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

Nonadiabatic resonances in a noisy Fitzhugh-Nagumo neuron model

We have analyzed the response of a noisy Fitzhugh-Nagumo neuronlike model (FN) to subthreshold external stimuli. In contrast to previous studies we have focused our attention on high-frequency signals which could be of interest for real systems such as nervous fibers in the auditory system. We show that the noisy FN behaves as a stochastic oscillator with a characteristic time scale whose effects remain in a wide range of situations. In the nonadiabatic regime of frequencies considered in this work we report several resonant behaviors which resemble those of classical deterministic oscillators but never the typical stochastic resonance phenomenon so often observed for low-frequency signals

Determination of biosorption mechanism in biomass of agave, using spectroscopic and microscopic techniques for the purification of contaminated water

[Abstract] Lead (Pb2+) and copper (Cu2+) are polluting metals due to their toxicity; however, the extraction of these metals is essential for economic development, so it is important to look for efficient and low-cost alternatives that can remove heavy metals from the various bodies of water. One of the alternatives used in this work is biosorption, for which an agroindustrial waste (epidermis from Agave atrovirens) was used to evaluate the affinity of removal of lead and copper in aqueous solutions; in addition, spectroscopy and microscopy techniques were used to elucidate and corroborate the removal and affinity capacity of the agave epidermis for both metals studied. The optimal pH value for the removal of both metals was 3. The adsorption isotherms yielded a qmax of 25.7 and 8.6 mg/g for lead and copper, respectively. Adjusting to the Langmuir-Freundlich model, the adsorption kinetics were pseudo-second order, and it was found that the equilibrium time was at 140 min. The spectroscopy and microscopy analyses corroborated the affinity between metals and functional groups of the agave, as well as with the elemental analysis, which reported 17.38% of lead and 4.25% of copper.[Resumen] El plomo (Pb2+) y el cobre (Cu2+) son metales contaminantes debido a su toxicidad; sin embargo, la extracción de estos metales es indispensable para el desarrollo económico, por lo que es importante buscar alternativas eficientes y de bajo costo que puedan remover metales pesados de los diversos cuerpos de agua. Una de las alternativas utilizadas en este trabajo es la biosorción, para la cual se utilizó un residuo agroindustrial (epidermis de Agave atrovirens), para evaluar la afinidad de remoción del plomo y cobre en soluciones acuosas; adicionalmente, se emplearon técnicas de espesctroscopía y microscopía que permitieron elucidar y corroborar la capacidad de remoción y afinidad que tuvo la epidermis de A. atrovirens para ambos metales estudiados. El valor óptimo de pH para la remoción de ambos metales fue 3. Las isotermas de adsorción arrojaron una qmax de 25.7 y 8.6 mg/g para el plomo y cobre, respectivamente. Ajustando al modelo de Langmuir-Freundlich, las cinéticas de adsorción resultaron de pseudo-segundo orden, se encontró que el tiempo de equilibrio es a los 140 min. El análisis espectroscópico y microscópico, corroboró la afinidad entre metales y grupos funcionales del agave, así como con el análisis elemental, el cual reportó 17.38% de plomo y 4.25% de cobre

Synchronization reveals topological scales in complex networks

We study the relationship between topological scales and dynamic time scales in complex networks. The analysis is based on the full dynamics towards synchronization of a system of coupled oscillators. In the synchronization process, modular structures corresponding to well defined communities of nodes emerge in different time scales, ordered in a hierarchical way. The analysis also provides a useful connection between synchronization dynamics, complex networks topology and spectral graph analysis.Comment: 4 pages, 3 figure

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

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). Efficient computation of the 2-D Green’s function for 1-D periodic structures using the Ewald method. IEEE Transactions on Antennas and Propagation, 53(9), 2977-2984. doi:10.1109/tap.2005.854556Kustepeli, A., & Martin, A. Q. (2000). On the splitting parameter in the Ewald method. IEEE Microwave and Guided Wave Letters, 10(5), 168-170. doi:10.1109/75.85036

Agilidad, flexibilidad de producción e innovación en la empresa manufacturera espa-ñola

Este artículo analiza en una muestra de empresas manufactureras españolas la relación de la producción ágil con el esfuerzo interno y la cooperación externa en innovación tecnológica. Los resultados del estudio indican que las empresas con mayor capacidad de agilidad utilizan con más intensidad un amplio conjunto de tecnologías agiles de desarrollo, fabricación y suministro. Las empresas más ágiles también cooperan externamente más en innovación y dicha cooperación modera la flexibilidad de producción de las empresas, indicando con ello que, gracias a la cooperación externa en innovación las empresas con menor flexibilidad de producción pueden aun así conseguir mayor capacidad de agilidad

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

Sequential repeated tibial tubercle osteotomy in a two-stage exchange strategy : a superior approach to treating a chronically infected knee arthroplasty?

Surgical approach can impact the reliability of the debridement after a chronic total knee periprosthetic joint infection (PJI), a factor of utmost importance to eradicate the infection. The most adequate knee surgical approach in cases of PJI is a matter of debate. The purpose of this study was to determine the influence of performing a tibial tubercle osteotomy (TTO) in a two-stage exchange protocol for knee PJI treatment. Retrospective cohort study examining patients managed with two-stage arthroplasty due to chronic knee PJI (2010-2019). Performance and timing of the TTO were collected. Primary end-point was infection control with a minimum FU of 12 months and according to internationally accepted criteria. Correlation between TTO timing and reinfection rate was reviewed. Fifty-two cases were finally included. Overall success (average follow-up: 46.2 months) was 90.4%. Treatment success was significantly higher among cases addressed using TTO during the second stage (97.1% vs. 76.5%, pvalue 0.03). Only 4.8% of the patients relapsed after performing a sequential repeated TTO, that is, during both first and second stages, compared to 23.1% cases in which TTO was not done (p value 0.28). No complications were observed among patients in the TTO group with a significant decrease in soft tissue necrosis (p: 0.052). Sequential repeated tibial tubercle osteotomy during a two-stage strategy is a reasonable option and offers high rates of infection control in complex cases of knee PJI with a low rate of complications