Pattern formation at cellular membranes by phosphorylation and dephosphorylation of proteins

We consider a classical model on activation of proteins, based in two reciprocal enzymatic biochemical reactions. The combination of phosphorylation and dephosphorylation reactions of proteins is a well established mechanism for protein activation in cell signalling. We introduce different affinity of the two versions of the proteins to the membrane and to the cytoplasm. The difference in the diffusion coefficient at the membrane and in the cytoplasm together with the high density of proteins at the membrane which reduces the accessible area produces domain formation of protein concentration at the membrane. We differentiate two mechanisms responsible for the pattern formation inside of living cells and discuss the consequences of these models for cell biology.Peer ReviewedPreprin

Reentry produced by small-scale heterogeneities in a discrete model of cardiac tissue

Reentries are reexcitations of cardiac tissue after the passing of an excitation wave which can cause dangerous arrhythmias like tachycardia or life-threatening heart failures like fibrillation. The heart is formed by a network of cells connected by gap junctions. Under ischemic conditions some of the cells lose their connections, because gap junctions are blocked and the excitability is decreased. We model a circular region of the tissue where a fraction of connections among individual cells are removed and substituted by non-conducting material in a twodimensional (2D) discrete model of a heterogeneous excitable medium with local kinetics based on electrophysiology. Thus, two neighbouring cells are connected (disconnected) with a probability f (1 - f). Such a region is assumed to be surrounded by homogeneous tissue. The circular heterogeneous area is shown to act as a source of new waves which reenter into the tissue and reexcitate the whole domain. We employ the Fenton-Karma equations to model the action potential for the local kinetics of the discrete nodes to study the statistics of the reentries in two dimensional networks with different topologies. We conclude that the probability of reentry is determined by the proximity of the fraction of disrupted connections between neighboring nodes (Peer ReviewedPostprint (published version

Reentry near the percolation threshold in a heterogeneous discrete model for cardiac tissue

Arrhythmias in cardiac tissue are related to irregular electrical wave propagation in the heart. Cardiac tissue is formed by a discrete cell network, which is often heterogeneous. A localized region with a fraction of nonconducting links surrounded by homogeneous conducting tissue can become a source of reentry and ectopic beats. Extensive simulations in a discrete model of cardiac tissue show that a wave crossing a heterogeneous region of cardiac tissue can disintegrate into irregular patterns, provided the fraction of nonconducting links is close to the percolation threshold of the cell network. The dependence of the reentry probability on this fraction, the system size, and the degree of excitability can be inferred from the size distribution of nonconducting clusters near the percolation threshold.Peer ReviewedPostprint (published version

Improving Fixed-Point Implementation of QR Decomposition by Rounding-to-Nearest

QR decomposition is a key operation in many current communication systems. This paper shows how to reduce the area of a fixed-point QR decomposition implementation based on Givens rotations by using a new number representation system. This new representation allows performing round-tonearest at the same cost of truncation. Consequently, the rounding errors of the results are halved, which allows it to reduce the word-length by one bit. This reduction positively impacts on the area, delay and power consumption of the design.Ministry of Education and Science of Spain and Junta of Andalucía under contracts TIN2013-42253-P and TIC-1692, respectively, and Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Heterogeneous Kohonen networks

A large number of practical problems involves elements that are described as a mixture of qualitative and quantitative infomation, and whose description is probably incomplete. The self-organizing map is an effective tool for visualization of high-dimensional continuous data. In this work, we extend the network and training algorithm to cope with heterogeneous information, as well as missing values. The classification performance on a collection of benchmarking data sets is compared in different configurations. Various visualization methods are suggested to aid users interpret post-training results.Peer ReviewedPostprint (author's final draft

Effective medium approach for heterogeneous reaction-diffusion media

An effective medium theory that can be used to calculate effective diffusion and reaction rate coefficients in random heterogeneous reaction-diffusion systems is described. The predictions of the theory are compared with simulations of spatially distributed media with different types of heterogeneity. The magnitude of the front velocity in bistable media is used to gauge the accuracy of the theoretical predictions. Quantitative agreement is found if the diffusion length in the heterogeneities is large compared to the characteristic width of the front. However, for small diffusion lengths the agreement depends on the type of heterogeneity. The effective medium predictions are also compared with simulations on systems with regular or temporal disorder.Peer ReviewedPostprint (published version

Complex wave patterns in an effective reaction–diffusion model for chemical reactions in microemulsions

An effective medium theory is employed to derive a simple qualitative model of a pattern forming chemical reaction in a microemulsion. This spatially heterogeneous system is composed of water nanodroplets randomly distributed in oil. While some steps of the reaction are performed only inside the droplets, the transport through the extended medium occurs by diffusion of intermediate chemical reactants as well as by collisions of the droplets. We start to model the system with heterogeneous reaction–diffusion equations and then derive an equivalent effective spatially homogeneous reaction–diffusion model by using earlier results on homogenization in heterogeneous reaction–diffusion systems [ S. Alonso, M. Bär, and R. Kapral, J. Chem. Phys. 134, 214102 (2009)]. We study the linear stability of the spatially homogeneous state in the resulting effective model and obtain a phase diagram of pattern formation, that is qualitatively similar to earlier experimental results for the Belousov–Zhabotinsky reaction in an aerosol OT (AOT)-water-in-oil microemulsion [ V. K. Vanag and I. R. Epstein, Phys. Rev. Lett. 87, 228301 (2001)]. Moreover, we reproduce many patterns that have been observed in experiments with the Belousov–Zhabotinsky reaction in an AOT oil-in-water microemulsion by direct numerical simulations.Peer ReviewedPostprint (published version

Nonlinear physics of electrical wave propagation in the heart: a review

The beating of the heart is a synchronized contraction of muscle cells (myocytes) that are triggered by a periodic sequence of electrical waves (action potentials) originating in the sino-atrial node and propagating over the atria and the ventricles. Cardiac arrhythmias like atrial and ventricular fibrillation (AF,VF) or ventricular tachycardia (VT) are caused by disruptions and instabilities of these electrical excitations, that lead to the emergence of rotating waves (VT) and turbulent wave patterns (AF,VF). Numerous simulation and experimental studies during the last 20 years have addressed these topics. In this review we focus on the nonlinear dynamics of wave propagation in the heart with an emphasis on the theory of pulses, spirals and scroll waves and their instabilities in excitable media and their application to cardiac modeling. After an introduction into electrophysiological models for action potential propagation, the modeling and analysis of spatiotemporal alternans, spiral and scroll meandering, spiral breakup and scroll wave instabilities like negative line tension and sproing are reviewed in depth and discussed with emphasis on their impact in cardiac arrhythmias.Peer ReviewedPreprin

Web 2.0, language resources and standards to automatically build a multilingual named entity lexicon

This paper proposes to advance in the current state-of-the-art of automatic Language Resource (LR) building by taking into consideration three elements: (i) the knowledge available in existing LRs, (ii) the vast amount of information available from the collaborative paradigm that has emerged from the Web 2.0 and (iii) the use of standards to improve interoperability. We present a case study in which a set of LRs for different languages (WordNet for English and Spanish and Parole-Simple-Clips for Italian) are extended with Named Entities (NE) by exploiting Wikipedia and the aforementioned LRs. The practical result is a multilingual NE lexicon connected to these LRs and to two ontologies: SUMO and SIMPLE. Furthermore, the paper addresses an important problem which affects the Computational Linguistics area in the present, interoperability, by making use of the ISO LMF standard to encode this lexicon. The different steps of the procedure (mapping, disambiguation, extraction, NE identification and postprocessing) are comprehensively explained and evaluated. The resulting resource contains 974,567, 137,583 and 125,806 NEs for English, Spanish and Italian respectively. Finally, in order to check the usefulness of the constructed resource, we apply it into a state-of-the-art Question Answering system and evaluate its impact; the NE lexicon improves the system’s accuracy by 28.1%. Compared to previous approaches to build NE repositories, the current proposal represents a step forward in terms of automation, language independence, amount of NEs acquired and richness of the information represented