indirect effects of species loss through interconnected modular networks.

  11. 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

  12. Pairwise additivity in the nuclear magnetic resonance interactions of atomic xenon.

    Science.gov (United States)

    Hanni, Matti; Lantto, Perttu; Vaara, Juha

    2009-04-14

    Nuclear magnetic resonance (NMR) of atomic (129/131)Xe is used as a versatile probe of the structure and dynamics of various host materials, due to the sensitivity of the Xe NMR parameters to intermolecular interactions. The principles governing this sensitivity can be investigated using the prototypic system of interacting Xe atoms. In the pairwise additive approximation (PAA), the binary NMR chemical shift, nuclear quadrupole coupling (NQC), and spin-rotation (SR) curves for the xenon dimer are utilized for fast and efficient evaluation of the corresponding NMR tensors in small xenon clusters Xe(n) (n = 2-12). If accurate, the preparametrized PAA enables the analysis of the NMR properties of xenon clusters, condensed xenon phases, and xenon gas without having to resort to electronic structure calculations of instantaneous configurations for n > 2. The binary parameters for Xe(2) at different internuclear distances were obtained at the nonrelativistic Hartree-Fock level of theory. Quantum-chemical (QC) calculations at the corresponding level were used to obtain the NMR parameters of the Xe(n) (n = 2-12) clusters at the equilibrium geometries. Comparison of PAA and QC data indicates that the direct use of the binary property curves of Xe(2) can be expected to be well-suited for the analysis of Xe NMR in the gaseous phase dominated by binary collisions. For use in condensed phases where many-body effects should be considered, effective binary property functions were fitted using the principal components of QC tensors from Xe(n) clusters. Particularly, the chemical shift in Xe(n) is strikingly well-described by the effective PAA. The coordination number Z of the Xe site is found to be the most important factor determining the chemical shift, with the largest shifts being found for high-symmetry sites with the largest Z. This is rationalized in terms of the density of virtual electronic states available for response to magnetic perturbations.

  13. Social Networking Sites as Communication, Interaction, and Learning Environments: Perceptions and Preferences of Distance Education Students

    Science.gov (United States)

    Bozkurt, Aras; Karadeniz, Abdulkadir; Kocdar, Serpil

    2017-01-01

    The advent of Web 2.0 technologies transformed online networks into interactive spaces in which user-generated content has become the core material. With the possibilities that emerged from Web 2.0, social networking sites became very popular. The capability of social networking sites promises opportunities for communication and interaction,…

  14. User-Centric Secure Cross-Site Interaction Framework for Online Social Networking Services

    Science.gov (United States)

    Ko, Moo Nam

    2011-01-01

    Social networking service is one of major technological phenomena on Web 2.0. Hundreds of millions of users are posting message, photos, and videos on their profiles and interacting with other users, but the sharing and interaction are limited within the same social networking site. Although users can share some content on a social networking site…

  15. Nanoparticle-nanoparticle interactions in biological media by Atomic Force Microscopy

    Science.gov (United States)

    Pyrgiotakis, Georgios; Blattmann, Christoph O.; Pratsinis, Sotiris; Demokritou, Philip

    2015-01-01

    Particle-particle interactions in physiological media are important determinants for nanoparticle fate and transport. Herein, such interactions are assessed by a novel Atomic Force Microscopy (AFM) based platform. Industry-relevant CeO2, Fe2O3, and SiO2 nanoparticles of various diameters were made by the flame spray pyrolysis (FSP) based Harvard Versatile Engineering Nanomaterials Generation System (Harvard VENGES). The nanoparticles were fully characterized structurally and morphologically and their properties in water and biological media were also assessed. The nanoparticles were attached on AFM tips and deposited on Si substrates to measure particle–particle interactions. The corresponding force was measured in air, water and biological media that are widely used in toxicological studies. The presented AFM based approach can be used to assess the agglomeration potential of nanoparticles in physiological fluids. The agglomeration potential of CeO2 nanoparticles in water and RPMI 1640 (Roswell Park Memorial Institute formulation 1640) was inversely proportional to their primary particle (PP) diameter, but for Fe2O3 nanoparticles, that potential is independent of PP diameter in these media. Moreover, in RPMI+10% Fetal Bovine Serum (FBS) the corona thickness and dispersibility of the CeO2 is independent of PP diameter while for Fe2O3, the corona thickness and dispersibility were inversely proportional to PP diameter. The present method can be combined with (dynamic light scattering (DLS), proteomics, and computer simulations to understand the nano-bio interactions, with emphasis on the agglomeration potential of nanoparticles and their transport in physiological media. PMID:23978039

  16. Atomic force imaging microscopy investigation of the interaction of ultraviolet radiation with collagen thin films

    Science.gov (United States)

    Stylianou, A.; Yova, D.; Alexandratou, E.; Petri, A.

    2013-02-01

    Collagen is the major fibrous protein in the extracellular matrix and consists a significant component of skin, bone, cartilage and tendon. Due to its unique properties, it has been widely used as scaffold or culture substrate for tissue regeneration or/and cell-substrate interaction studies. The ultraviolet light-collagen interaction investigations are crucial for the improvement of many applications such as that of the UV irradiation in the field of biomaterials, as sterilizing and photo-cross-linking method. The aim of this paper was to investigate the mechanisms of UV-collagen interactions by developing a collagen-based, well characterized, surface with controlled topography of collagen thin films in the nanoscale range. The methodology was to quantify the collagen surface modification induced on ultraviolet radiation and correlate it with changes induced in cells. Surface nanoscale characterization was performed by Atomic Force Microscopy (AFM) which is a powerful tool and offers quantitative and qualitative information with a non-destructive manner. In order to investigate cells behavior, the irradiated films were used for in vitro cultivation of human skin fibroblasts and the cells morphology, migration and alignment were assessed with fluorescence microscopy imaging and image processing methods. The clarification of the effects of UV light on collagen thin films and the way of cells behavior to the different modifications that UV induced to the collagen-based surfaces will contribute to the better understanding of cell-matrix interactions in the nanoscale and will assist the appropriate use of UV light for developing biomaterials.

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

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Lijin; Guan, Pengfei, E-mail: pguan@csrc.ac.cn [Beijing Computational Science Research Center, Beijing 100193 (China); Wang, W. H. [Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China)

    2016-07-21

    The fragility that controls the temperature-dependent viscous properties of liquids as the glass transition is approached, in various glass-forming liquids with different softness of the repulsive part of atomic interactions at different densities, is investigated by molecular dynamic simulations. We show that the landscape of fragility in purely repulsive systems can be separated into three regions denoted as R{sub I,} R{sub II}, and R{sub III}, respectively, with qualitatively disparate dynamic behaviors: R{sub I} which can be described by “softness makes strong glasses,” R{sub II} where fragility is independent of softness and can only be tuned by density, and R{sub III} with constant fragility, suggesting that density plays an unexpected role for understanding the repulsive softness dependence of fragility. What is more important is that we unify the long-standing inconsistence with respect to the repulsive softness dependence of fragility by observing that a glass former can be tuned more fragile if nonperturbative attraction is added into it. Moreover, we find that the vastly dissimilar influences of attractive interaction on fragility could be estimated from the structural properties of related zero-temperature glasses.

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

    International Nuclear Information System (INIS)

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

    2016-01-01

    The fragility that controls the temperature-dependent viscous properties of liquids as the glass transition is approached, in various glass-forming liquids with different softness of the repulsive part of atomic interactions at different densities, is investigated by molecular dynamic simulations. We show that the landscape of fragility in purely repulsive systems can be separated into three regions denoted as R I, R II , and R III , respectively, with qualitatively disparate dynamic behaviors: R I which can be described by “softness makes strong glasses,” R II where fragility is independent of softness and can only be tuned by density, and R III with constant fragility, suggesting that density plays an unexpected role for understanding the repulsive softness dependence of fragility. What is more important is that we unify the long-standing inconsistence with respect to the repulsive softness dependence of fragility by observing that a glass former can be tuned more fragile if nonperturbative attraction is added into it. Moreover, we find that the vastly dissimilar influences of attractive interaction on fragility could be estimated from the structural properties of related zero-temperature glasses.

  20. Emerging bosons with three-body interactions from spin-1 atoms in optical lattices

    International Nuclear Information System (INIS)

    Mazza, L.; Rizzi, M.; Cirac, J. I.; Lewenstein, M.

    2010-01-01

    We study two many-body systems of bosons interacting via an infinite three-body contact repulsion in a lattice: a pairs quasicondensate induced by correlated hopping and the discrete version of the Pfaffian wave function. We propose to experimentally realize systems characterized by such interaction by means of a proper spin-1 lattice Hamiltonian: spin degrees of freedom are locally mapped into occupation numbers of emerging bosons, in a fashion similar to spin-1/2 and hardcore bosons. Such a system can be realized with ultracold spin-1 atoms in a Mott insulator with a filling factor of 1. The high versatility of these setups allows us to engineer spin-hopping operators breaking the SU(2) symmetry, as needed to approximate interesting bosonic Hamiltonians with three-body hardcore constraint. For this purpose we combine bichromatic spin-independent superlattices and Raman transitions to induce a different hopping rate for each spin orientation. Finally, we illustrate how our setup could be used to experimentally realize the first setup, that is, the transition to a pairs quasicondensed phase of the emerging bosons. We also report on a route toward the realization of a discrete bosonic Pfaffian wave function and list some open problems for reaching this goal.

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

    Science.gov (United States)

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

    2016-07-21

    The fragility that controls the temperature-dependent viscous properties of liquids as the glass transition is approached, in various glass-forming liquids with different softness of the repulsive part of atomic interactions at different densities, is investigated by molecular dynamic simulations. We show that the landscape of fragility in purely repulsive systems can be separated into three regions denoted as RI, RII, and RIII, respectively, with qualitatively disparate dynamic behaviors: RI which can be described by "softness makes strong glasses," RII where fragility is independent of softness and can only be tuned by density, and RIII with constant fragility, suggesting that density plays an unexpected role for understanding the repulsive softness dependence of fragility. What is more important is that we unify the long-standing inconsistence with respect to the repulsive softness dependence of fragility by observing that a glass former can be tuned more fragile if nonperturbative attraction is added into it. Moreover, we find that the vastly dissimilar influences of attractive interaction on fragility could be estimated from the structural properties of related zero-temperature glasses.

  2. 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. Published by Elsevier Inc.

  3. 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

  4. NatalieQ: A web server for protein-protein interaction network querying

    NARCIS (Netherlands)

    El-Kebir, M.; Brandt, B.W.; Heringa, J.; Klau, G.W.

    2014-01-01

    Background Molecular interactions need to be taken into account to adequately model the complex behavior of biological systems. These interactions are captured by various types of biological networks, such as metabolic, gene-regulatory, signal transduction and protein-protein interaction networks.

  5. Cancer risk at low doses of ionizing radiation. Artificial neural networks inference from atomic bomb survivors

    International Nuclear Information System (INIS)

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

    2014-01-01

    Cancer risk at low doses of ionizing radiation remains poorly defined because of ambiguity in the quantitative link to doses below 0.2 Sv in atomic bomb survivors in Hiroshima and Nagasaki arising from limitations in the statistical power and information available on overall radiation dose. To deal with these difficulties, a novel nonparametric statistics based on the ‘integrate-and-fire’ algorithm of artificial neural networks was developed and tested in cancer databases established by the Radiation Effects Research Foundation. The analysis revealed unique features at low doses that could not be accounted for by nominal exposure dose, including (1) the presence of a threshold that varied with organ, gender and age at exposure, and (2) 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. (author)

  6. 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%.

  7. 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.

  8. Specialization of mutualistic interaction networks decreases toward tropical latitudes

    DEFF Research Database (Denmark)

    Schleuning, M.; Fründ, J.; Klein, A.-M.

    2012-01-01

    that current conditions have a stronger effect on biotic specialization than historical community stability. Biotic specialization decreased with increasing local and regional plant diversity. This suggests that high specialization of mutualistic interactions is a response of pollinators and seed dispersers......] or differences in plant diversity [10, 11]. Thus, the direction of the latitudinal specialization gradient remains contentious. With an unprecedented global data set, we investigated how biotic specialization between plants and animal pollinators or seed dispersers is associated with latitude, past...... and contemporary climate, and plant diversity. We show that in contrast to expectation, biotic specialization of mutualistic networks is significantly lower at tropical than at temperate latitudes. Specialization was more closely related to contemporary climate than to past climate stability, suggesting...

  9. Co-creating value through agents interaction within service network

    Energy Technology Data Exchange (ETDEWEB)

    Okdinawati, L.; Simatupang, T.M.; Sunitiyoso, Y.

    2017-07-01

    The purpose of this paper is to gives further understanding on value co-creation mechanisms in B-to-B service network by reinforcing the processes, the relationships, and influences of other agents where Collaborative Transportation Management (CTM) forms might be best employed. Design/methodology/approach: In order to model the interactions among agents in the collaboration processes and the value co-creation processes, this research used three collaboration cases in Indonesia. Then, the agent-based simulation was used to capture both the collaboration process and the value co-creation process of the three collaboration cases. Findings: The interactions among the agents both inside and outside their collaboration environment determined agent’s role as a value co-creator. The willingness of an agent to accept the opinion of another agent determined the degree of their willingness to co-operate and to change their strategies, and perceptions. Therefore, influenced the size of the value obtained by them in each collaboration process. Research limitations/implications: The findings of the simulations subject to assumptions based on the collaboration cases. Further research is related to how to encourage agents to co-operate and adjust their perceptions. Practical implications: It is crucial for the practitioners to interact with another agent both inside and outside their collaboration environment. The opinions of another agent inside the collaboration environment also need to be considered. Originality/value: This research is derived from its emphasis on how a value is co-created by reinforcing both the collaborative processes and the interactions among agents as well as on how CTM might be best employed.

  10. Co-creating value through agents interaction within service network

    International Nuclear Information System (INIS)

    Okdinawati, L.; Simatupang, T.M.; Sunitiyoso, Y.

    2017-01-01

    The purpose of this paper is to gives further understanding on value co-creation mechanisms in B-to-B service network by reinforcing the processes, the relationships, and influences of other agents where Collaborative Transportation Management (CTM) forms might be best employed. Design/methodology/approach: In order to model the interactions among agents in the collaboration processes and the value co-creation processes, this research used three collaboration cases in Indonesia. Then, the agent-based simulation was used to capture both the collaboration process and the value co-creation process of the three collaboration cases. Findings: The interactions among the agents both inside and outside their collaboration environment determined agent’s role as a value co-creator. The willingness of an agent to accept the opinion of another agent determined the degree of their willingness to co-operate and to change their strategies, and perceptions. Therefore, influenced the size of the value obtained by them in each collaboration process. Research limitations/implications: The findings of the simulations subject to assumptions based on the collaboration cases. Further research is related to how to encourage agents to co-operate and adjust their perceptions. Practical implications: It is crucial for the practitioners to interact with another agent both inside and outside their collaboration environment. The opinions of another agent inside the collaboration environment also need to be considered. Originality/value: This research is derived from its emphasis on how a value is co-created by reinforcing both the collaborative processes and the interactions among agents as well as on how CTM might be best employed.

  11. Pleistocene megafaunal interaction networks became more vulnerable after human arrival.

    Science.gov (United States)

    Pires, Mathias M; Koch, Paul L; Fariña, Richard A; de Aguiar, Marcus A M; dos Reis, Sérgio F; Guimarães, Paulo R

    2015-09-07

    The end of the Pleistocene was marked by the extinction of almost all large land mammals worldwide except in Africa. Although the debate on Pleistocene extinctions has focused on the roles of climate change and humans, the impact of perturbations depends on properties of ecological communities, such as species composition and the organization of ecological interactions. Here, we combined palaeoecological and ecological data, food-web models and community stability analysis to investigate if differences between Pleistocene and modern mammalian assemblages help us understand why the megafauna died out in the Americas while persisting in Africa. We show Pleistocene and modern assemblages share similar network topology, but differences in richness and body size distributions made Pleistocene communities significantly more vulnerable to the effects of human arrival. The structural changes promoted by humans in Pleistocene networks would have increased the likelihood of unstable dynamics, which may favour extinction cascades in communities facing extrinsic perturbations. Our findings suggest that the basic aspects of the organization of ecological communities may have played an important role in major extinction events in the past. Knowledge of community-level properties and their consequences to dynamics may be critical to understand past and future extinctions. © 2015 The Author(s).

  12. CombiMotif: A new algorithm for network motifs discovery in protein-protein interaction networks

    Science.gov (United States)

    Luo, Jiawei; Li, Guanghui; Song, Dan; Liang, Cheng

    2014-12-01

    Discovering motifs in protein-protein interaction networks is becoming a current major challenge in computational biology, since the distribution of the number of network motifs can reveal significant systemic differences among species. However, this task can be computationally expensive because of the involvement of graph isomorphic detection. In this paper, we present a new algorithm (CombiMotif) that incorporates combinatorial techniques to count non-induced occurrences of subgraph topologies in the form of trees. The efficiency of our algorithm is demonstrated by comparing the obtained results with the current state-of-the art subgraph counting algorithms. We also show major differences between unicellular and multicellular organisms. The datasets and source code of CombiMotif are freely available upon request.

  13. Dynamics of entanglement of a three-level atom in motion interacting with two coupled modes including parametric down conversion

    Science.gov (United States)

    Faghihi, M. J.; Tavassoly, M. K.; Hatami, M.

    In this paper, a model by which we study the interaction between a motional three-level atom and two-mode field injected simultaneously in a bichromatic cavity is considered; the three-level atom is assumed to be in a Λ-type configuration. As a result, the atom-field and the field-field interaction (parametric down conversion) will be appeared. It is shown that, by applying a canonical transformation, the introduced model can be reduced to a well-known form of the generalized Jaynes-Cummings model. Under particular initial conditions, which may be prepared for the atom and the field, the time evolution of state vector of the entire system is analytically evaluated. Then, the dynamics of atom by considering ‘atomic population inversion’ and two different measures of entanglement, i.e., ‘von Neumann entropy’ and ‘idempotency defect’ is discussed, in detail. It is deduced from the numerical results that, the duration and the maximum amount of the considered physical quantities can be suitably tuned by selecting the proper field-mode structure parameter p and the detuning parameters.

  14. Interaction between interstitial atoms and 1/2 (110) edge dislocations, and its influence on the Peierls stress

    International Nuclear Information System (INIS)

    de Hosson, J.T.M.

    1976-01-01

    The positions of the metal atoms around a 1 / 2 (111) (110) edge dislocation in Mo and W are calculated using the Wilson-Johnson potentials. The boundary conditions are given by anisotropic elasticity theory. After the lattices have been relaxed the potential energy of a He atom was calculated for a grid of positions within a block around the dislocation core, which extends over six planes in the (112) direction. The He-metal potential, also developed by Johnson and Wilson was used to calculate the position with maximum energy gain for a He atom. The binding energies of the He atom in the dislocated lattice for Mo and W were 1.55 eV and 1.53 eV, respectively. The second part of the investigation concerns the Peierls stresses for a 1 / 2 (111) (110) edge dislocation in α-Fe, with and without a carbon atom. The Peierls energy and stress are calculated for this slip-system based on the method originally used by Nabarro. The Peierls stresses (at zero absolute temperature) for the lattice with and without a carbon atom, are 0.006 μ and 0.009 μ, respectively. These calculations were carried out utilizing the Wilson-Johnson potential for the Fe-Fe interaction and the Johnson potential was used for the Fe-C interaction

  15. Interaction of epitaxial silicene with overlayers formed by exposure to Al atoms and O{sub 2} molecules

    Energy Technology Data Exchange (ETDEWEB)

    Friedlein, R.; Yamada-Takamura, Y. [Japan Advanced Institute of Science and Technology, School of Materials Science, Nomi, Ishikawa 923-1292 (Japan); Van Bui, H.; Wiggers, F. B.; Kovalgin, A. Y.; Jong, M. P. de, E-mail: M.P.deJong@utwente.nl [MESA Institute for Nanotechnology, University of Twente, 7500 AE Enschede (Netherlands)

    2014-05-28

    As silicene is not chemically inert, the study and exploitation of its electronic properties outside of ultrahigh vacuum environments require the use of insulating capping layers. In order to understand if aluminum oxide might be a suitable encapsulation material, we used high-resolution synchrotron photoelectron spectroscopy to study the interactions of Al atoms and O{sub 2} molecules, as well as the combination of both, with epitaxial silicene on thin ZrB{sub 2}(0001) films grown on Si(111). The deposition of Al atoms onto silicene, up to the coverage of about 0.4 Al per Si atoms, has little effect on the chemical state of the Si atoms. The silicene-terminated surface is also hardly affected by exposure to O{sub 2} gas, up to a dose of 4500 L. In contrast, when Al-covered silicene is exposed to the same dose, a large fraction of the Si atoms becomes oxidized. This is attributed to dissociative chemisorption of O{sub 2} molecules by Al atoms at the surface, producing reactive atomic oxygen species that cause the oxidation. It is concluded that aluminum oxide overlayers prepared in this fashion are not suitable for encapsulation since they do not prevent but actually enhance the degradation of silicene.

  16. Simulation of multi-atomic interactions in H-O-W system with the MD code CADAC

    International Nuclear Information System (INIS)

    Landman, I.S.

    2005-01-01

    For future tokamak reactors, chemical erosion of tungsten armour surfaces under impact of hot deuterium-tritium plasma that contains impurities, for instance oxygen, is an important issue. Oxygen can form volatile molecular complexes O x W y at the surface, and the retained H-atoms form the volatile complexes H x O y , which mitigates the erosion (H states for hydrogen isotopes). The plasma impact can substantially destroy the complexes. To describe this H-O-W system, the molecular dynamics (MD) code CADAC was earlier developed using only pair-atomic interactions. Now CADAC is extended for multi-body forces to simulate molecular organization of atoms near the tungsten surface. The approach uses the Abell's model of empirical bond-order potentials in addition combined, for the first time, with a valence concept. CADAC simulates chemical features using atomic valences and the Morse potentials. The new model is introduced and model parameters are estimated

  17. Constraints on T-odd and P-even hadronic interactions from nucleon, nuclear, and atomic electric dipole moments

    International Nuclear Information System (INIS)

    Haxton, W.C.; Hoering, A.; Musolf, M.J.; Old Dominion Univ., Norfolk, VA

    1994-01-01

    We deduce constraints on time-reversal-noninvariant (TRNI), parity-conserving (PC) hadronic interactions from nucleon, nuclear, and atomic electric dipole moment (edm) limits. Such interactions generate edm's through weak radiative corrections. We consider long-ranged mechanisms, i.e., those mediated by meson exchanges in contrast to short-range two-loop mechanisms. We find that the ratio of typical TRNI. PC nuclear matrix elements to those of the strong interaction are approx-lt 10 -5 , a limit about two orders of magnitude more stringent than those from direct detailed balance studies of such interactions

  18. 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.

  19. 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.

  20. Dynamics of bad-cavity-enhanced interaction with cold Sr atoms for laser stabilization

    DEFF Research Database (Denmark)

    Schäffer, S. A.; Christensen, B. T.R.; Henriksen, M. R.

    2017-01-01

    Hybrid systems of cold atoms and optical cavities are promising systems for increasing the stability of laser oscillators used in quantum metrology and atomic clocks. In this paper we map out the atom-cavity dynamics in such a system and demonstrate limitations as well as robustness of the approach....... We investigate the phase response of an ensemble of cold Sr88 atoms inside an optical cavity for use as an error signal in laser frequency stabilization. With this system we realize a regime where the high atomic phase shift limits the dynamical locking range. The limitation is caused by the cavity...

  1. 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 (InWeb_InBioMap,......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...

  2. Quantum state detection and state preparation based on cavity-enhanced nonlinear interaction of atoms with single photon

    Science.gov (United States)

    Hosseini, Mahdi

    Our ability to engineer quantum states of light and matter has significantly advanced over the past two decades, resulting in the production of both Gaussian and non-Gaussian optical states. The resulting tailored quantum states enable quantum technologies such as quantum optical communication, quantum sensing as well as quantum photonic computation. The strong nonlinear light-atom interaction is the key to deterministic quantum state preparation and quantum photonic processing. One route to enhancing the usually weak nonlinear light-atom interactions is to approach the regime of cavity quantum electrodynamics (cQED) interaction by means of high finesse optical resonators. I present results from the MIT experiment of large conditional cross-phase modulation between a signal photon, stored inside an atomic quantum memory, and a control photon that traverses a high-finesse optical cavity containing the atomic memory. I also present a scheme to probabilistically change the amplitude and phase of a signal photon qubit to, in principle, arbitrary values by postselection on a control photon that has interacted with that state. Notably, small changes of the control photon polarization measurement basis by few degrees can substantially change the amplitude and phase of the signal state. Finally, I present our ongoing effort at Purdue to realize similar peculiar quantum phenomena at the single photon level on chip scale photonic systems.

  3. Open quantum systems and the two-level atom interacting with a single mode of the electromagnetic field

    International Nuclear Information System (INIS)

    Sandulescu, A.; Stefanescu, E.

    1987-07-01

    On the basis of Lindblad theory of open quantum systems we obtain new optical equations for the system of two-level atom interacting with a single mode of the electromagnetic field. The conventional Block equations in a generalized form with field phases are obtained in the hypothesis that all the terms are slowly varying in the rotating frame.(authors)

  4. 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…

  5. Differential MS2 Interaction with Food Contact Surfaces Determined by Atomic Force Microscopy and Virus Recovery.

    Science.gov (United States)

    Shim, J; Stewart, D S; Nikolov, A D; Wasan, D T; Wang, R; Yan, R; Shieh, Y C

    2017-12-15

    Enteric viruses are recognized as major etiologies of U.S. foodborne infections. These viruses are easily transmitted via food contact surfaces. Understanding virus interactions with surfaces may facilitate the development of improved means for their removal, thus reducing transmission. Using MS2 coliphage as a virus surrogate, the strength of virus adhesion to common food processing and preparation surfaces of polyvinyl chloride (PVC) and glass was assessed by atomic force microscopy (AFM) and virus recovery assays. The interaction forces of MS2 with various surfaces were measured from adhesion peaks in force-distance curves registered using a spherical bead probe preconjugated with MS2 particles. MS2 in phosphate-buffered saline (PBS) demonstrated approximately 5 times less adhesion force to glass (0.54 nN) than to PVC (2.87 nN) ( P force for PVC (∼0 nN) and consistently increased virus recovery by 19%. With direct and indirect evidence of virus adhesion, this study illustrated a two-way assessment of virus adhesion for the initial evaluation of potential means to mitigate virus adhesion to food contact surfaces. IMPORTANCE The spread of foodborne viruses is likely associated with their adhesive nature. Virus attachment on food contact surfaces has been evaluated by quantitating virus recoveries from inoculated surfaces. This study aimed to evaluate the microenvironment in which nanometer-sized viruses interact with food contact surfaces and to compare the virus adhesion differences using AFM. The virus surrogate MS2 demonstrated less adhesion force to glass than to PVC via AFM, with the force-contributing factors including the intrinsic nature and the topography of the contact surfaces. This adhesion finding is consistent with the virus recoveries, which were determined indirectly. Greater numbers of viruses were recovered from glass than from PVC, after application at the same levels. The stronger MS2 adhesion onto PVC could be interrupted by incorporating a

  6. Exchange and Dzyaloshinskii-Moriya interactions in bulk FeGe: Effects of atomic vacancies

    Science.gov (United States)

    Loh, G. C.; Gan, C. K.

    2017-05-01

    We examine the effects of atomic vacancies on the (1) spin interaction, and (2) electronic character in the cubic B20 chiral magnet FeGe. For the former, Heisenberg exchange and Dzyaloshinskii-Moriya (DM) interactions are studied. The latter is done via a particular Wannier flavor of the Hamiltonian in the form of maximally-localized Wannier functions (MLWFs). Using first-principles calculations based on full-potential linearized augmented plane-wave (FLAPW)-based density functional theory (DFT), the spin order of bulk FeGe, in its pristine form, and with a Fe (Fe75%Ge100%) or Ge vacancy (Fe100%Ge75%) is investigated. Despite the presence of vacancies, the ground state of FeGe remains helimagnetic, i.e. spin spirals in FeGe are fairly robust. The energetic stability of FeGe increases in the presence of the vacancies. The spiral size is increased by approximately 40%, suggesting that vacancies can be introduced to manipulate the chiral order. The vacancies lift the band degeneracy in the valence manifold of the Wannier-interpolated band structures. Only the spin-down Fermi surfaces are substantially different between the pristine and defective FeGe; it is electron-like in the pristine case, but largely hole-like in the defective ones. The Ge vacancy splits the Fermi surface more than the Fe vacancy. The Heisenberg exchange between nearest Fe pairs is ferromagnetic in pristine FeGe. This Fe-Fe interaction remains ferromagnetic, albeit a slight decrease in strength, in the presence of a Fe vacancy. In contrast, a Ge vacancy in FeGe induces anti-ferromagnetism between nearest Fe pairs. By including spin-orbit coupling effects, we find that the DM interaction of defective FeGe is reversed in sign, and it is more uniform in strength along the three highly symmetric directions, relative to that in pristine FeGe. All in all, the versatility of FeGe makes it an excellent functional material, especially in data storage and spintronics applications.

  7. Stimulated cold fusion by positronium atoms, cross sections, and wall interactions in plasmas, used to diagnostics

    International Nuclear Information System (INIS)

    Emami, Z.

    2005-01-01

    Because of the technical complexities, involved in the controlled thermonuclear, reactions, a simple vicegerent agent cold plasma, stimulated by positronium atoms (achieved through a ring storage) as stimulus, introduced by this author in ITC 12 conference. In the present paper, the interaction between γ rays emitted through positronium atoms annihilation (in the forms of doublet and triplet electromagnetic photonic radiation) with plasma particles (including electrons, ions and neutral particles) investigated. Proper lifetime of singlet γ rays τs are about 100 ns and from that of triplet γ rays, i.e τt about 100 fems, reside in the following transition times in Ne and Argon elements in He-Ne and Ar lasers respectively: Ne*(3S2) [transition time τ = 105 ns] -> Ne*(2P4); Ar+*(3P4 4S) [transition time τ = 105 fems] -> Ar+(3P5). Then the interactions of γ rays with mater in plasma could follow up as treated from that of the laser and mater in one extreme while the comparison of this situation with normal plasmas in other extreme could serve as diagnostics key role in magnetically confined plasmas reactors. Collisions between charge and neutral species in plasma with electromagnetic radiation (γ photonic radiation) including the energy loss and scattering lead to different consequences. Light electrons can take up appreciably amounts of energy from the incident rays, lead to heating cold plasma, whereas massive ions absorb very little energy. Thus loss of incident energy in radiation occurs almost entirely in collisions with electrons , which, referred to the γ rays energy this would led to plasma heating about thermonuclear reaction ( Eγ = hν = 0.5 MeV). The heavy ions and neutral species in interaction with electromagnetic γ radiation, result on the other hand in scattering, in turn may increase the ionization level of the cold plasma, toward fully ionized plasma. Although all the essential features of these different interaction cross sections deduced

  8. Second meeting of the Atomic and Molecular Data Centre network. Fontenay aux Roses, 23-24 May 1980

    International Nuclear Information System (INIS)

    Katsonis, K.

    1980-11-01

    Summary report of the Second A+M Data Centre Network (DCN) meeting convened by the IAEA Nuclear Data Section at the CEA Laboratory at Fontenay-aux-Roses, France, 23-24 May 1980. The meeting was attended by 20 representatives from centres and groups from six Member States concerned with the coordinated international management of atomic and molecular data pertinent to controlled fusion research and technology

  9. Interrogating the architecture of protein assemblies and protein interaction networks by cross-linking mass spectrometry

    NARCIS (Netherlands)

    Liu, Fan; Heck, Albert J R

    2015-01-01

    Proteins are involved in almost all processes of the living cell. They are organized through extensive networks of interaction, by tightly bound macromolecular assemblies or more transiently via signaling nodes. Therefore, revealing the architecture of protein complexes and protein interaction

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

    International Nuclear Information System (INIS)

    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 βE 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 Δ/sub M/ = -2M/(BETAE). It is used to calibrate the analyzing efficiency. The polarization due to epsilon/sub P/ is Δ/sub P/ = 2i epsilon/sub P//(βE), and can be distinguished from Δ/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

  11. 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.

  12. Electron correlation in the interacting quantum atoms partition via coupled-cluster lagrangian densities.

    Science.gov (United States)

    Holguín-Gallego, Fernando José; Chávez-Calvillo, Rodrigo; García-Revilla, Marco; Francisco, Evelio; Pendás, Ángel Martín; Rocha-Rinza, Tomás

    2016-07-15

    The electronic energy partition established by the Interacting Quantum Atoms (IQA) approach is an important method of wavefunction analyses which has yielded valuable insights about different phenomena in physical chemistry. Most of the IQA applications have relied upon approximations, which do not include either dynamical correlation (DC) such as Hartree-Fock (HF) or external DC like CASSCF theory. Recently, DC was included in the IQA method by means of HF/Coupled-Cluster (CC) transition densities (Chávez-Calvillo et al., Comput. Theory Chem. 2015, 1053, 90). Despite the potential utility of this approach, it has a few drawbacks, for example, it is not consistent with the calculation of CC properties different from the total electronic energy. To improve this situation, we have implemented the IQA energy partition based on CC Lagrangian one- and two-electron orbital density matrices. The development presented in this article is tested and illustrated with the H2 , LiH, H2 O, H2 S, N2 , and CO molecules for which the IQA results obtained under the consideration of (i) the CC Lagrangian, (ii) HF/CC transition densities, and (iii) HF are critically analyzed and compared. Additionally, the effect of the DC in the different components of the electronic energy in the formation of the T-shaped (H2 )2 van der Waals cluster and the bimolecular nucleophilic substitution between F(-) and CH3 F is examined. We anticipate that the approach put forward in this article will provide new understandings on subjects in physical chemistry wherein DC plays a crucial role like molecular interactions along with chemical bonding and reactivity. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  13. Adsorption of Cu, Ag, and Au atoms on graphene including van der Waals interactions

    International Nuclear Information System (INIS)

    Amft, Martin; Eriksson, Olle; Skorodumova, Natalia V; Lebegue, Sebastien

    2011-01-01

    We performed a systematic density functional (DF) study of the adsorption of copper, silver, and gold adatoms on pristine graphene, especially accounting for van der Waals (vdW) interactions by the vdW-DF and PBE + D2 methods. In particular, we analyze the preferred adsorption site (among top, bridge, and hollow positions) together with the corresponding distortion of the graphene sheet and identify diffusion paths. Both vdW schemes show that the coinage metal atoms do bind to the graphene sheet and that in some cases the buckling of the graphene layer can be significant. Only the results for silver are qualitatively at variance with those obtained with the generalized gradient approximation, which gives no binding in this case. However in all three cases, we observe some quantitative differences between the vdW-DF and PBE + D2 methods. For instance the adsorption energies calculated with the PBE + D2 method are systematically higher than the ones obtained with vdW-DF. Moreover, the equilibrium distances computed with PBE + D2 are shorter than those calculated with the vdW-DF method. (paper)

  14. Predicting Ligand Binding Sites on Protein Surfaces by 3-Dimensional Probability Density Distributions of Interacting Atoms

    Science.gov (United States)

    Jian, Jhih-Wei; Elumalai, Pavadai; Pitti, Thejkiran; Wu, Chih Yuan; Tsai, Keng-Chang; Chang, Jeng-Yih; Peng, Hung-Pin; Yang, An-Suei

    2016-01-01

    Predicting ligand binding sites (LBSs) on protein structures, which are obtained either from experimental or computational methods, is a useful first step in functional annotation or structure-based drug design for the protein structures. In this work, the structure-based machine learning algorithm ISMBLab-LIG was developed to predict LBSs on protein surfaces with input attributes derived from the three-dimensional probability density maps of interacting atoms, which were reconstructed on the query protein surfaces and were relatively insensitive to local conformational variations of the tentative ligand binding sites. The prediction accuracy of the ISMBLab-LIG predictors is comparable to that of the best LBS predictors benchmarked on several well-established testing datasets. More importantly, the ISMBLab-LIG algorithm has substantial tolerance to the prediction uncertainties of computationally derived protein structure models. As such, the method is particularly useful for predicting LBSs not only on experimental protein structures without known LBS templates in the database but also on computationally predicted model protein structures with structural uncertainties in the tentative ligand binding sites. PMID:27513851

  15. Magnetic properties of point defect interaction with impurity atoms in Fe-Cr alloys

    Science.gov (United States)

    Nguyen-Manh, D.; Lavrentiev, M. Yu.; Dudarev, S. L.

    2009-04-01

    An integrated ab initio and statistical Monte Carlo investigation has been recently carried out to model the thermodynamic and kinetic properties of Fe-Cr alloys. We found that the conventional Fe-Cr phase diagram is not adequate at low temperature region where the magnetic contribution to the free energy plays an important role in the prediction of an ordered Fe 15Cr phase and its negative enthalpy of formation. The origin of the anomalous thermodynamic and magnetic properties of Fe-Cr alloys can be understood using a tight-binding Stoner model combined with the charge neutrality condition. We investigate the environmental dependence of magnetic moment distributions for various self-interstitial atom dumbbells configurations using spin density maps found using density functional theory calculations. The mixed dumbbell Fe-Cr and Fe-Mn binding energies are found to be positive due to magnetic interactions. Finally, we discuss the relationship between the migration energy of vacancy in Fe-Cr alloys and magnetism at the saddle point configuration.

  16. Weighted Protein Interaction Network Analysis of Frontotemporal Dementia.

    Science.gov (United States)

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

    2017-02-03

    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 interaction network analysis (W-PPI-NA), to highlight key functional players within relevant biological processes associated with a given trait. This is exemplified in the current study by applying W-PPI-NA to frontotemporal dementia (FTD): We first built the state of the art FTD protein network (FTD-PN) and then analyzed both its topological and functional features. The FTD-PN resulted from the sum of the individual interactomes built around FTD-spectrum genes, leading to a total of 4198 nodes. Twenty nine of 4198 nodes, called inter-interactome hubs (IIHs), represented those interactors able to bridge over 60% of the individual interactomes. Functional annotation analysis not only reiterated and reinforced previous findings from single genes and gene-coexpression analyses but also indicated a number of novel potential disease related mechanisms, including DNA damage response, gene expression regulation, and cell waste disposal and potential biomarkers or therapeutic targets including EP300. These processes and targets likely represent the functional core impacted in FTD, reflecting the underlying genetic architecture contributing to disease. The approach presented in this study can be applied to other complex traits for which risk-causative genes are known as it provides a promising tool for setting the foundations for collating genomics and wet laboratory data in a bidirectional manner. This is and will be critical to accelerate molecular target prioritization and drug discovery.

  17. Topology-function conservation in protein-protein interaction networks.

    Science.gov (United States)

    Davis, Darren; Yaveroğlu, Ömer Nebil; Malod-Dognin, Noël; Stojmirovic, Aleksandar; Pržulj, Nataša

    2015-05-15

    Proteins underlay the functioning of a cell and the wiring of proteins in protein-protein interaction network (PIN) relates to their biological functions. Proteins with similar wiring in the PIN (topology around them) have been shown to have similar functions. This property has been successfully exploited for predicting protein functions. Topological similarity is also used to guide network alignment algorithms that find similarly wired proteins between PINs of different species; these similarities are used to transfer annotation across PINs, e.g. from model organisms to human. To refine these functional predictions and annotation transfers, we need to gain insight into the variability of the topology-function relationships. For example, a function may be significantly associated with specific topologies, while another function may be weakly associated with several different topologies. Also, the topology-function relationships may differ between different species. To improve our understanding of topology-function relationships and of their conservation among species, we develop a statistical framework that is built upon canonical correlation analysis. Using the graphlet degrees to represent the wiring around proteins in PINs and gene ontology (GO) annotations to describe their functions, our framework: (i) characterizes statistically significant topology-function relationships in a given species, and (ii) uncovers the functions that have conserved topology in PINs of different species, which we term topologically orthologous functions. We apply our framework to PINs of yeast and human, identifying seven biological process and two cellular component GO terms to be topologically orthologous for the two organisms. © The Author 2015. Published by Oxford University Press.

  18. Topology and weights in a protein domain interaction network--a novel way to predict protein interactions.

    Science.gov (United States)

    Wuchty, Stefan

    2006-05-23

    While the analysis of unweighted biological webs as diverse as genetic, protein and metabolic networks allowed spectacular insights in the inner workings of a cell, biological networks are not only determined by their static grid of links. In fact, we expect that the heterogeneity in the utilization of connections has a major impact on the organization of cellular activities as well. We consider a web of interactions between protein domains of the Protein Family database (PFAM), which are weighted by a probability score. We apply metrics that combine the static layout and the weights of the underlying interactions. We observe that unweighted measures as well as their weighted counterparts largely share the same trends in the underlying domain interaction network. However, we only find weak signals that weights and the static grid of interactions are connected entities. Therefore assuming that a protein interaction is governed by a single domain interaction, we observe strong and significant correlations of the highest scoring domain interaction and the confidence of protein interactions in the underlying interactions of yeast and fly. Modeling an interaction between proteins if we find a high scoring protein domain interaction we obtain 1, 428 protein interactions among 361 proteins in the human malaria parasite Plasmodium falciparum. Assessing their quality by a logistic regression method we observe that increasing confidence of predicted interactions is accompanied by high scoring domain interactions and elevated levels of functional similarity and evolutionary conservation. Our results indicate that probability scores are randomly distributed, allowing to treat static grid and weights of domain interactions as separate entities. In particular, these finding confirms earlier observations that a protein interaction is a matter of a single interaction event on domain level. As an immediate application, we show a simple way to predict potential protein interactions

  19. Topology and weights in a protein domain interaction network – a novel way to predict protein interactions

    Directory of Open Access Journals (Sweden)

    Wuchty Stefan

    2006-05-01

    Full Text Available Abstract Background While the analysis of unweighted biological webs as diverse as genetic, protein and metabolic networks allowed spectacular insights in the inner workings of a cell, biological networks are not only determined by their static grid of links. In fact, we expect that the heterogeneity in the utilization of connections has a major impact on the organization of cellular activities as well. Results We consider a web of interactions between protein domains of the Protein Family database (PFAM, which are weighted by a probability score. We apply metrics that combine the static layout and the weights of the underlying interactions. We observe that unweighted measures as well as their weighted counterparts largely share the same trends in the underlying domain interaction network. However, we only find weak signals that weights and the static grid of interactions are connected entities. Therefore assuming that a protein interaction is governed by a single domain interaction, we observe strong and significant correlations of the highest scoring domain interaction and the confidence of protein interactions in the underlying interactions of yeast and fly. Modeling an interaction between proteins if we find a high scoring protein domain interaction we obtain 1, 428 protein interactions among 361 proteins in the human malaria parasite Plasmodium falciparum. Assessing their quality by a logistic regression method we observe that increasing confidence of predicted interactions is accompanied by high scoring domain interactions and elevated levels of functional similarity and evolutionary conservation. Conclusion Our results indicate that probability scores are randomly distributed, allowing to treat static grid and weights of domain interactions as separate entities. In particular, these finding confirms earlier observations that a protein interaction is a matter of a single interaction event on domain level. As an immediate application, we

  20. Tripartite entanglement dynamics and entropic squeezing of a three-level atom interacting with a bimodal cavity field

    Science.gov (United States)

    Faghihi, M. J.; Tavassoly, M. K.; Bagheri Harouni, M.

    2014-04-01

    In this paper, we study the interaction between a Λ-type three-level atom and two quantized electromagnetic fields which are simultaneously injected in a bichromatic cavity surrounded by a Kerr medium in the presence of field-field interaction (parametric down conversion) and detuning parameters. By applying a canonical transformation, the introduced model is reduced to a well-known form of the generalized Jaynes-Cummings model. Under particular initial conditions which may be prepared for the atom and the field, the time evolution of the state vector of the entire system is analytically evaluated. Then, the dynamics of the atom is studied through the evolution of the atomic population inversion. In addition, two different measures of entanglement between the tripartite system (three entities make the system: two field modes and one atom), i.e., von Neumann and linear entropy are investigated. Also, two kinds of entropic uncertainty relations, from which entropy squeezing can be obtained, are discussed. In each case, the influences of the detuning parameters and Kerr medium on the above nonclassicality features are analyzed in detail via numerical results. It is illustrated that the amount of the above-mentioned physical phenomena can be tuned by choosing the evolved parameters, appropriately.

  1. Tripartite entanglement dynamics and entropic squeezing of a three-level atom interacting with a bimodal cavity field

    International Nuclear Information System (INIS)

    Faghihi, M J; Tavassoly, M K; Bagheri Harouni, M

    2014-01-01

    In this paper, we study the interaction between a Λ-type three-level atom and two quantized electromagnetic fields which are simultaneously injected in a bichromatic cavity surrounded by a Kerr medium in the presence of field–field interaction (parametric down conversion) and detuning parameters. By applying a canonical transformation, the introduced model is reduced to a well-known form of the generalized Jaynes–Cummings model. Under particular initial conditions which may be prepared for the atom and the field, the time evolution of the state vector of the entire system is analytically evaluated. Then, the dynamics of the atom is studied through the evolution of the atomic population inversion. In addition, two different measures of entanglement between the tripartite system (three entities make the system: two field modes and one atom), i.e., von Neumann and linear entropy are investigated. Also, two kinds of entropic uncertainty relations, from which entropy squeezing can be obtained, are discussed. In each case, the influences of the detuning parameters and Kerr medium on the above nonclassicality features are analyzed in detail via numerical results. It is illustrated that the amount of the above-mentioned physical phenomena can be tuned by choosing the evolved parameters, appropriately. (paper)

  2. A partitioned correlation function interaction approach for describing electron correlation in atoms

    International Nuclear Information System (INIS)

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

    2013-01-01

    The traditional multiconfiguration Hartree–Fock (MCHF) and configuration interaction (CI) methods are based on a single orthonormal orbital basis. For atoms with many closed core shells, or complicated shell structures, a large orbital basis is needed to saturate the different electron correlation effects such as valence, core–valence and correlation within the core shells. The large orbital basis leads to massive configuration state function (CSF) expansions that are difficult to handle, even on large computer systems. We show that it is possible to relax the orthonormality restriction on the orbital basis and break down the originally very large calculations into a series of smaller calculations 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 expansion coefficients of the PCFs are determined from a low dimensional generalized eigenvalue problem. The interaction and overlap matrices are computed using a biorthonormal transformation technique (Verdebout et al 2010 J. Phys. B: At. Mol. Phys. 43 074017). The new method, called partitioned correlation function interaction (PCFI), converges rapidly with respect to the orbital basis and gives total energies that are lower than the ones from ordinary MCHF and CI calculations. The PCFI method is also very flexible when it comes to targeting different electron correlation effects. Focusing our attention on neutral lithium, we show that by dedicating a PCF to the single excitations from the core, spin- and orbital-polarization effects can be captured very efficiently, leading to highly improved convergence patterns for hyperfine parameters compared with MCHF calculations based on a single orthogonal radial orbital basis. By collecting separately optimized PCFs to correct the

  3. A partitioned correlation function interaction approach for describing electron correlation in atoms

    Science.gov (United States)

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

    2013-04-01

    The traditional multiconfiguration Hartree-Fock (MCHF) and configuration interaction (CI) methods are based on a single orthonormal orbital basis. For atoms with many closed core shells, or complicated shell structures, a large orbital basis is needed to saturate the different electron correlation effects such as valence, core-valence and correlation within the core shells. The large orbital basis leads to massive configuration state function (CSF) expansions that are difficult to handle, even on large computer systems. We show that it is possible to relax the orthonormality restriction on the orbital basis and break down the originally very large calculations into a series of smaller calculations 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 expansion coefficients of the PCFs are determined from a low dimensional generalized eigenvalue problem. The interaction and overlap matrices are computed using a biorthonormal transformation technique (Verdebout et al 2010 J. Phys. B: At. Mol. Phys. 43 074017). The new method, called partitioned correlation function interaction (PCFI), converges rapidly with respect to the orbital basis and gives total energies that are lower than the ones from ordinary MCHF and CI calculations. The PCFI method is also very flexible when it comes to targeting different electron correlation effects. Focusing our attention on neutral lithium, we show that by dedicating a PCF to the single excitations from the core, spin- and orbital-polarization effects can be captured very efficiently, leading to highly improved convergence patterns for hyperfine parameters compared with MCHF calculations based on a single orthogonal radial orbital basis. By collecting separately optimized PCFs to correct the MR

  4. Effect of interaction strength on robustness of controlling edge dynamics in complex networks

    Science.gov (United States)

    Pang, Shao-Peng; Hao, Fei

    2018-05-01

    Robustness plays a critical role in the controllability of complex networks to withstand failures and perturbations. Recent advances in the edge controllability show that the interaction strength among edges plays a more important role than network structure. Therefore, we focus on the effect of interaction strength on the robustness of edge controllability. Using three categories of all edges to quantify the robustness, we develop a universal framework to evaluate and analyze the robustness in complex networks with arbitrary structures and interaction strengths. Applying our framework to a large number of model and real-world networks, we find that the interaction strength is a dominant factor for the robustness in undirected networks. Meanwhile, the strongest robustness and the optimal edge controllability in undirected networks can be achieved simultaneously. Different from the case of undirected networks, the robustness in directed networks is determined jointly by the interaction strength and the network's degree distribution. Moreover, a stronger robustness is usually associated with a larger number of driver nodes required to maintain full control in directed networks. This prompts us to provide an optimization method by adjusting the interaction strength to optimize the robustness of edge controllability.

  5. Ab initio study of neutral (TiO2)n clusters and their interactions with water and transition metal atoms

    International Nuclear Information System (INIS)

    Çakır, D; Gülseren, O

    2012-01-01

    We have systematically investigated the growth behavior and stability of small stoichiometric (TiO 2 ) n (n = 1-10) clusters as well as their structural, electronic and magnetic properties by using the first-principles plane wave pseudopotential method within density functional theory. In order to find out the ground state geometries, a large number of initial cluster structures for each n has been searched via total energy calculations. Generally, the ground state structures for the case of n = 1-9 clusters have at least one monovalent O atom, which only binds to a single Ti atom. However, the most stable structure of the n = 10 cluster does not have any monovalent O atom. On the other hand, Ti atoms are at least fourfold coordinated for the ground state structures for n ≥ 4 clusters. Our calculations have revealed that clusters prefer to form three-dimensional structures. Furthermore, all these stoichiometric clusters have nonmagnetic ground state. The formation energy and the highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) gap for the most stable structure of (TiO 2 ) n clusters for each n have also been calculated. The formation energy and hence the stability increases as the cluster size grows. In addition, the interactions between the ground state structure of the (TiO 2 ) n cluster and a single water molecule have been studied. The binding energy (E b ) of the H 2 O molecule exhibits an oscillatory behavior with the size of the clusters. A single water molecule preferably binds to the cluster Ti atom through its oxygen atom, resulting an average binding energy of 1.1 eV. We have also reported the interaction of the selected clusters (n = 3, 4, 10) with multiple water molecules. We have found that additional water molecules lead to a decrease in the binding energy of these molecules to the (TiO 2 ) n clusters. Finally, the adsorption of transition metal (TM) atoms (V, Co and Pt) on the n = 10 cluster has been

  6. Robust determination of effective atomic numbers for electron interactions with TLD-100 and TLD-100H thermoluminescent dosimeters

    International Nuclear Information System (INIS)

    Taylor, M.L.

    2011-01-01

    Lithium fluoride thermoluminescent dosimeters (TLD) are the most commonly implemented for clinical dosimetry. The small physical magnitude of TLDs makes them attractive for applications such as small field measurement, in vivo dosimetry and measurement of out-of-field doses to critical structures. The most broadly used TLD is TLD-100 (LiF:Mg,Ti) and, for applications requiring higher sensitivity to low-doses, TLD-100H (LiF:Mg,Cu,P) is frequently employed. The radiological properties of these TLDs are therefore of significant interest. For the first time, in this study effective atomic numbers for radiative, collisional and total electron interaction processes are calculated for TLD-100 and TLD-100H dosimeters over the energy range 1 keV-100 MeV. This is undertaken using a robust, energy-dependent method of calculation rather than typical power-law approximations. The influence of dopant concentrations and unwanted impurities is also investigated. The two TLDs exhibit similar effective atomic numbers, ranging from approximately 5.77-6.51. Differences arising from the different dopants are most pronounced in low-energy radiative effects. The TLDs have atomic numbers approximately 1.48-2.06 times that of water. The effective atomic number of TLD-100H is consistently higher than that of TLD-100 over a broad energy range, due to the greater influence of the higher-Z dopants on the electron interaction cross sections. Typical variation in dopant concentration does not significantly influence the effective atomic number. The influence on TLD-100H is comparatively more pronounced than that on TLD-100. Contrariwise, unwanted hydroxide impurities influence TLD-100 more than TLD-100H. The effective atomic number is a key parameter that influences the radiological properties and energy response of TLDs. Although many properties of these TLDs have been studied rigorously, as yet there has been no investigation of their effective atomic numbers for electron interactions. The

  7. 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.

  8. 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....

  9. Semiclassical interaction between monochromatic electromagnetic radiation and an atom with two unstable levels; some fallacious works by Kamenov-Bonchev

    International Nuclear Information System (INIS)

    Romashev, Yu. A.; Skorobogatov, G.A.

    1999-01-01

    The solution of the time-dependent Hamiltonian for the classical dipole interaction of a two-level atom with a monochromatic electromagnetic wave is presented. Both atomic energy levels are assumed to be unstable. The amplitudes and probabilities of transitions between the energy levels as well as the cross-sections of resonance absorption and induced emission are obtained explicitly. It is shown that in both stationary and nonstationary limits the instability of the lower level does not lead to a differential cross section of induced emission larger than those obtained from the Breit-Wigner formula in the standard collision theory. (authors)

  10. The complete treatment of the time evolution in the case of a discretized atom-field interaction model

    International Nuclear Information System (INIS)

    Seke, J.; Adam, G.; Soldatov, A.V.; Bogolubov, N.N.

    2002-01-01

    Full text: The dynamics of a discretized atom-field interaction model with a physically relevant form factor is analyzed. It is shown that after some short time interval only a small fraction of eigenvalues and eigenstates (belonging to the close vicinity of the excited atomic state energy E=ω 0 /2) contributes to the nondecay probability amplitudes in the long-time regime, whereas the contribution of all other eigenstates and eigenvalues is negligible. Nevertheless, to describe correctly the non-Markovian dynamics in the short-time regime the contribution of all eigenstates and eigenvalues must be taken into account. (author)

  11. The interaction between network ties and business modeling : Case studies of sustainability-oriented innovations

    NARCIS (Netherlands)

    Oskam, Inge; Bossink, Bart; de Man, Ard Pieter

    2018-01-01

    A stream of literature is emerging where network development and business modeling intersect. Various authors emphasize that networks influence business models. This paper extends this stream of literature by studying two cases in which we analyze how business modeling and networking interact over

  12. The Interaction between network ties and business modeling : case studies of sustainability-oriented innovations

    NARCIS (Netherlands)

    Oskam, Inge; Bossink, Bart; de Man, Ard-Pieter

    2018-01-01

    A stream of literature is emerging where network development and business modeling intersect. Various authors emphasize that networks influence business models. This paper extends this stream of literature by studying two cases in which we analyze how business modeling and networking interact over

  13. Strategic interactions in DRAM and RISC technology: A network approach

    NARCIS (Netherlands)

    Duysters, G.M.; Vanhaverbeke, W.P.M.

    1996-01-01

    Interorganizational cooperation in some high-tech industries is no longer confined to two-company alliances, but entails industry-wide alliance networks. This article examines how industry analysis and network analysis can be combined to provide a thorough understanding of how network positions, and

  14. Interaction in agent-based economics: A survey on the network approach

    Science.gov (United States)

    Bargigli, Leonardo; Tedeschi, Gabriele

    2014-04-01

    In this paper we aim to introduce the reader to some basic concepts and instruments used in a wide range of economic networks models. In particular, we adopt the theory of random networks as the main tool to describe the relationship between the organization of interaction among individuals within different components of the economy and overall aggregate behavior. The focus is on the ways in which economic agents interact and the possible consequences of their interaction on the system. We show that network models are able to introduce complex phenomena in economic systems by allowing for the endogenous evolution of networks.

  15. Analysis of protein-protein interaction networks by means of annotated graph mining algorithms

    NARCIS (Netherlands)

    Rahmani, Hossein

    2012-01-01

    This thesis discusses solutions to several open problems in Protein-Protein Interaction (PPI) networks with the aid of Knowledge Discovery. PPI networks are usually represented as undirected graphs, with nodes corresponding to proteins and edges representing interactions among protein pairs. A large

  16. Impedance-Based Harmonic Instability Assessment in Multiple Electric Trains and Traction Network Interaction System

    DEFF Research Database (Denmark)

    Tao, Haidong; Hu, Haitao; Wang, Xiongfei

    2018-01-01

    This paper presents an impedance-based method to systematically investigate the interaction between multi-train and traction networks, focusing on evaluating the harmonic instability problems. Firstly, the interaction mechanism of multi-train and the traction network is represented as a feedback ...

  17. Non-criticality of interaction network over system's crises: A percolation analysis.

    Science.gov (United States)

    Shirazi, Amir Hossein; Saberi, Abbas Ali; Hosseiny, Ali; Amirzadeh, Ehsan; Toranj Simin, Pourya

    2017-11-20

    Extraction of interaction networks from multi-variate time-series is one of the topics of broad interest in complex systems. Although this method has a wide range of applications, most of the previous analyses have focused on the pairwise relations. Here we establish the potential of such a method to elicit aggregated behavior of the system by making a connection with the concepts from percolation theory. We study the dynamical interaction networks of a financial market extracted from the correlation network of indices, and build a weighted network. In correspondence with the percolation model, we find that away from financial crises the interaction network behaves like a critical random network of Erdős-Rényi, while close to a financial crisis, our model deviates from the critical random network and behaves differently at different size scales. We perform further analysis to clarify that our observation is not a simple consequence of the growth in correlations over the crises.

  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. A channeling investigation of the interaction between solute atoms and irradiation-produced defects in magnesium

    International Nuclear Information System (INIS)

    Howe, L.M.; Swanson, M.L.; Quenneville, A.F.

    1978-01-01

    The trapping of irradiation-produced defects by solute atoms in Mg crystals was monitored by measuring the displacement of the solute atoms from lattice sites using the backscattering-channeling technique. In Mg-0.2 at.% Ag crystals, irradiation at 30 K with 1 MeVHe + ions resulted in a very large fraction of Ag atoms being displaced from their lattice sites. The Ag atom displacement appeared to be along directions and is attributed to the trapping of migrating Mg interstitial atoms by Ag atoms to form Mg-Ag mixed dumbbells. Recovery of the Ag atom displacements and the irradiation-induced dechanneling increment occurred principally in two stages, 80-160 K (stage III) and 200-280 K (stage IV). Stage III is attributed mainly to some type of interstitial migration and stage IV is attributed to the migration of single vacancies. In contrast to the Mg-Ag results, a very small displaced fraction of Bi atoms occurred in an irradiated Mg-0.08 at.% Bi crystal; hence Mg-Bi mixed dumbbells do not appear to be formed. (author)

  20. Interactions between neural networks: a mechanism for tuning chaos and oscillations.

    Science.gov (United States)

    Wang, Lipo

    2007-06-01

    We show that chaos and oscillations in a higher-order binary neural network can be tuned effectively using interactions between neural networks. Our results suggest that network interactions may be useful as a means of adjusting the level of dynamic activities in systems that employ chaos and oscillations for information processing, or as a means of suppressing oscillatory behaviors in systems that require stability.