Generating functional analysis of complex formation and dissociation in large protein interaction networks

We analyze large systems of interacting proteins, using techniques from the non-equilibrium statistical mechanics of disordered many-particle systems. Apart from protein production and removal, the most relevant microscopic processes in the proteome are complex formation and dissociation, and the microscopic degrees of freedom are the evolving concentrations of unbound proteins (in multiple post-translational states) and of protein complexes. Here we only include dimer-complexes, for mathematical simplicity, and we draw the network that describes which proteins are reaction partners from an ensemble of random graphs with an arbitrary degree distribution. We show how generating functional analysis methods can be used successfully to derive closed equations for dynamical order parameters, representing an exact macroscopic description of the complex formation and dissociation dynamics in the infinite system limit. We end this paper with a discussion of the possible routes towards solving the nontrivial order parameter equations, either exactly (in specific limits) or approximately.Comment: 14 pages, to be published in Proc of IW-SMI-2009 in Kyoto (Journal of Phys Conference Series

Tailored graph ensembles as proxies or null models for real networks I: tools for quantifying structure

We study the tailoring of structured random graph ensembles to real networks, with the objective of generating precise and practical mathematical tools for quantifying and comparing network topologies macroscopically, beyond the level of degree statistics. Our family of ensembles can produce graphs with any prescribed degree distribution and any degree-degree correlation function, its control parameters can be calculated fully analytically, and as a result we can calculate (asymptotically) formulae for entropies and complexities, and for information-theoretic distances between networks, expressed directly and explicitly in terms of their measured degree distribution and degree correlations.Comment: 25 pages, 3 figure

Diffusion dynamics on multiplex networks

We study the time scales associated to diffusion processes that take place on multiplex networks, i.e. on a set of networks linked through interconnected layers. To this end, we propose the construction of a supra-Laplacian matrix, which consists of a dimensional lifting of the Laplacian matrix of each layer of the multiplex network. We use perturbative analysis to reveal analytically the structure of eigenvectors and eigenvalues of the complete network in terms of the spectral properties of the individual layers. The spectrum of the supra-Laplacian allows us to understand the physics of diffusion-like processes on top of multiplex networks.Comment: 6 Pages including supplemental material. To appear in Physical Review Letter

Multipactor radiation analysis within a waveguide region based on a frequency-domain representation of the dynamics of charged particles

[EN] A technique for the accurate computation of the electromagnetic fields radiated by a charged particle moving within a parallel-plate waveguide is presented. Based on a transformation of the time-varying current density of the particle into a time-harmonic current density, this technique allows the evaluation of the radiated electromagnetic fields both in the frequency and time domains, as well as in the near- and far-field regions. For this purpose, several accelerated versions of the parallel-plate Green's function in the frequency domain have been considered. The theory has been successfully applied to the multipactor discharge occurring within a two metal-plates region. The proposed formulation has been tested with a particle-in-cell code based on the finite-difference time-domain method, obtaining good agreement.The authors would like to thank ESA/ESTEC for having funded this research activity through the Contract "RF Breakdown in Multicarrier Systems" (Contract No. 19918/06/NL/GLC).Gimeno, B.; Sorolla, E.; Anza, S.; Vicente, C.; Gil, J.; Pérez, AM.; Boria Esbert, VE.... (2009). Multipactor radiation analysis within a waveguide region based on a frequency-domain representation of the dynamics of charged particles. Physical review. E, Statistical, nonlinear, and soft matter physics. 79(4):1-9. https://doi.org/10.1103/PhysRevE.79.046604S19794Figueroa, H., Gai, W., Konecny, R., Norem, J., Ruggiero, A., Schoessow, P., & Simpson, J. (1988). Direct Measurement of Beam-Induced Fields in Accelerating Structures. Physical Review Letters, 60(21), 2144-2147. doi:10.1103/physrevlett.60.2144Ng, K.-Y. (1990). Wake fields in a dielectric-lined waveguide. Physical Review D, 42(5), 1819-1828. doi:10.1103/physrevd.42.1819Rosing, M., & Gai, W. (1990). Longitudinal- and transverse-wake-field effects in dielectric structures. Physical Review D, 42(5), 1829-1834. doi:10.1103/physrevd.42.1829Gai, W., Kanareykin, A. D., Kustov, A. L., & Simpson, J. (1997). Numerical simulations of intense charged-particle beam propagation in a dielectric wake-field accelerator. Physical Review E, 55(3), 3481-3488. doi:10.1103/physreve.55.3481Burov, A., & Danilov, V. (1999). Suppression of Transverse Bunch Instabilities by Asymmetries in the Chamber Geometry. Physical Review Letters, 82(11), 2286-2289. doi:10.1103/physrevlett.82.2286Xiao, L., Gai, W., & Sun, X. (2001). Field analysis of a dielectric-loaded rectangular waveguide accelerating structure. Physical Review E, 65(1). doi:10.1103/physreve.65.016505Jing, C., Liu, W., Xiao, L., Gai, W., Schoessow, P., & Wong, T. (2003). Dipole-mode wakefields in dielectric-loaded rectangular waveguide accelerating structures. Physical Review E, 68(1). doi:10.1103/physreve.68.016502Stupakov, G., Bane, K. L. F., & Zagorodnov, I. (2007). Optical approximation in the theory of geometric impedance. Physical Review Special Topics - Accelerators and Beams, 10(5). doi:10.1103/physrevstab.10.054401Hatch, A. J., & Williams, H. B. (1954). The Secondary Electron Resonance Mechanism of Low‐Pressure High‐Frequency Gas Breakdown. Journal of Applied Physics, 25(4), 417-423. doi:10.1063/1.1721656Hatch, A. J., & Williams, H. B. (1958). Multipacting Modes of High-Frequency Gaseous Breakdown. Physical Review, 112(3), 681-685. doi:10.1103/physrev.112.681Vaughan, J. R. M. (1988). Multipactor. IEEE Transactions on Electron Devices, 35(7), 1172-1180. doi:10.1109/16.3387Gilardini, A. L. (1995). Multipacting discharges: Constant‐ktheory and simulation results. Journal of Applied Physics, 78(2), 783-795. doi:10.1063/1.360336Riyopoulos, S. (1997). Multipactor saturation due to space-charge-induced debunching. Physics of Plasmas, 4(5), 1448-1462. doi:10.1063/1.872319Kryazhev, A., Buyanova, M., Semenov, V., Anderson, D., Lisak, M., Puech, J., … Sombrin, J. (2002). Hybrid resonant modes of two-sided multipactor and transition to the polyphase regime. Physics of Plasmas, 9(11), 4736-4743. doi:10.1063/1.1514969Udiljak, R., Anderson, D., Ingvarson, P., Jordan, U., Jostell, U., Lapierre, L., … Sombrin, J. (2003). New method for detection of multipaction. IEEE Transactions on Plasma Science, 31(3), 396-404. doi:10.1109/tps.2003.811646De Lara, J., Perez, F., Alfonseca, M., Galan, L., Montero, I., Roman, E., & Garcia-Baquero, D. R. (2006). Multipactor prediction for on-board spacecraft RF equipment with the MEST software tool. IEEE Transactions on Plasma Science, 34(2), 476-484. doi:10.1109/tps.2006.872450Torregrosa, G., Coves, A., Vicente, C. P., Perez, A. M., Gimeno, B., & Boria, V. E. (2006). Time evolution of an electron discharge in a parallel-plate dielectric-loaded waveguide. IEEE Electron Device Letters, 27(7), 619-621. doi:10.1109/led.2006.877284Udiljak, R., Anderson, D., Lisak, M., Semenov, V. E., & Puech, J. (2007). Multipactor in a coaxial transmission line. I. Analytical study. Physics of Plasmas, 14(3), 033508. doi:10.1063/1.2710464Semenov, V. E., Zharova, N., Udiljak, R., Anderson, D., Lisak, M., & Puech, J. (2007). Multipactor in a coaxial transmission line. II. Particle-in-cell simulations. Physics of Plasmas, 14(3), 033509. doi:10.1063/1.2710466Anza, S., Vicente, C., Gimeno, B., Boria, V. E., & Armendáriz, J. (2007). Long-term multipactor discharge in multicarrier systems. Physics of Plasmas, 14(8), 082112. doi:10.1063/1.2768019Udiljak, R., Anderson, D., Lisak, M., Puech, J., & Semenov, V. E. (2007). Multipactor in a Waveguide Iris. IEEE Transactions on Plasma Science, 35(2), 388-395. doi:10.1109/tps.2007.892737Burton, R. J., de Jong, M. S., & Funk, L. W. (1991). Vacuum and multipactor performance of the hadron electron ring accelerator 52 MHz cavities. Journal of Vacuum Science & Technology A: Vacuum, Surfaces, and Films, 9(3), 2081-2084. doi:10.1116/1.577417Yamaguchi, S., Saito, Y., Anami, S., & Michizono, S. (1992). Trajectory simulation of multipactoring electrons in an S-band pillbox RF window. IEEE Transactions on Nuclear Science, 39(2), 278-282. doi:10.1109/23.277497Kishek, R., & Lau, Y. Y. (1995). Interaction of Multipactor Discharge and rf Circuit. Physical Review Letters, 75(6), 1218-1221. doi:10.1103/physrevlett.75.1218Lay-Kee Ang, Lau, Y. Y., Kishek, R. A., & Gilgenbach, R. M. (1998). Power deposited on a dielectric by multipactor. IEEE Transactions on Plasma Science, 26(3), 290-295. doi:10.1109/27.700756Kishek, R. A., Lau, Y. Y., Ang, L. K., Valfells, A., & Gilgenbach, R. M. (1998). Multipactor discharge on metals and dielectrics: Historical review and recent theories. Physics of Plasmas, 5(5), 2120-2126. doi:10.1063/1.872883Neuber, A., Hemmert, D., Krompholz, H., Hatfield, L., & Kristiansen, M. (1999). Initiation of high power microwave dielectric interface breakdown. Journal of Applied Physics, 86(3), 1724-1728. doi:10.1063/1.370953Chojnacki, E. (2000). Simulations of a multipactor-inhibited waveguide geometry. Physical Review Special Topics - Accelerators and Beams, 3(3). doi:10.1103/physrevstab.3.032001Cimino, R., Collins, I. R., Furman, M. A., Pivi, M., Ruggiero, F., Rumolo, G., & Zimmermann, F. (2004). Can Low-Energy Electrons Affect High-Energy Physics Accelerators? Physical Review Letters, 93(1). doi:10.1103/physrevlett.93.014801Abe, T., Kageyama, T., Akai, K., Ebihara, K., Sakai, H., & Takeuchi, Y. (2006). Multipactoring zone map of an rf input coupler and its application to high beam current storage rings. Physical Review Special Topics - Accelerators and Beams, 9(6). doi:10.1103/physrevstab.9.062002Sorolla, E., Anza, S., Gimeno, B., Perez, A. M. P., Vicente, C., Gil, J., … Boria, V. E. (2008). An Analytical Model to Evaluate the Radiated Power Spectrum of a Multipactor Discharge in a Parallel-Plate Region. IEEE Transactions on Electron Devices, 55(8), 2252-2258. doi:10.1109/ted.2008.926271Harrington, R. F. (2001). Time-Harmonic Electromagnetic Fields. doi:10.1109/9780470546710Hanson, G. W., & Yakovlev, A. B. (2002). Operator Theory for Electromagnetics. doi:10.1007/978-1-4757-3679-3Ewald, P. P. (1921). Die Berechnung optischer und elektrostatischer Gitterpotentiale. Annalen der Physik, 369(3), 253-287. doi:10.1002/andp.19213690304Myun-Joo Park, & Sangwook Nam. (1998). Rapid summation of the Green’s function for the rectangular waveguide. IEEE Transactions on Microwave Theory and Techniques, 46(12), 2164-2166. doi:10.1109/22.739301Capolino, F., Wilton, D. R., & Johnson, W. A. (2005). 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Spectral density of random graphs with topological constraints

The spectral density of random graphs with topological constraints is analysed using the replica method. We consider graph ensembles featuring generalised degree-degree correlations, as well as those with a community structure. In each case an exact solution is found for the spectral density in the form of consistency equations depending on the statistical properties of the graph ensemble in question. We highlight the effect of these topological constraints on the resulting spectral density.Comment: 24 pages, 6 figure

Spin models on random graphs with controlled topologies beyond degree constraints

We study Ising spin models on finitely connected random interaction graphs which are drawn from an ensemble in which not only the degree distribution $p(k)$ can be chosen arbitrarily, but which allows for further fine-tuning of the topology via preferential attachment of edges on the basis of an arbitrary function Q(k,k') of the degrees of the vertices involved. We solve these models using finite connectivity equilibrium replica theory, within the replica symmetric ansatz. In our ensemble of graphs, phase diagrams of the spin system are found to depend no longer only on the chosen degree distribution, but also on the choice made for Q(k,k'). The increased ability to control interaction topology in solvable models beyond prescribing only the degree distribution of the interaction graph enables a more accurate modeling of real-world interacting particle systems by spin systems on suitably defined random graphs.Comment: 21 pages, 4 figures, submitted to J Phys

A school-based motivational intervention to promote physical activity from a self-determination theory perspective

This study analyzed the effects of a multidimensional intervention to promote physical activity (PA) in school, based on self-determination theory. The study involved 88 students, aged between 14 and 17 years, who were divided into a control group (n = 59) and an experimental group (n = 29). In the experimental group, a 6-month intervention was conducted, applying a teaching unit of fitness and health in physical education (PE) classes, an extracurricular program of healthy PA, and meetings with families. Questionnaires were administered to measure different motivational variables and PA levels at four time points. Significant differences were found in favor of the experimental group in parental and peer autonomy support; integrated regulation in PE; autonomy, intrinsic and identified regulation in leisure-time PA; moderate, hard, and very hard PA; and physical self-worth. Motivational effects were maintained over time but the effects on PA levels disappeared at 6 month

36th Cordoba Guitar Festival: Spectator Analysis Using Structural Equation Modelling (SEM)

The Cordoba Guitar Festival is one of the most important cultural events in Spain. This article analyses the musical preferences, satisfaction, attitudinal loyalty, and behavioural loyalty of spectators who attended the 36th festival held in July 2016, as well as the festival’s economic impact on the city. These characteristics of the public give rise to the four hypotheses of this study. To achieve this aim, a structural equation model (SEM) was used. The results −χ2 = 27.79, with the p-value found to be p = P (χ2 ≥ 27.79) = 0.224—show the goodness-of-fit of the model and indicate that the observed data do fit the expected dataset. The results therefore allow us to accept the proposed hypotheses concerning the influence of different latent factors, such as musical preferences, loyalty, and satisfaction with the festival. This is the main focus with which the present study has been written. Regarding the economic impact, the Festival raised 1.2 million euros, that is, slightly more than 73,000 euros per day. The amount, although not very high, is important as additional income for the city. The conclusions show the need to consider the preferences of the spectator as an essential tool to enable the continuation and longevity of the Cordoba Guitar Festival—an important cultural destination

Physical activity quantification in elder women

Cuantificación de la actividad física en mujeres mayores