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

Towards a Method to Conceptualize Domain Ontologies

This paper presents the suite of principles, designs criteria and verification process used in the knowledge conceptualization process of a consensuated domain ontology in the domain of chemicals. To achieve agreement between different development teams we propose the use of a common and shared conceptual model as starting point. To capture domain knowledge of a given domain and organize it in a shared and consensuated conceptual model, we recommend an approach that integrates the following intermediate representation techniques: Data Dictionary, Concepts Classification Trees, Tables of Instance Attributes, Table of Class Attributes, Table of Constants, Tables of Formulas, Attributes Classification Trees, and Tables of Instances. We also provide a set of guidelines to verify the knowledge gathered inside each intermediate representations and between intermediate representations

Groundwater pollution in quaternary aquifer of Vitoria - Gasteiz (Basque Country, Spain)

As a result of diverse changes in land use and in water-resource management in the high basin of the Zadorra River (Basque Country), an important loss of water resources and an intense contamination by nitrogen compounds has taken place. The purpose of this paper is to detail the land transformations that have taken place on the aquifer since the 1950s: increase of drainage network, change from dry to irrigated farming, and diversion of rivers at the aquifer unit inlet. Furthermore, we analyze the impact of these transformations on the hydrodynamics and water quality of this aquifer system

Reflectionless discrete perfectly matched layers for higher-order finite difference schemes

This paper introduces discrete-holomorphic Perfectly Matched Layers (PMLs) specifically designed for high-order finite difference (FD) discretizations of the scalar wave equation. In contrast to standard PDE-based PMLs, the proposed method achieves the remarkable outcome of completely eliminating numerical reflections at the PML interface, in practice achieving errors at the level of machine precision. Our approach builds upon the ideas put forth in a recent publication [Journal of Computational Physics 381 (2019): 91-109] expanding the scope from the standard second-order FD method to arbitrary high-order schemes. This generalization uses additional localized PML variables to accommodate the larger stencils employed. We establish that the numerical solutions generated by our proposed schemes exhibit an exponential decay rate as they propagate within the PML domain. To showcase the effectiveness of our method, we present a variety of numerical examples, including waveguide problems. These examples highlight the importance of employing high-order schemes to effectively address and minimize undesired numerical dispersion errors, emphasizing the practical advantages and applicability of our approach

The Kuramoto model: A simple paradigm for synchronization phenomena

Synchronization phenomena in large populations of interacting elements are the subject of intense research efforts in physical, biological, chemical, and social systems. A successful approach to the problem of synchronization consists of modeling each member of the population as a phase oscillator. In this review, synchronization is analyzed in one of the most representative models of coupled phase oscillators, the Kuramoto model. A rigorous mathematical treatment, specific numerical methods, and many variations and extensions of the original model that have appeared in the last few years are presented. Relevant applications of the model in different contexts are also included

Evenly convex sets, and evenly quasiconvex functions, revisited

Since its appearance, even convexity has become a remarkable notion in convex analysis. In the fifties, W. Fenchel introduced the evenly convex sets as those sets solving linear systems containing strict inequalities. Later on, in the eighties, evenly quasiconvex functions were introduced as those whose sublevel sets are evenly convex. The significance of even convexity relies on the different areas where it enjoys applications, ranging from convex optimization to microeconomics. In this paper, we review some of the main properties of evenly convex sets and evenly quasiconvex functions, provide further characterizations of evenly convex sets, and present some new results for evenly quasiconvex functions.This research has been partially supported by MINECO of Spain and ERDF of EU, Grants PGC2018-097960-B-C22 and ECO2016-77200-P

Editorial: New insights into adult neurogenesis and neurodegeneration: challenges for brain repair

The formation of new neurons in the brain is probably one of the most controversial topics in the scientific community since in the 1960's Joseph Altman described for the first time that proliferating cells give rise to new neurons in the adult brain of rats and other mammals. This Research Topic includes 1 brief research report, 3 mini review, 4 review and 9 original research papers gathering different contributions highlighting new developments in the field of neurogenesis

Robust solutions to multi-objective linear programs with uncertain data

In this paper we examine multi-objective linear programming problems in the face of data uncertainty both in the objective function and the constraints. First, we derive a formula for the radius of robust feasibility guaranteeing constraint feasibility for all possible scenarios within a specified uncertainty set under affine data parametrization. We then present numerically tractable optimality conditions for minmax robust weakly efficient solutions, i.e., the weakly efficient solutions of the robust counterpart. We also consider highly robust weakly efficient solutions, i.e., robust feasible solutions which are weakly efficient for any possible instance of the objective matrix within a specified uncertainty set, providing lower bounds for the radius of highly robust efficiency guaranteeing the existence of this type of solutions under affine and rank-1 objective data uncertainty. Finally, we provide numerically tractable optimality conditions for highly robust weakly efficient solutions.This research was partially supported by the Australian Research Council, Discovery Project DP120100467, the MICINN of Spain, grant number MTM2011-29064-C03-02, and Generalitat Valenciana, grant number ACOMP/2013/062

Multi-resonant scatterers in sonic crystals: Locally multi-resonant acoustic metamaterial

An acoustic metamaterial made of a two-dimensional (2D) periodic array of multi-resonant acoustic scatterers is analyzed both experimentally and theoretically. The building blocks consist of a combination of elastic beams of low-density polyethylene foam (LDPF) with cavities of known area. Elastic resonances of the beams and acoustic resonances of the cavities can be excited by sound producing several attenuation peaks in the low frequency range. Due to this behavior the periodic array with long wavelength multi-resonant structural units can be classified as a locally multi-resonant acoustic metamaterial (LMRAM) with strong dispersion of its effective properties. The results presented in this paper could be used to design effective tunable acoustic filters for the low frequency range. (C) 2012 Elsevier Ltd. All rights reserved.This work was supported by MCI Secretaria de Estado de Investigacion (Spanish government) and FEDER funds, under Grants MAT2009-09438 and MTM2009-14483-C02-02. V.R.G. is grateful for the support of "Programa de Contratos Post-Doctorales con Movilidad UPV (CEI-01-11)". A.K. and O.U. are grateful for the support of EPSRC (UK) through research Grant EP/E063136/1.Romero García, V.; Krynkin, A.; García-Raffi, LM.; Umnova, O.; Sánchez Pérez, JV. (2013). Multi-resonant scatterers in sonic crystals: Locally multi-resonant acoustic metamaterial. Journal of Sound and Vibration. 332(1):184-198. doi:10.1016/j.jsv.2012.08.003S184198332