Network theory approach for data evaluation in the dynamic force spectroscopy of biomolecular interactions

Investigations of molecular bonds between single molecules and molecular complexes by the dynamic force spectroscopy are subject to large fluctuations at nanoscale and possible other aspecific binding, which mask the experimental output. Big efforts are devoted to develop methods for effective selection of the relevant experimental data, before taking the quantitative analysis of bond parameters. Here we present a methodology which is based on the application of graph theory. The force-distance curves corresponding to repeated pulling events are mapped onto their correlation network (mathematical graph). On these graphs the groups of similar curves appear as topological modules, which are identified using the spectral analysis of graphs. We demonstrate the approach by analyzing a large ensemble of the force-distance curves measured on: ssDNA-ssDNA, peptide-RNA (system from HIV1), and peptide-Au surface. Within our data sets the methodology systematically separates subgroups of curves which are related to different intermolecular interactions and to spatial arrangements in which the molecules are brought together and/or pulling speeds. This demonstrates the sensitivity of the method to the spatial degrees of freedom, suggesting potential applications in the case of large molecular complexes and situations with multiple binding sites

Thermodynamics of a model for RNA folding

We analyze the thermodynamic properties of a simplified model for folded RNA molecules recently studied by G. Vernizzi, H. Orland, A. Zee (in {\it Phys. Rev. Lett.} {\bf 94} (2005) 168103). The model consists of a chain of one-flavor base molecules with a flexible backbone and all possible pairing interactions equally allowed. The spatial pseudoknot structure of the model can be efficiently studied by introducing a $N \times N$ hermitian random matrix model at each chain site, and associating Feynman diagrams of these models to spatial configurations of the molecules. We obtain an exact expression for the topological expansion of the partition function of the system. We calculate exact and asymptotic expressions for the free energy, specific heat, entanglement and chemical potential and study their behavior as a function of temperature. Our results are consistent with the interpretation of $1/N$ as being a measure of the concentration of $\rm{Mg}^{++}$ in solution.Comment: 11 pages, 4 figure

Site-selective quantum correlations revealed by magnetic anisotropy in the tetramer system SeCuO3

We present the investigation of a monoclinic compound SeCuO3 using x-ray powder diffraction, magnetization, torque and electron-spin-resonance (ESR). Structurally based analysis suggests that SeCuO3 can be considered as a 3D network of tetramers. The values of intra-tetramer exchange interactions are extracted from the temperature dependence of the susceptibility and amount to ~200 K. The inter-tetramer coupling leads to the development of long-range antiferromagnetic order at TN = 8 K. An unusual temperature dependence of the effective g-tensors is observed, accompanied with a rotation of macroscopic magnetic axes. We explain this unique observation as due to site-selective quantum correlations

Bloggers Behavior and Emergent Communities in Blog Space

Interactions between users in cyberspace may lead to phenomena different from those observed in common social networks. Here we analyse large data sets about users and Blogs which they write and comment, mapped onto a bipartite graph. In such enlarged Blog space we trace user activity over time, which results in robust temporal patterns of user--Blog behavior and the emergence of communities. With the spectral methods applied to the projection on weighted user network we detect clusters of users related to their common interests and habits. Our results suggest that different mechanisms may play the role in the case of very popular Blogs. Our analysis makes a suitable basis for theoretical modeling of the evolution of cyber communities and for practical study of the data, in particular for an efficient search of interesting Blog clusters and further retrieval of their contents by text analysis

Z boson production in p+Pb collisions at sNN√=5.02 TeV measured with the ATLAS detector

The ATLAS Collaboration has measured the inclusive production of Z bosons via their decays into electron and muon pairs in p+Pb collisions at √ sNN = 5.02 TeV at the Large Hadron Collider. The measurements are made using data corresponding to integrated luminosities of 29.4 nb−1 and 28.1 nb−1 for Z → ee and Z → µµ, respectively. The results from the two channels are consistent and combined to obtain a cross section times the Z → `` branching ratio, integrated over the rapidity region |y ∗ Z | < 3.5, of 139.8 ± 4.8 (stat.) ± 6.2 (syst.) ± 3.8 (lumi.) nb. Differential cross sections are presented as functions of the Z boson rapidity and transverse momentum, and compared with models based on parton distributions both with and without nuclear corrections. The centrality dependence of Z boson production in p+Pb collisions is measured and analyzed within the framework of a standard Glauber model and the model’s extension for fluctuations of the underlying nucleon-nucleon scattering cross sectionFil: Aad, G.. Aix-Marseille Université; FranciaFil: Abbott, B.. Oklahoma State University; Estados UnidosFil: Abdallah, J.. Academia Sinica; ChinaFil: Abdinov, O.. Azerbaijan Academy of Sciences; AzerbaiyánFil: Aben, R.. University of Amsterdam; Países BajosFil: Alconada Verzini, María Josefina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física La Plata; ArgentinaFil: Alonso, Francisco. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física La Plata; ArgentinaFil: Arduh, Francisco Anuar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física La Plata; ArgentinaFil: Dova, Maria Teresa. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física La Plata; ArgentinaFil: Monticelli, Fernando Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física La Plata; ArgentinaFil: Wahlberg, Hernan Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física La Plata; ArgentinaFil: Otero y Garzon, Gustavo Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Física de Buenos Aires; ArgentinaFil: Piegaia, Ricardo Nestor. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Física de Buenos Aires; ArgentinaFil: Reisin, Hernan Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Física de Buenos Aires; ArgentinaFil: Sacerdoti, Sabrina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Física de Buenos Aires; ArgentinaFil: Zieminska, D.. Indiana University; Estados UnidosFil: Zimine, N. I.. Joint Institute for Nuclear Research ; RusiaFil: Zimmermann, C.. Universität Mainz; AlemaniaFil: Zimmermann, S.. Albert-Ludwigs-Universität; AlemaniaFil: Zinonos, Z.. Georg-August-Universität; AlemaniaFil: Zinser, M.. Universität Mainz; AlemaniaFil: Ziolkowski, M.. Universität Siegen ; AlemaniaFil: Živković, L.. University of Belgrade; SerbiaFil: Zobernig, G.. University of Wisconsin; Estados UnidosFil: Zoccoli, A.. Università di Bologna; ItaliaFil: Nedden, M. zur. Humboldt University; AlemaniaFil: Zurzolo, G.. Università di Napoli; ItaliaFil: Zwalinski, L.. Cern - European Organization For Nuclear Research; SuizaFil: The ATLAS Collaboration. No especifica

Magneto-transport study of intra- and intergrain transitions in the magnetic superconductors RuSr2GdCu2O8 and RuSr2(Gd1.5Ce0.5)Cu2O10

A characterization of the magnetic superconductors RuSr2GdCu2O8 [Ru-(1212)] and RuSr2(Gd1.5Ce0.5)Cu2O10 [Ru-(1222)] through resistance measurements as a function of temperature and magnetic field is presented. Two peaks in the derivative of the resistive curves are identified as intra- and intergrain superconducting transitions. Strong intragrain granularity effects are observed, and explained by considering the antiphase boundaries between structural domains of coherently rotated RuO6 octahedra as intragrain Josephson-junctions. A different field dependence of the intragrain transition temperature in these compounds was found. For Ru-(1212) it remains unchanged up to 0.1 T, decreasing for higher fields. In Ru-(1222) it smoothly diminishes with the increase in field even for a value as low as 100 Oe. These results are interpreted as a consequence of a spin-flop transition of the Ru moments. The large separation between the RuO2 layers in Ru-(1222) promotes a weak interlayer coupling, leading the magnetic transition to occur at lower fields. The suppression rate of the intragrain transition temperature is about five times higher for Ru-(1222), a result we relate to an enhancement of the 2D character of the vortex structure. A distinctive difference with conventional cuprates is the sharp increase in amplitude of the intergrain peak in both systems, as the field is raised, which is ascribed to percolation through a fraction of high quality intergrain junctions.Comment: Submitted for Physical Review

Endogenous and exogenous dynamics in the fluctuations of capital fluxes: An empirical analysis of the Chinese stock market

A phenomenological investigation of the endogenous and exogenous dynamics in the fluctuations of capital fluxes is investigated on the Chinese stock market using mean-variance analysis, fluctuation analysis and their generalizations to higher orders. Non-universal dynamics have been found not only in $\alpha$ exponents different from the universal value 1/2 and 1 but also in the distributions of the ratios $\eta_i = \sigma_i^{\rm{exo}} / \sigma_i^{\rm{endo}}$. Both the scaling exponent $\alpha$ of fluctuations and the Hurst exponent $H_i$ increase in logarithmic form with the time scale $\Delta t$ and the mean traded value per minute $$, respectively. We find that the scaling exponent $\alpha^{\rm{endo}}$ of the endogenous fluctuations is found to be independent of the time scale, while the exponent of exogenous fluctuations $\alpha^{\rm{exo}}=1$. Multiscaling and multifractal features are observed in the data as well. However, the inhomogeneous impact model is not verified.Comment: 9 Latx pages for EPJB including 13 figure

Triggers for displaced decays of long-lived neutral particles in the ATLAS detector

A set of three dedicated triggers designed to detect long-lived neutral particles decaying throughout the ATLAS detector to a pair of hadronic jets is described. The efficiencies of the triggers for selecting displaced decays as a function of the decay position are presented for simulated events. The effect of pile-up interactions on the trigger efficiencies and the dependence of the trigger rate on instantaneous luminosity during the 2012 data-taking period at the LHC are discussedFil: Aad, G.. Albert Ludwigs Universität; AlemaniaFil: Abajyan, T.. Universitaet Bonn; AlemaniaFil: Abbott, B.. University of Oklahoma; Estados UnidosFil: Abdallah, J.. Universitat Autònoma de Barcelona; EspañaFil: Abdel Khalek, S.. Universite Paris Sud; FranciaFil: Alconada Verzini, María Josefina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física La Plata; ArgentinaFil: Alonso, Francisco. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física La Plata; ArgentinaFil: Anduaga, Xabier Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física La Plata; ArgentinaFil: Dova, Maria Teresa. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física La Plata; ArgentinaFil: González Silva, María Laura. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Física; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Monticelli, Fernando Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física La Plata; ArgentinaFil: Otero y Garzon, Gustavo Javier. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Física; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Piegaia, Ricardo Nestor. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Física; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Romeo, Gaston Leonardo. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Física; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Tripiana, Martin Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física La Plata. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física La Plata; ArgentinaFil: Zhuang, X.. Ludwig Maximilians Universitat; AlemaniaFil: Zhuravlov, V.. Max-Planck Institut für Physik; AlemaniaFil: Zieminska, D.. Indiana University; Estados UnidosFil: Zimin, N. I.. Joint Institute for Nuclear Research; RusiaFil: Zimmermann, R.. Universitaet Bonn; AlemaniaFil: Zimmermann, S.. Universitaet Bonn; AlemaniaFil: Zimmermann, S.. Albert Ludwigs Universität; AlemaniaFil: Ziolkowski, M.. Universität Siegen; AlemaniaFil: Zitoun, R.. Université de Savoie; FranciaFil: Živković, L.. Columbia University; Estados UnidosFil: Zmouchko, V. V.. State Research Center Institute for High Energy Physics; RusiaFil: Zobernig, G.. University of Wisconsin; Estados UnidosFil: Zoccoli, A.. Università di Bologna; ItaliaFil: zur Nedden, M.. Humboldt University; AlemaniaFil: Zutshi, V.. Northern Illinois University; Estados Unido

Thermal relaxation of magnetic clusters in amorphous Hf_{57}Fe_{43} alloy

The magnetization processes in binary magnetic/nonmagnetic amorphous alloy Hf_{57}Fe_{43} are investigated by the detailed measurements of magnetic hysteresis loops, temperature dependence of magnetization, relaxation of magnetization and magnetic ac susceptibility, including a nonlinear term. Blocking of magnetic moments at lower temperatures is accompanied with the slow relaxation of magnetization and magnetic hysteresis loops. All of the observed properties are explained with the superparamagnetic behaviour of the single domain magnetic clusters inside the nonmagnetic host, their blocking by the anisotropy barriers and thermal fluctuation over the barriers accompanied by relaxation of magnetization. From magnetic viscosity analysis based on thermal relaxation over the anisotropy barriers it is found out that magnetic clusters occupy the characteristic volume from 25 up to 200 nm3 . The validity of the superparamagnetic model of Hf_{57}Fe_{43} is based on the concentration of iron in the Hf_{100-x}Fe_{43} system that is just below the threshold for the long range magnetic ordering. This work throws more light on magnetic behaviour of other amorphous alloys, too