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  • Exploiting nonlinearity and noise in optical tweezers and semiconductor lasers: from resonant damping to stochastic logic gates and extreme pulses.

     Perrone, Sandro
    Defense's date: 2014-02-07
    Department of Applied Physics, Universitat Politècnica de Catalunya
    Theses

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    El tema central de esta tesis es el estudio de las dinámicas estocásticas y no lineales en sistemas ópticos. En primer lugar, se ha observado experimentalmente la dinámica estocástica de una partícula colloidal en una trampa óptica sometida a una fuerza externa. Los resultados se han relacionado a los efectos de un ruido paramétrico externo agregado a trampas ópticas monoestables y biestables. Específicamente hemos descubierto un nuevo efecto que hemos nombrado resonancia estocástica amortiguada (SRD), que se refiere a la minimización de la varianza de la posición de la partícula atrapada en un potencial harmonico, en funcion de la intensidad de un ruido paramétrico externo, añadido a la fuerza que actua sobre la particula. Se ha comparado la resonancia estocástica clásica con la amortiguada, y hemos demonstrado que se trata de dos fenómenos que coexisten en el mismo sistema, pero en diferentes regímenes. Además, hemos investigado experimentalmente un sistema monoestable, que exhibe un máximo en el cociente señal-ruido, que no se habia observado anteriormente en una trampa optica. Para estas investigaciones, hemos desarrollado una nueva técnica que aumenta 10 veces el rango de detección del fotodiodo, que explota el crosstalk entre canales.En segundo lugar, hemos estudiado la dinámica estocástica de un láser de semiconductor (SCL) de emision vertical (VCSEL), que presenta biestabilidad en las polarización de la luz emitida y fenomenos de histéresis, al variar la corriente inyectada o al variar la potencia óptica inyectada.Hemos demostrado que estas propiedades se pueden utilizar para realizar operaciones lógicas gracias al efecto del ruido de emisión espontánea. Dos señales de entrada lógicas han sido codificadas en tres niveles de potencia inyectada desde un láser guia (llamado master), y la respuesta lógica del laser injectado (slave) fue decodificada a partir de la polarización de la luz emitida. Se ha logrado una respuesta lógica correcta cuando se ajusta la potencia de la injeccion para favorecer, en dos de los niveles de injeccion, a una de las dos polarizaciones, y para favorecer a la otra polarización, en el tercer nivel de injeccion. Hemos demostrado numéricamente que el operador logico basado en la polarizacion emitida por un VCSEL con injeccion optica permite reproducir la tabla de verdad para los operadores lógicos OR y NOR. La extensión a los operadores logicos AND y NAND es de muy simple implementaciòn. Codificando las señales de entrada en forma optica hemos sido capaces de reducir el tiempo mínimo de bit requerido para realizar operaciones logicas correctamente, desde 30 ns, obtenido previamente mediante codificacion optoelectrónica, hasta 5 ns.El tercer objetivo de esta tesis es el estudio de la dinámica no lineal caótica de un SCL inyectado ópticamente en la region de parametros donde se observan esporadicamente picos extremos de intensidad, llamados Rogue Waves (RWs). Nuestros estudios nos permiten concluir que, agregando ruido moderado de intensidad apropiada, el número de pulsos extremos aumenta respecto al caso determinista. Por el contrario, en algunas regiones de parametros, agregar un ruido de baja intensidad da lugar a una significativa disminución de los pulsos extremos. Con el fin de suprimir o inducir estos pulsos extremos, hemos investigado los efectos de una modulación periódica de la corriente del láser. Hemos observado que esta modulacion puede efectivamente suprimir o inducir RWs, dependiendo de la frecuencia de la modulacion.

  • A mesoscopic study of the excitatory/inhibitory coupling effect on synchronization and segregation

     Pons Rivero, Antonio Javier; Malagarriga Guasch, Daniel; Garcia Ojalvo, Jorge
    NETT Summer School
    Presentation's date: 2013-07-01
    Presentation of work at congresses

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  • Emergent bimodal firing patterns implement different encoding strategies during gamma-band oscillations

     De Sancristobal Alonso, Belen; Vicente, Raul; Sancho Herrero, José María; Garcia Ojalvo, Jorge
    Frontiers in Computational Neuroscience
    Date of publication: 2013-03-26
    Journal article

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    Upon sensory stimulation, primary cortical areas readily engage in narrow-band rhythmic activity between 30 to 90 Hz, the so-called gamma oscillations. Here we show that, when embedded in a balanced network, type-I excitable neurons entrained to the collective rhythm show a discontinuity in their firing rates between a slow and a fast spiking mode. This jump in the spiking frequencies is characteristic to type II neurons, but is not present in the frequency-current curve (f-I curve) of isolated type I neurons. There-fore, this rate bimodality arises as an emerging network property in type I population models. We have studied the mechanisms underlying the generation of these two firing modes, in order to reproduce the spiking activity of in vivo cortical recordings, which is known to be highly irregular and sparse. We have also analyzed the relation between afferent inputs and the single unit activity...

  • Neuronal oscillations: from single-unit activity to emergent dynamics and back  Open access

     De Sancristobal Alonso, Belen
    Defense's date: 2013-07-22
    Department of Physics and Nuclear Engineering, Universitat Politècnica de Catalunya
    Theses

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    L’objectiu principal d’aquesta tesi és avançar en la comprensió del processament d’informació en xarxes neuronals en presència d’oscil lacions subumbrals. La majoria de neurones propaguen la seva activitat elèctrica a través de sinapsis químiques que són activades, exclusivament, quan el corrent elèctric que les travessa supera un cert llindar. És per aquest motiu que les descàrregues ràpides i intenses produïdes al soma neuronal, els anomenats potencials d’acció, són considerades la unitat bàsica d’informació neuronal, és a dir, el senyal mínim i necessari per a iniciar la comunicació entre dues neurones. El codi neuronal és entès, doncs, com un llenguatge binari que expressa qualsevol missatge (estímul sensorial, memòries, etc.) en un tren de potencials d’acció. Tanmateix, cap funció cognitiva rau en la dinàmica d’una única neurona. Circuits de milers de neurones connectades entre sí donen lloc a determinats ritmes, palesos en registres d’activitat colectiva com els electroencefalogrames (EEG) o els potencials de camp local (LFP). Si els potencials d’acció de cada cèl lula, desencadenats per fluctuacions estocàstiques de les corrents sinàptiques, no assolissin un cert grau de sincronia, no apareixeria aquesta periodicitat a nivell de xarxa. Per tal de poder entendre si aquests ritmes intervenen en el codi neuronal hem estudiat tres situacions. Primer, en el Capítol 2, hem mostrat com una cadena oberta de neurones amb un potencial de membrana intrínsecament oscil latori filtra un senyal periòdic arribant per un dels extrems. La resposta de cada neurona (pulsar o no pulsar) depèn de la seva fase, de forma que cada una d’elles rep un missatge filtrat per la precedent. A més, cada potencial d’acció presinàptic provoca un canvi de fase en la neurona postsinàptica que depèn de la seva posició en l’espai de fases. Els períodes d’entrada capaços de sincronitzar les oscil lacions subumbrals són aquells que mantenen la fase d’arribada dels potencials d’acció fixa al llarg de la cadena. Per tal de què el missatge arribi intacte a la darrera neurona cal, a més a més, que aquesta fase permeti la descàrrega del voltatge transmembrana. En segon cas, hem estudiat una xarxa neuronal amb connexions tant a veïns propers com de llarg abast, on les oscil lacions subumbrals emergeixen de l’activitat col lectiva reflectida en els corrents sinàptics (o equivalentment en el LFP). Les neurones inhibidores aporten un ritme a l’excitabilitat de la xarxa, és a dir, que els episodis en què la inhibició és baixa, la probabilitat d’una descàrrega global de la població neuronal és alta. En el Capítol 3 mostrem com aquest ritme implica l’aparició d’una bretxa en la freqüència de descàrrega de les neurones: o bé polsen espaiadament en el temps o bé en ràfegues d’elevada intensitat. La fase del LFP determina l’estat de la xarxa neuronal codificant l’activitat de la població: els mínims indiquen la descàrrega simultània de moltes neurones que, ocasionalment, han superat el llindar d’excitabilitat degut a un decreixement global de la inhibició, mentre que els màxims indiquen la coexistència de ràfegues en diferents punts de la xarxa degut a decreixements locals de la inhibició en estats globals d’excitació. Aquesta dinàmica és possible gràcies al domini de la inhibició sobre l’excitació. En el Capítol 4 considerem acoblament entre dues xarxes neuronals per tal d’estudiar la interacció entre ritmes diferents. Les oscil lacions indiquen recurrència en la sincronització de l’activitat col lectiva, de manera que durant aquestes finestres temporals una població optimitza el seu impacte en una xarxa diana. Quan el ritme de la població receptora i el de l’emissora difereixen significativament, l’eficiència en la comunicació decreix, ja que les fases de màxima resposta de cada senyal LFP no mantenen una diferència constant entre elles. Finalment, en el Capítol 5 hem estudiat com les oscil lacions col lectives pròpies de l’estat de son donen lloc al fenomen de coherència estocàstica. Per a una intensitat òptima del soroll, modulat per l’excitabilitat de la xarxa, el LFP assoleix una regularitat màxima donant lloc a un període refractari de la població neuronal. En resum, aquesta Tesi mostra escenaris d’interacció entre els potencials d’acció, característics de la dinàmica de neurones individuals, i les oscil lacions subumbrals, fruit de l’acoblament entre les cèl lules i ubiqües en la dinàmica de poblacions neuronals. Els resultats obtinguts aporten funcionalitat a aquests ritmes emergents, agents sincronitzadors i moduladors de les descàrregues neuronals i reguladors de la comunicació entre xarxes neuronals.

    The main objective of this thesis is to better understand information processing in neuronal networks in the presence of subthreshold oscillations. Most neurons propagate their electrical activity via chemical synapses, which are only activated when the electric current that passes through them surpasses a certain threshold. Therefore, fast and intense discharges produced at the neuronal soma (the action potentials or spikes) are considered the basic unit of neuronal information. The neuronal code is understood, then, as a binary language that expresses any message (sensory stimulus, memories, etc.) in a train of action potentials. Circuits of thousands of interconnected neurons give rise to certain rhythms, revealed in collective activity measures such as electroencephalograms (EEG) and local field potentials (LFP). Synchronization of action potentials of each cell, triggered by stochastic fluctuations of the synaptic currents, cause this periodicity at the network level.To understand whether these rhythms are involved in the neuronal code we studied three situations. First, in Chapter 2, we showed how an open chain of neurons with an intrinsically oscillatory membrane potential filters a periodic signal coming from one of its ends. The response of each neuron (to spike or not) depends on its phase, so that each cell receives a message filtered by the preceding one. Each presynaptic action potential causes a phase change in the postsynaptic neuron, which depends on its position in the phase space. Those incoming periods that are able to synchronize the subthreshold oscillations, keep the phase of arrival of action potentials fixed along the chain. The original message reaches intact the last neuron provided that this phase allows the discharge of the transmembrane voltage.I the second case, we studied a neuronal network with connections to both long range and close neighbors, in which the subthreshold oscillations emerge from the collective activity apparent in the synaptic currents. The inhibitory neurons provide a rhythm to the excitability of the network. When inhibition is low, the likelihood of a global discharge of the neuronal population is high. In Chapter 3 we show how this rhythm causes a gap in the discharge frequency of neurons: either they pulse single spikes or they fire bursts of high intensity. The LFP phase determines the state of the neuronal network, coding the activity of the population: its minima indicate the simultaneous discharge of many neurons, while its maxima indicate the coexistence of bursts due to local decreases of inhibition at global states of excitation. In Chapter 4 we consider coupling between two neural networks in order to study the interaction between different rhythms. The oscillations indicate recurrence in the synchronization of collective activity, so that during these time windows a population optimizes its impact on a target network. When the rhythm of the emitter and receiver population differ significantly, the communication efficiency decreases as the phases of maximum response of each LFP signal do not maintain a constant difference between them.Finally, in Chapter 5 we studied how oscillations typical of the collective sleep state give rise to stochastic coherence. For an optimal noise intensity, modulated by the excitability of the network, the LFP reaches a maximal regularity leading to a refractory period of the neuronal population.In summary, this Thesis shows scenarios of interaction between action potentials, characteristics of the dynamics of individual neurons, and the subthreshold oscillations, outcome of the coupling between the cells and ubiquitous in the dynamics of neuronal populations . The results obtained provide functionality to these emerging rhythms, triggers of synchronization and modulator agents of the neuronal discharges and regulators of the communication between neuronal networks.

  • Transient and stochastic dynamics in cellular processes  Open access

     Rue Queralt, Pau
    Defense's date: 2013-07-25
    Department of Applied Physics, Universitat Politècnica de Catalunya
    Theses

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    This Thesis studies different cellular and cell population processes driven by non-linear and stochastic dynamics. The problems addressed here gravitate around the concepts of transient dynamics and relaxation from a perturbed to a steady state. In this regard, in all processes studied, stochastic fluctuations, either intrinsically present in or externally applied to these systems play an important and constructive role, by either driving the systems out of equilibrium, interfering with the underlying deterministic laws, or establishing suitable levels of heterogeneity. The first part of the Thesis is committed the analysis of genetically regulated transient cellular processes. Here, we analyse, from a theoretical standpoint, three genetic circuits with pulsed excitable dynamics. We show that all circuits can work in two different excitable regimes, in contrast to what was previously speculated. We also study how, in the presence of molecular noise, these excitable circuits can generate periodic polymodal pulses due to the combination of two noise induced phenomena: stabilisation of an unstable spiral point and coherence resonance. We also studied an excitable genetic mechanism for the regulation of the transcriptional fluctuations observed in some pluripotency factors in Embryonic Stem cells. In the embryo, pluripotency is a transient cellular state and the exit of cells from it seems to be associated with transcriptional fluctuations. In regard to pluripotency control, we also propose a novel mechanism based on the post-translational regulation of a small set of four pluripotency factors. We have validated the theoretical model, based on the formation of binary complexes among these factors, with quantitative experimental data at the single-cell level. The model suggests that the pluripotency state does not depend on the cellular levels of a single factor, but rather on the equilibrium of correlations between the different proteins. In addition, the model is able to anticipate the phenotype of several mutant cell types and suggests that the regulatory function of the protein interactions is to buffer the transcriptional activity of Oc4, a key pluripotency factor. In the second part of the Thesis we studied the behaviour of a computational cell signalling network of the human fibroblast in the presence of external fluctuations and signals. The results obtained here indicate that the network responds in a nontrivial manner to background chatter, both intrinsically and in the presence of external periodic signals. We show that these responses are consequence of the rerouting of the signal to different network information-transmission paths that emerge as noise is modulated. Finally, we also study the cell population dynamics during the formation of microbial biofilms, wrinkled pellicles of bacteria glued by an extracellular matrix that are one of the simplest cases of self-organised multicellular structures. In this Thesis we develop a spatiotemporal model of cellular growth and death that accounts for the experimentally observed patterns of massive bacterial death that precede wrinkle formation in biofilms. These localised patterns focus mechanical forces during biofilm expansion and trigger the formation of the characteristic ridges. In this sense, the proposed model suggests that the death patterns emerge from the mobility changes in bacteria due to the production of extracellular matrix and the spatially inhomogeneous cellular growth. An important prediction of the model is that matrix productions is crucial for the appearance of the patterns and, therefore for winkle formation. We have also experimentally validated validated this prediction with matrix deficient bacterial strains, which show neither death patterns nor wrinkles.

    En aquesta Tesi s’estudien diferents processos intracel·lulars i de poblacions cel·lulars regits per dinàmica estocàstica i no lineal. El problemes biològics tractats graviten al voltant el concepte de dinàmica transitòria i de relaxació d’un estat dinàmic pertorbat a l’estat estacionari. En aquest sentit, en tots els processos estudiats, les fluctuacions estocàstiques, presents intrínsecament o aplicades de forma externa, hi tenen un paper constructiu, ja sigui empenyent els sistemes fora de l’equilibri, interferint amb les lleis deterministes subjacents, o establint els nivells d’heterogeneïtat necessaris. La primera part de la Tesi es dedica a l’estudi de processos cel·lulars transitoris regulats genèticament. En ella analitzem des d’un punt de vista teòric tres circuits genètics de control de polsos excitables i, contràriament al que s’havia especulat anteriorment, establim que tots ells poden treballar en dos tipus de règim excitable. Analitzem també com, en presència de soroll molecular, aquests circuits excitables poden generar polsos periòdics i multimodals degut a la combinació de dos fenòmens induïts per soroll: l’estabilització estocàstica d’estats inestables i la ressonància de coherència. D’altra banda, estudiem com un mecanisme genètic excitable pot ser el responsable de regular a nivell transcripcional les fluctuacions que s’observen experimentalment en alguns factors de pluripotència en cèl·lules mare embrionàries. En l’embrió, la pluripotència és un estat cel·lular transitori i la sortida de les cèl·lules d’aquest sembla que està associada a fluctuacions transcripcionals. En relació al control de la pluripotència, presentem també un nou mecanisme basat en la regulació post-traduccional d’un petit conjunt de 4 factors de pluripotència. El model teòric proposat, basat en la formació de complexos entre els diferents factors de pluripotència, l’hem validat mitjançant experiments quantitatius en cèl·lules individuals. El model postula que l’estat de pluripotència no depèn dels nivells cel·lulars d’un únic factor, sinó d’un equilibri de correlacions entre diverses proteïnes. A més, prediu el fenotip de cèl·lules mutants i suggereix que la funció reguladora de les interaccions entre les quatre proteïnes és la d’esmorteir l’activitat transcripcional d’Oct4, un dels principals factors de pluripotència. En el segon apartat de la Tesi estudiem el comportament d’una xarxa computacional de senyalització cel·lular de fibroblast humà en presència de senyals externs fluctuants i cíclics. Els resultats obtinguts mostren que la xarxa respon de forma no trivial a les fluctuacions ambientals, fins i tot en presència d’una senyal externa. Diferents nivells de soroll permeten modular la resposta de la xarxa, mitjançant la selecció de rutes alternatives de transmissió de la informació. Finalment, estudiem la dinàmica de poblacions cel·lulars durant la formació de biofilms, pel·lícules arrugades d’aglomerats de bacteris que conformen un dels exemples més simples d’estructures multicel·lulars autoorganitzades. En aquesta Tesi presentem un model espai-temporal de creixement i mort cel·lular motivat per l’evidència experimental sobre l’aparició de patrons de mort massiva de bacteris previs a la formació de les arrugues dels biofilms. Aquests patrons localitzats concentren les forces mecàniques durant l’expansió del biofilm i inicien la formació de les arrugues característiques. En aquest sentit, el model proposat explica com es formen els patrons de mort a partir dels canvis de mobilitat dels bacteris deguts a la producció de matriu extracel·lular combinats amb un creixement espacialment heterogeni. Una important predicció del model és que la producció de matriu és un procés clau per a l’aparició dels patrons i, per tant de les arrugues. En aquest aspecte, els nostres resultats experimentals en bacteris mutants que no produeixen components essencials de la matriu, confirmen les prediccions.

  • ESTOCASTICIDAD EN SISTEMAS COMPLEJOS NOLINEALES

     Pons Rivero, Antonio Javier; Torrent Serra, Maria Del Carmen; Masoller Alonso, Cristina; Pigolotti, Simone; Ramirez de La Piscina Millan, Laureano; Peñaranda Ayllon, Angelina; Malagarriga Guasch, Daniel; Dies Miracle, Marta; Aragoneses Aguado, Andres; Deza, Juan Ignacio; Garcia Ojalvo, Jorge
    Participation in a competitive project

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  • Synchronizability and dynamics of coupled neural mass oscillators

     Malagarriga Guasch, Daniel; Garcia Ojalvo, Jorge; Pons Rivero, Antonio Javier
    International Symposium on Nonlinear Theory and its Applications
    Presentation's date: 2012-10-24
    Presentation of work at congresses

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  • Modelos físicos de actividad cerebral: de la micro- a la macro-escala

     Pons Rivero, Antonio Javier; Garcia Ojalvo, Jorge
    Revista española de física
    Date of publication: 2012-09-01
    Journal article

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  • Localized cell death focuses mechanical forces during 3D patterning in a biofilm

     Asally, M.; Kittisopikul, M.; Rue Queralt, Pau; Du, Yingjie; Hu, Zheng; Cagatay, Tolga; Robinson, A.B.; Lu, Hongliang; Garcia Ojalvo, Jorge; Süel, Gürol M.
    Proceedings of the National Academy of Sciences of the United States of America
    Date of publication: 2012-11-13
    Journal article

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  • Zero-lag synchronization and bubbling in delay-coupled lasers

     Tiana Alsina, Jordi; Hicke, K.; Porte, X.; Soriano, M.C.; Torrent Serra, Maria Del Carmen; Garcia Ojalvo, Jorge
    Physical review E: statistical, nonlinear, and soft matter physics
    Date of publication: 2012-02-21
    Journal article

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  • Interspike-interval correlations induced by two-state switching in an excitable system

     Schwalger, T.; Tiana Alsina, Jordi; Torrent Serra, Maria Del Carmen; Garcia Ojalvo, Jorge; Lindner, B.
    Europhysics letters
    Date of publication: 2012-07
    Journal article

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  • Correlations between the levels of Oct4 and nanog as a signature for naive pluripotency in mouse embryonic stem cells

     Muñoz Descalzo, Silvia; Rue Queralt, Pau; Garcia Ojalvo, Jorge; Martinez Arias, Alfonso
    Stem cells
    Date of publication: 2012-12
    Journal article

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  • Towards a statistical mechanics of cell fate decisions

     Garcia Ojalvo, Jorge; Martinez Arias, Alfonso
    Current opinion in genetics and development
    Date of publication: 2012-12
    Journal article

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  • Dinámica de circuitos de regulación genética en bacterias  Open access

     Espinar Calvo, Maria Lorena
    Defense's date: 2012-12-21
    Department of Applied Physics, Universitat Politècnica de Catalunya
    Theses

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    El objetivo de esta Tesis es el estudio de diferentes comportamientos celulares dinámicos en Escherichia coli y Bacillus subtilis. Es interesante comprender cómo estos organismos sencillos poseen mecanismos complejos para responder al entorno en el que se encuentran. Dicha respuesta está regulada por complicadas redes de regulación formadas por genes y proteínas, donde al igual que los instrumentistas de una orquesta, cada elemento de las redes genéticas debe tomar parte en armonía, en el momento justo y la cantidad adecuada para dar lugar a la respuesta celular apropiada. La Parte I introduce aspectos básicos de la metodología utilizada y conceptos fundamentales para la comprensión de los resultados. El Capítulo 1 es una breve introducción a los circuitos de regulación genética y el uso de proteínas fluorescentes para el estudio in vivo y en células individuales de la dinámica de dichos circuitos. El Capítulo 2 describe los materiales y técnicas utilizadas, desde el cultivo y obtención de cepas bacterianas, los métodos para filmar dichas cepas con microscopía de fluorescencia temporalizada, al análisis de las imágenes. El Capítulo 3 describe las características básicas de los procesos biológicos de estudio. El Capítulo 4 describe ciertos aspectos de la dinámica celular como el comportamiento oscilatorio o excitable de algunos sistemas biológicos, y las herramientas matemáticas usadas para contrastar los datos experimentales. La Parte II corresponde a los resultados. El Capítulo 5 describe los resultados del estudio del control del inicio de la replicación cromosómica en E. coli. Mediante una serie de perturbaciones en las proteínas que regulan este proceso, y mediante el análisis de las imágenes obtenidas por microscopía, se cuantificó el efecto ejercido sobre el inicio de replicación, comparando los resultados con una cepa control. El Capítulo 6 describe los resultados del estudio de la forma en que el circuito genético que regula la competencia en B. subtilis integra múltiples señales simultáneas. Se caracterizó experimentalmente y con un análisis de bifurcación del modelo matemático del circuito, la respuesta en células individuales e in vivo a señales químicas de diferente intensidad que controlan la expresión constitutiva de los genes que forman el circuito, y a la variación del número de copias de uno de estos genes. El Capítulo 7 describe los resultados del estudio del proceso de toma de decisión celular en B. subtilis, basado en la decisión de estas bacterias por optar entre los programas de diferenciación en competencia genética y esporulación, los cuales compiten entre sí en el tiempo. El análisis simultáneo y en células individuales de ambos programas permitió descubrir por qué las bacterias optan por uno u otro mediante un mecanismo de carrera molecular entre estos dos programas en competición. El Capítulo 8 describe los resultados del estudio de la adaptación celular al estrés mediante esporulación y la toma de decisión de una forma robusta en B. subtilis. Se analizó de forma cuantitativa la expresión de los genes implicados en la progresión hacia la formación de esporas y se desarrolló un modelo matemático poblacional para estudiar el efecto de la reversibilidad en el proceso de adaptación celular a cambios en los niveles de estrés. La Parte III corresponde a las Conclusiones y la perspectiva futura para los resultados descritos en la Parte II. Los resultados obtenidos contribuyen a la comprensión de determinados comportamientos en E. coli y B. subtilis. Estas bacterias, sencillas si se comparan con organismos superiores, ofrecen la posibilidad de estudiar mecanismos utilizados por sistemas más complejos, pero que para su estudio se requieren técnicas complicadas. El estudio en células individuales de la dinámica de redes de regulación mediante las técnicas utilizadas nos permite el análisis in vivo y en tiempo real de lo que sucede con dichas redes en el interior de las células respecto al exterior celular.

    The aim of this Thesis is the study of different dynamic cellular behaviors in Escherichia coli and Bacillus subtilis. It is interesting to understand how these simple organisms have not so simple mechanisms to respond to their environment. This response is regulated by complex regulatory networks consisting of genes and proteins, where as instrumentalists in an orchestra, each element of the network should operates in harmony, at the right time and the right amount to give an appropriate cellular response. Part I introduces basic aspects of the methodology and concepts for the understanding of the results presented in this Thesis. Chapter 1 provides a brief introduction to genetic regulatory circuits and the fluorescent proteins used for the study of the dynamics of such circuits in vivo and in individual cells. Chapter 2 describes the materials and techniques used, from growing and obtaining bacterial strains, to the methodology used for filming these strains by temporalized fluorescence microscopy, and to the analysis of the obtained images. Chapter 3 describes the main features of the dynamical biological processes studied in E. coli and B. subtilis. Chapter 4 refers to certain aspects of cellular dynamics such as oscillatory or excitable behavior of some biological systems, as well as the mathematical tools used to compare the data obtained experimentally. Part II corresponds to the results. Chapter 5 describes the results of the study of the control of chromosome replication initiation in E. coli. We implemented a set of perturbations in the main proteins that regulate this process, and their effect on the initiation of replication, quantified by analyzing the images obtained by fluorescence microscopy, comparing the results with a control strain. Chapter 6 describes the results obtained from the study of how a genetic circuit in B. subtilis, namely the one regulating competence, integrates multiple simultaneous inputs. We characterized experimentally the response of individual cells in vivo to different chemical signals that control the strength of the constitutive expression of genes forming the circuit, in addition to the copy number variation of one of these genes. The results were compared with a bifurcation analysis of the mathematical model of the circuit. Chapter 7 describes the results obtained in a study of the decision making process of microorganism B. subtilis. Specifically, we studied the decision of these bacteria between two differentiation programs such as genetic competence and sporulation, which compete with each other in time. The simultaneous analysis in individual cells of both programs allowed us to uncover the way in which bacteria choose between these two competing programs, showing that the competition occurs through a molecular race. Finally, Chapter 8 describes the results obtained in the study of reversible progression towards an all-or-none switch in the sporulation of B. subtilis. We quantitatively analyzed the expression of genes involved in the progression towards spore formation and a population model was developed to study the effect of reversibility in the process of cellular adaptation to changes in stress levels. Part III details the conclusions and a description of the possible future perspectives for each of the results described in Part II. The results obtained contribute to the understanding of certain dynamic behaviors in the microorganisms E. coli and B. subtilis. These bacteria, although simple when compared with higher organisms, offer the possibility of studying mechanisms that are frequently utilized by more complex systems, which require more sophisticated analysis techniques. The study at the single cell level of network dynamics of gene regulation by the techniques used in this Thesis, allows the analysis in vivo and in real time of the underlying dynamic of such networks inside cells in response to the cell environment.

  • Study on conduction mechanismes of mediun voltage cable XLPE insulation in the melting range of temperatures.  Open access

     Òrrit Prat, Jordi
    Defense's date: 2012-03-07
    Department of Applied Physics, Universitat Politècnica de Catalunya
    Theses

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    D’ençà que el polietilè reticulat (XLPE) es va començar a utilitzar com aïllament elèctric per cables de subministrament elèctric, s’han destinat molts esforços a l’estudi de les propietats dielèctriques del polietilè i l’efecte que la càrrega d’espai té sobre el seu comportament. En aquest sentit, les corrents de despolarització estimulades tèrmicament (TSDC) s’han utilitzat extensament per estudiar les relaxacions de càrrega d’espai. Aquesta tècnica ha demostrat tenir prou resolució per distingir diferències en aïllaments de XLPE amb composicions o processos de fabricació diferents. En aquesta tesi, els mecanismes de conducció dels aïllaments XLPE de cables de mitjana tensió (MV) han estat estudiats per TSDC i diverses tècniques complementàries, com l’anàlisi dinàmica elèctrica (DEA), les corrents d’absorció/resorció (ARC), el pols electroacústic (PEA) i les corrents de despolarització isotèrmiques (IDC). Altres tècniques, com l’espectroscòpia d’infrarojos (FTIR) o la difracció de raigs X, han estat també utilitzades per caracteritzar el material. S’han obtingut espectres TSDC per diferents mostres de cable, les quals en condicions de servei treballen en un rang de tensió AC de 12 a 20kV i a temperatures al voltant dels 90ºC. D’altra banda, s’han realitzat mesures de la conductivitat per ARC i DEA en mostres de cable, en cilindres de XLPE i en films. Les mesures s’han dut a terme a temperatures pertanyents al rang de fusió del XLPE (50–110ºC), en mostres sotmeses a aquestes temperatures durant diferents períodes de temps. Els resultats mostren diferències importants entre el comportament de les propietats conductives de les mostres de cable amb pantalles semiconductores (SC) i sense (cilindres de XLPE). El comportament observat ha estat explicat mitjançant la coexistència de dos mecanismes de conducció. La difusió d’impureses des de les pantalles SC determina el comportament d’una d’aquestes contribucions a mig i llarg termini. Els resultats obtinguts per FTIR són consistents amb aquest model. Respecte la microestructura, tant les mesures DSC com la difracció per raigs X mostren que existeixen processos de recristal•lització quan les mostres són sotmeses a temperatures ubicades dins del rang de fusió. Els electrets formats mitjançant el mètode de la polarització per finestres (WP) mostren una descàrrega TSDC amb un ample pic heteropolar en el rang de fusió, amb el màxim al voltant dels 105ºC. En treballs previs, aquest pic es va associar a la fusió de la fracció cristal•lina. Tanmateix, en lloc de decréixer quan la temperatura de polarització augmenta, el pic presenta una temperatura de polarització òptima al voltant de 90-95ºC. Aquest comportament ha estat explicat tenint en compte els processos de recristal•lització que es produeixen quan el material es polaritza isotèrmicament. Durant la recristal•lització, una nova fracció cristal•lina creix en un estat polaritzat degut el camp aplicat, i origina una corrent de despolarització quan es fon durant la mesura TSDC. Amb l’objectiu de determinar l’origen d’altres pics que apareixen en l’espectre TSDC del XLPE, s’han emprat les IDC com a tècnica complementària. Les corrents IDC obtingudes de mostres no tractades es poden representar com la combinació de dues contribucions diferenciades: un terme que és una funció potencial del temps i un d’exponencial. La segona relaxació es correspon amb un pic TSDC que apareix a 95ºC. D’aquesta manera s’ha pogut determinar l’origen dipolar del pic. Finalment, mitjançant la tècnica PEA s’ha obtingut la distribució de la càrrega d’espai en mostres polaritzades que havien estat sotmeses a diferents tractaments tèrmics. S’ha observat un comportament transitori tant per PEA com per TSDC. Tanmateix no s’ha pogut establir cap relació directa entre les descàrregues TSDC i mesures PEA. En conseqüència, s’ha proposat una explicació per les corbes TSDC que considera mecanismes que no són detectables en els perfils de càrrega obtinguts per PEA

    Since cross-linked polyethylene (XLPE) started to be used as electrical insulation for power cables, much research has been focused on polyethylene dielectric properties and the effect of the space charge on its behavior. In this sense, thermally stimulated depolarization currents (TSDC) have been widely used to study space charge relaxation. This technique has proved to have enough resolution to determine differences in charge trapping properties among XLPE insulations with different composition and manufacturing processes. In this thesis work, the conduction mechanisms of medium voltage (MV) cable XLPE insulation have been studied by TSDC and several complementary techniques, such as dynamic electrical analysis (DEA), absorption/resorption currents (ARC), pulsed electroacoustic (PEA) and isothermal depolarization currents (IDC). Other techniques, like Fourier transform infrared (FTIR) spectroscopy or X-ray diffractometry, have been used to characterize the material. TSDC spectra have been obtained for different cable samples, which in service conditions work under AC voltages ranging from 12 to 20kV and at temperatures around 90ºC. On the other hand, conductivity measurements by ARC and DEA have been performed in cable samples and in XLPE cylinders, as well as XLPE films. Measurements have been carried out at temperatures within the melting temperature range of XLPE (50–110ºC) on samples annealed at such temperatures during several annealing times. Results show significant differences in the behavior of the conductive properties of XLPE cable samples with semiconducting (SC) screens and without them (XLPE cylinders). The observed behavior has been explained by the coexistence of two conduction mechanisms. Diffusion of impurities from SC screens determines the medium and long-term behavior of one of these contributions and, hence, of cable conductivity. FTIR results are consistent with this model. With respect to microstructure, DSC and X-ray diffractometry results show that recrystallization processes exist when samples are annealed in the melting range of temperatures. Electrets formed by means of the windowing polarization method (WP) showed a TSDC discharge with a wide heteropolar peak in the melting temperature range, and with the maximum at about 105ºC. This peak was associated with the melting of the crystalline fraction in previous works. However, in spite of decreasing with the temperature of polarization, an optimal polarization temperature around 90–95ºC is found. This behavior has been explained by taking into account recrystallization processes when the insulation is isothermally polarized. During recrystallization, the new crystalline fraction grows in a polarized state due to the applied electric field, and it causes the depolarization current when it melts during the TSDC measurement. Results obtained from different experiments are consistent with this assumption. With the aim to find out the origin of other TSDC peaks present in the spectrum of XLPE cable samples, IDC has been used as complementary technique. IDC currents obtained from as-received cable samples at temperatures close to service conditions can be considered as the combination of two different contributions: a power law current and a stretched exponential contribution. The last relaxation process has been successfully associated with with a TSDC peak found at 95ºC. By this way the dipolar origin of the peak has been determined. Finally, PEA measurements have provided the space charge distribution profiles of polarized samples with different annealings. A transient behavior has been observed in both PEA and TSDC measurements. However, no straightforward relation between TSDC discharges and space charge detected by PEA can be established. Therefore, an explanation for TSDC curves has been proposed, which considers mechanisms that are not noticeable in charge profiles obtained by PEA.

  • Premi ICREA Acadèmia

     Masoller Alonso, Cristina; Garcia Ojalvo, Jorge; Llorca Pique, Jordi
    Award or recognition

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  • NEURAL ENGINEERING TRANSFORMATIVE TECHNOLOGIES

     Pons Rivero, Antonio Javier; Torrent Serra, Maria Del Carmen; Masoller Alonso, Cristina; Garcia Ojalvo, Jorge
    Participation in a competitive project

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  • Noise-induced up/down dynamics in scale-free neuronal networks

     Grau Moya, Jordi; Pons Rivero, Antonio Javier; Garcia Ojalvo, Jorge
    International journal of bifurcation and chaos
    Date of publication: 2012-07-31
    Journal article

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    Cortical neuronal networks are known to exhibit regimes of dynamical activity characterized by periods of elevated firing (up states) separated by silent phases (down states). Here, we show that up/down dynamics may emerge spontaneously in scale-free neuronal networks, provided an optimal amount of noise acts upon all network nodes. Our conclusions are drawn from numerical simulations of networks of subthreshold integrate-and-fire neurons, connected to each other according to a scale-free topology. We study the structure of the up/down regime both in time and in terms of the node degree. We also examine whether localized random perturbations applied to specific network nodes are able to generate up/down dynamics, showing that this regime arises when noisy inputs are applied to low-degree (nonhub) network nodes, but not when they act upon network hubs.

  • Integration of cellular signals in chattering environments

     Rué Queralt, Pau; Domedel Puig, Nuria; Garcia Ojalvo, Jorge; Pons Rivero, Antonio Javier
    Progress in biophysics and molecular biology
    Date of publication: 2012-09-08
    Journal article

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  • Speed-dependent cellular decision making in nonequilibrium genetic circuits

     Nené, N.R.; Garcia Ojalvo, Jorge; Zaikin, Alexey
    PLoS One
    Date of publication: 2012-03-13
    Journal article

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  • Dynamical and synchronization properties of delay-coupled lasers

     Martinez Gonzalez, Maria Cristina; Soriano, M. C.; Torrent Serra, Maria Del Carmen; Garcia Ojalvo, Jorge; Fischer, Ingho
    Date of publication: 2011
    Book chapter

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  • Neural oscillations: from mechanisms to functionality

     Pons Rivero, Antonio Javier; De Sancristobal Alonso, Belen; Garcia Ojalvo, Jorge
    Barcelona Computational and Systems Neuroscience Meeting
    Presentation's date: 2011-06-14
    Presentation of work at congresses

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  • Modulating the Phase Coherence of Neuronal Population Oscillations in the Gamma Band

     De Sancristobal Alonso, Belen; Vicente, Raul; Pons Rivero, Antonio Javier; Pipa, Gordon; Garcia Ojalvo, Jorge
    International Conference on Cognitive Neurodynamics
    Presentation of work at congresses

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  • Modeling signaling information processing through a Boolean network

     Pons Rivero, Antonio Javier; Domedel Puig, Nuria; Rué Queralt, Pau; Garcia Ojalvo, Jorge
    International Congress on Molecular Systems Biology
    Presentation's date: 2011-05-12
    Presentation of work at congresses

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  • Modeling the effector - regulatory T cell cross-regulation reveals the intrinsic character of relapses in Multiple Sclerosis

     Velez de Mendizabal, Nieves; Carneiro, Jorge; Solé, Ricard V.; Goñi, Joaquín; Bragard, Jean; Martinez Forero, Ivan; Martinez Pasamar, Sara; Sepulcre, Jorge; Torrealdea, Javier; Bagnato, Francesca; Garcia Ojalvo, Jorge; Villoslada, Pablo
    BMC systems biology
    Date of publication: 2011-07-15
    Journal article

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  • Physical approaches to the dynamics of genetic circuits: a tutorial

     Garcia Ojalvo, Jorge
    Contemporary physics
    Date of publication: 2011-09
    Journal article

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  • Access to the full text
    Information routing driven by background chatter in a signaling network  Open access

     Domedel Puig, Nuria; Rué Queralt, Pau; Pons Rivero, Antonio Javier; Garcia Ojalvo, Jorge
    PLOS computational biology
    Date of publication: 2011-12-08
    Journal article

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    Living systems are capable of processing multiple sources of information simultaneously. This is true even at the cellular level, where not only coexisting signals stimulate the cell, but also the presence of fluctuating conditions is significant. When information is received by a cell signaling network via one specific input, the existence of other stimuli can provide a background activity –or chatter– that may affect signal transmission through the network and, therefore, the response of the cell. Here we study the modulation of information processing by chatter in the signaling network of a human cell, specifically, in a Boolean model of the signal transduction network of a fibroblast. We observe that the level of external chatter shapes the response of the system to information carrying signals in a nontrivial manner, modulates the activity levels of the network outputs, and effectively determines the paths of information flow. Our results show that the interactions and node dynamics, far from being random, confer versatility to the signaling network and allow transitions between different information-processing scenarios.

  • Gene circuit designs for noisy excitable dynamics

     Rue Queralt, Pau; Garcia Ojalvo, Jorge
    Mathematical biosciences
    Date of publication: 2011-05
    Journal article

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  • Dynamical consequences of bandpass feedback loops in a bacterial phosphorelay

     Sen, S.; Garcia Ojalvo, Jorge; Elowitz, Michael B.
    PLoS One
    Date of publication: 2011-09-29
    Journal article

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  • Dual-lag synchronization between coupled chaotic lasers due to path-delay interference

     Tiana Alsina, Jordi; Garcia Lopez, Pedro; Torrent, M.C.; Garcia Ojalvo, Jorge
    Chaos
    Date of publication: 2011-12
    Journal article

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  • Nonlinear frequency conversion under general phase mismatched condition: the role of phase locking and random nonlinear domains  Open access  awarded activity

     Roppo, Vito
    Defense's date: 2011-06-15
    Department of Applied Physics, Universitat Politècnica de Catalunya
    Theses

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    In the field of second harmonic (SH) generation most studies have been concerned with maximizing conversion efficiencies, generally achievable at the phase matching (PM) condition. Outside of the PM the conversion efficiency drastically decreases. This has caused that the possible working conditions out of PM to remain largely unexplored. In this thesis work we initiated a systematic study of the SH behavior in under conditions of large phase mismatch. When a pump pulse crosses an interface between a linear and a nonlinear medium there are always two generated SH components. These components may be understood on the basis of the mathematical solution of the inhomogeneous wave equations at the SH frequency. The homogeneous (HOM) solution is a component with wave-vector k(2¿) as expected from the dispersion relation and exchanges energy with the pump until the inevitable walk-off. The inhomogeneous (INH) solution is a component with a wave-vector 2k(¿), twice the pump wave-vector, and travels locked to the pump pulse. We divide our work in two parts, one for each generated component. Inhomogeneous component. We start a systematic study of the behavior of the generated INH component, phase locked to the pump. The consequences of phase locking (PL) can guide us towards new scenarios by allowing working conditions hitherto assumed inaccessible for absorbing materials. We show that while the HOM component travels with the group velocity given by material dispersion, the IHN component is captured by the pump pulse and experiences the same effective dispersion of the pump. It does not follow the PM condition. It naturally follows that the suppression of absorption at the SH wavelengths will occur if the pump is tuned to a region of transparency. We extended the same theory for the generated third harmonic (TH). We then studied the surprising behavior of SH and TH INH components with frequencies above the absorption edge when the material is placed inside a cavity resonant only at the fundamental frequency. We have shown that the PL mechanism not only inhibits absorption but also fosters the enhancement of harmonic generation by several orders of magnitude compared to the no-cavity case. Finally, we tested the INH SH and TH behaviors in metallic frequency regime of material. Homogeneous component. The techniques used to PM the nonlinear interaction enable efficient nonlinear interactions but drastically limit the spectral bandwidth of the nonlinear optical process, making the designed frequency converter only suitable for a fixed input wavelength and single interaction only. It has been shown that the use of disordered nonlinear media relaxes the PM condition thus allowing one to achieve relatively efficient broad bandwidth regime of the frequency conversion. An example of a quadratic nonlinear medium with a disordered domain structure is an un-poled Strontium Barium Niobate (SBN) crystal. It is composed of a system of random size anti parallel ferroelectric domains that allow to phase-match any second-order parametric process over a broad range of wavelengths without any poling. We have initiated an experimental and theoretical investigation of the properties of the SH waves generated in SBN crystals, with an extension to the generated TH. This study covers the coherence and polarization properties of the generated signal, as well as its spatial distribution. In addition, we have made an experimental study of the noncollinear interaction of short optical pulses in a SBN crystal by using two fundamental waves intersecting inside the crystal. We have shown that this effect may be employed as a simple tool for monitoring both the pulse duration and initial chirp. This method offers a simple and economic alternative to the existing methods for pulse characterization.

  • STOCHASTICITY,COMPLEXITY AND SYNCHRONIZATION IN SEMICONDUCTOR LASERS  Open access

     Tiana Alsina, Jordi
    Defense's date: 2011-11-10
    Department of Applied Physics, Universitat Politècnica de Catalunya
    Theses

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    The purpose of this Thesis is study the dynamical behavior of semiconductor lasers with optical feedback, as well as analyze the synchronization of this kind of systems under different coupling arquitectures. This study has been done from an experimental point of view, but in some cases we have used numerical models in order to verify and/or extend the experimental results. A semiconductor laser in absence of any optical feedback emits light at constant power. If one wants to induce dynamics in the laser, a good strategy is to introduce an external cavity able to reflect the emitted light back into the laser. Due to this feedback, the laser can show a large variety of dynamical behaviors. In this Thesis we will focus mainly in a dynamical regime known as low frequency fluctuations regime (LFF). The LFF regime takes place when the pump current of the laser is close to its threshold current and the feedback strength is sufficiently large, and it consists in sudden intensity dropouts arising at irregular times, followed by a gradual and stepwise recovery. During this Thesis, we have characterized in detail the dynamical behavior of the time between intensity dropouts for a semiconductor laser with feedback, by using different statistical techniques based on information theory concepts. We have quantified the probability of appearance of certain patterns within the temporal series, as well as its degree of complexity. As a result of these studies, we can conclude that the dynamics of a semiconductor laser with optical feedback is stochastic for pump current values close to the laser threshold. On the other hand, for larger pump currents the dynamics is basically deterministic (chaotic). Numerical simulations have shown a good qualitative and quantitive agreement with the experimental results. During this Thesis we have also studied the ability of semiconductor lasers to synchronize under different coupling architectures. First, we have characterized the leader-laggard dynamics showed by two semiconductor lasers bidirectionally coupled operating at the LFF regime, with a method that takes into account the number of forbidden patterns that appears in the temporal series. We have quantified the degree of stochasticity of the system as a function of the pump current of both lasers. A second coupling architecture studied here, consists in two lasers unidirectionally coupled via two paths. In this case, we have analyzed how the synchronization is affected under different values of the coupling strength of both paths, as well as the potential of this system (or rather, the lack thereof) to be used in chaotic communications. Finally we have characterized the synchronization at zero lag for two lasers coupled bidirectionally via a passive relay. In particular, we have studied the desynchronization events and their statistics for different pump currents. The experimental results obtained in this Thesis give a global perspective of the dynamical statistical properties of semiconductor laser dynamics, both isolated or coupled to other lasers, which contributes to a better understanding of this kind of dynamical systems.

    L’objectiu d’aquesta Tesi ´es l’estudi de la din`amica de l`asers de semiconductor amb retroalimentaci´o `optica, aix´ý com l’an`alisis de la sincronitzaci´o d’aquest tipus de sistemes sota diferents arquitectures d’acoblament. Aquest estudi s’ha fet sempre des d’un punt de vista b`asicament experimental, tot i que en alguns casos hem utilitzat models num`erics per tal de verificar i/o ampliar els resultats experimentals. Un l`aser de semiconductor en abs`encia de retroalimentaci´o `optica o altres perturbacions externes, emet llum a una intensitat pr`acticament constant. Aix´ý doncs, si el que es vol ´es indu¨ýr din`amica en el l`aser, una bona estrat`egia ´es introdu¨ýr una cavitat externa capa¸c de reflexar la llum cap al l`aser. Un cop la llum ´es reinjectada, els l`asers de semiconductor poden mostrar una gran varietat de comportaments din`amics. En aquesta tesis ens centrarem principalment en un r`egim din`amic anomenat r`egim de fluctuacions de baixa frequ`encia (LFF en les seves sigles en angl`es). El r`egim d’LFF es d´ona quan el corrent d’injecci´o del l`aser es troba a prop del seu corrent llindar i la intensitat de la retroalimentaci´o ´es suficientment gran, i est`a caracteritzat per sobtades caigudes de la intensitat a temps irregulars, seguides per una recuperaci´o gradual i escalonada. Durant aquesta Tesi, hem caracteritzat de forma detallada el comportament din`amic de la distribuci´o dels temps entre les caigudes d’intensitat d’un l`aser de semiconductor amb retroalimentaci´o `optica, utilitzant diferents m`etodes estad´ýstics basats en conceptes de teoria de la informaci´o. En particular, hem quantificat la probabilitat d’aparici´o de certs patrons dins les s`eries temporals, aix´ý com el grau de complexitat d’aquestes. Durant aquest estudi hem observat que la din`amica d’un l`aser de semiconductor amb retroalimentaci´o es estoc`astica per valors del corrent d’injecci´o propers al corrent llindar del l`aser. D’altra banda, per a valors m´es grans del corrent d’injecci´o la din`amica ´es m´es determinista (ca`otica). Les simulacions num`eriques realitzades han mostrat un acord qualitatiu i quantitatiu amb els resultats experimentals. Durant aquesta Tesi tamb´e hem estudiat la sincronitzaci´o entre l`asers de semiconductor. Hem analitzat diferents arquitectures d’acoblament. Primer hem caracteritzat la din`amica leader-laggard que presenten dos l`asers de semiconductor acoblats bidireccionalment operant en r`egim de LFFs, amb un m`etode que t´e en compte el nombre de patrons prohibits que apareixen en la s`erie temporal. Hem quantificat el grau d’estocasticitat del sistema en funci´o del nivell de bombeig al qual est`an sotmesos els dos l`asers. La seg¨uent arquitectura d’acoblament que hem estudiat consisteix en dos l`asers acoblats unidireccionalment a trav´es de dos camins. En aquest cas hem analitzat com es veu afectada la sincronitzaci´o sota diferents valors de l’acoblament dels dos camins, aix´ý com el potencial d’aquest esquema experimental per realitzar comunicacions ca`otiques. Per ´ultim hem caracteritzat la sincronitzaci´o a retard zero per dos l`asers acoblats bidireccionalment, a on els dos l`asers tenen la seva pr`opia realimentaci´o `optica. En particular, hem estudiat els events de desincronitzaci´o i la seva estad´ýstica per a diferents corrents d’injecci´o. Els resultats experimentals obtinguts en aquesta Tesi, ofereixen una prespectiva global de les propietats estad´ýstiques de la din`amica de l`asers de semiconductor, tant a¨ýllats com acoblats a altres l`asers, que contribueixen a entendre millor aquests sistemes din`amics.

  • Nonlinear and Stochastic Dynamics of Semiconductor Lasers: Modulation, Transient Dynamics and Synchronization

     Zamora Munt, Jordi
    Defense's date: 2011-06-21
    Department of Physics and Nuclear Engineering, Universitat Politècnica de Catalunya
    Theses

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  • Laboratorio de dinámica de láseres

     Masoller Alonso, Cristina; Torrent, M.C.; Garcia Ojalvo, Jorge; Bonatto, Cristian; Tiana Alsina, Jordi; Zamora Munt, Jordi; Aragoneses Aguado, Andres; Rubido, Nicolás
    Date: 2011-03-17
    Report

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  • Mutual Inactivation of Notch Receptors and Ligands Facilitates Developmental Patterning

     Sprinzak, David; Lakhanpal, Amit; LeBon, Lauren; Garcia Ojalvo, Jorge; Elowitz, Michael B.
    PLOS computational biology
    Date of publication: 2011-06
    Journal article

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  • Research activities of the group on nonlinear dynamics, nonlinear optics and lasers (DONLL) at the universitat politècnica de catalunya (Campus de Terrassa)

     Tiana Alsina, Jordi; Zamora Munt, Jordi; Nistor, Ioan Cristian; Roppo, Vito; Maigyte, Lina; Aragoneses Aguado, Andres; Khumar, N.P.; Martinez Gonzalez, Maria Cristina; Fernandez Soler, Juanjo; Serrat Jurado, Carles; Font Garcia, Josep Lluís; Herrero Simon, Ramon; Cojocaru, Crina Maria; Trull, Jose; Masoller Alonso, Cristina; Staliunas, Kestutis; Torrent Serra, Maria Del Carmen; Garcia Ojalvo, Jorge; Vilaseca Alavedra, Ramon
    Óptica pura y aplicada
    Date of publication: 2011-06
    Journal article

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  • Access to the full text
    Optimizing periodicity and polymodality in noise-induced genetic oscillators  Open access

     Rue Queralt, Pau; Süel, Gürol M.; Garcia Ojalvo, Jorge
    Physical review E: statistical, nonlinear, and soft matter physics
    Date of publication: 2011
    Journal article

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    Many cellular functions are based on the rhythmic organization of biological processes into self-repeating cascades of events. Some of these periodic processes, such as the cell cycles of several species, exhibit conspicuous irregularities in the form of period skippings, which lead to polymodal distributions of cycle lengths. A recently proposed mechanism that accounts for this quantized behavior is the stabilization of a Hopf-unstable state by molecular noise. Here we investigate the effect of varying noise in a model system, namely an excitable activator-repressor genetic circuit, that displays this noise-induced stabilization effect. Our results show that an optimal noise level enhances the regularity (coherence) of the cycles, in a form of coherence resonance. Similar noise levels also optimize the multimodal nature of the cycle lengths. Together, these results illustrate how molecular noise within a minimal gene regulatory motif confers robust generation of polymodal patterns of periodicity.

  • Temporal competition between differentiation programs determines cell fate choice

     Kuchina, Anna; Espinar Calvo, Maria Lorena; Cagatay, Tolga; Balbin, A.O.; Zhang, F.; Alvarado, A.; Garcia Ojalvo, Jorge; Süel, Gürol M.
    Molecular systems biology
    Date of publication: 2011
    Journal article

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  • Reversible and Noisy Progression towards a Commitment Point Enables Adaptable and Reliable Cellular Decision-Making

     Kuchina, Anna; Espinar Calvo, Maria Lorena; Garcia Ojalvo, Jorge; Süel, Gürol M.
    PLOS computational biology
    Date of publication: 2011-11
    Journal article

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  • Language organization and temporal correlations in the spiking activity of an excitable laser: experiments and model comparison

     Rubido, Nicolás; Tiana Alsina, Jordi; Torrent Serra, Maria Del Carmen; Garcia Ojalvo, Jorge; Masoller Alonso, Cristina
    Physical review E: statistical, nonlinear, and soft matter physics
    Date of publication: 2011-08-09
    Journal article

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  • From structural to functional connectivity in aging brains: a neural mass modeling

     Pons Rivero, Antonio Javier; Cantero, José Luis; Atienza, Mercedes; Garcia Ojalvo, Jorge
    Annual Meeting of the Organization for Human Brain Mapping
    Presentation's date: 2010-06-07
    Presentation of work at congresses

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  • Transient low-frequency fluctuations in semiconductor lasers with optical feedback

     Zamora Munt, Jordi; Masoller Alonso, Cristina; Garcia Ojalvo, Jorge
    Physical review A
    Date of publication: 2010-03-11
    Journal article

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  • Quantifying the statistical complexity of low-frequency fluctuations in semiconductor lasers with optical feedback

     Tiana Alsina, Jordi; Torrent Serra, Maria Del Carmen; Rosso, Osvaldo A.; Masoller Alonso, Cristina; Garcia Ojalvo, Jorge
    Physical review A
    Date of publication: 2010
    Journal article

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  • Relaxation dynamics and frequency response of a noisy cell signaling network

     Rué Queralt, Pau; Pons Rivero, Antonio Javier; Domedel Puig, Nuria; Garcia Ojalvo, Jorge
    Chaos
    Date of publication: 2010-12-30
    Journal article

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  • Cooperative differentiation through clustering in multicellular populations

     Koseska, Aneta; Ullner, Ekkehard; Volkov, Evgenii; Kurths, Juergen; Garcia Ojalvo, Jorge
    Journal of theoretical biology
    Date of publication: 2010-03-21
    Journal article

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  • Cis-interactions between Notch and Delta generate mutually exclusive signalling states

     Sprinzak, David; Lakhanpal, Amit; LeBon, Lauren; Santat,, Leah A.; Fontes, Michelle E.; Anderson, Graham A.; Garcia Ojalvo, Jorge; Elowitz, Michael B.
    Nature
    Date of publication: 2010-05-06
    Journal article

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  • Quantifying stochasticity in the dynamics of delay-coupled semiconductor lasers via forbidden patterns

     Tiana Alsina, Jordi; Buldu, Jm; Torrent Serra, Maria Del Carmen; Garcia Ojalvo, Jorge
    Philosophical transactions of the Royal Society A. Mathematical physical and engineering sciences
    Date of publication: 2010-01
    Journal article

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  • Multi-stability and transient chaotic dynamics in semiconductor lasers with time-delayed optical feedback

     Zamora Munt, Jordi; Masoller Alonso, Cristina; Garcia Ojalvo, Jorge
    Date of publication: 2010
    Book chapter

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    We investigate numerically the chaotic transient dynamics of a semiconductor laser with time-delayed optical feedback. This transient behavior is seen in the low-frequency fluctuations (LFF) regime ocurring when the laser is pumped close to thereshold and is subjected to moderate feedback strengths. We characterize the transient dynamics in terms of its duration, the time intervals between consecutive dropouts, and the total in each transient event. We statistically analyze these quantities as a function of the noise strength and other system parameters related to different nonlinear mechanisms of light-matter interaction inside the laser active medium.

  • Individual-based modeling of Plasmodium falciparum erythrocyte infection in in vitro cultures  Open access

     Ferrer Savall, Jordi
    Defense's date: 2010-06-21
    Department of Physics and Nuclear Engineering, Universitat Politècnica de Catalunya
    Theses

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    La malària és encara avui en dia una malaltia que causa aproximadament un milió de morts a l'any a tot el món. La seva eradicació suposa un gran repte per a la humanitat i per a la comunitat científica, en particular. El cultiu in vitro del paràsit és essencial per al desenvolupament de nous medicaments. Els mètodes de cultiu actuals es basen en l'heurística i requereixen millores.En aquesta tesi es presenta una aproximació teòrica al procés d'infecció a eritròcits en cultius in vitro amb Plasmodium falciparum, un dels protozous paràsits causants de la malària. El treball està centrat en la construcció i avaluació de models d'una complexitat adequada per tractar els problemes específics detectats pels experts en l'àmbit, i inclou també la formulació d'algorismes de simulació i el disseny de protocols experimentals.Aquest tipus de treball requereix de la col·laboració multidisciplinària. La visió dels experts en malària es complementa amb la modelització i simulació, que permet la comprovació dels supòsits preestablerts, la comprensió de fenòmens observats i la millora dels mètodes de cultiu actuals. Així doncs, cal establir i desenvolupar eines que permetin crear, analitzar i compartir models amb grups que estudien la malària des d'altres perspectives. En aquesta tesi, s'ha optat per la modelització basada en l'individu (IbM) i orientada a la reproducció de múltiples patrons (PoM). El model s'ha formulat seguint l'ODD, un protocol estàndard en el camp de l'ecologia teòrica, que s'ha adaptat a la representació de comunitats microbianes.Els models basats en l'individu (IbMs) defineixen un conjunt de normes que regeixen el comportament de cada cèl·lula i les seves interaccions amb les altres cèl·lules i amb el seu entorn immediat. A partir d'aquestes regles, i tenint en compte una certa diversitat dins de la població i un cert grau d'aleatorietat en els processos individuals, els IbMs mostren explícitament el comportament emergent del sistema en conjunt. Complementàriament, s'han aplicat conceptes propis de la termodinàmica per tal d'entendrel'aparició de patrons macroscòpics a partir de l'estructura de la població (per exemple de la distribució de les fases d'infecció entre els glòbuls vermells infectats).Aquesta recerca ha comportat la la creació i aplicació del model i simulador INDISIM-RBC, que ha demostrat ser una bona eina per millorar la comprensió dels cultius estudiats. Es tracta d'un model mecanicista, basat en l'individu, que reprodueix quantitativament els patrons observats en cultius reals a diferents nivells de descripció, i que en prediu el comportament sota determinades condicions.Hem demostrat que INDISIM-RBC pot ser emprat per a estudiar en detall alguns aspectes del cultiu del paràsit causant de la malària que calia aclarir. Permet realitzar experiments virtuals i així impulsar noves línies de recerca i explorar noves tècniques de cultiu. En particular, INDISIM-RBC s'ha utilitzat per millorar els protocols experimentals actuals del cultius estàtics, definint la geometria òptima de l'hematòcrit i els protocols de subcultiu més adequats per als cultius continus.El treball realitzat en malària s'ha comparat amb la investigació duta a terme pel grup de recerca em relació amb d'altres comunitats microbianes. D'aquesta manera, podem estudiar les propietats emergents dels sistemes microbians en general en relació als efectes de la individualitat de la cèl·lula, la diversitat de les poblacions, l'heterogeneïtat en el medi, o el caràcter local de les interaccions, entre d'altres. Aquesta visió general proporciona eines conceptuals que poden ser emprades per refinar l'anàlisi dels processos d'infecció sota estudi.

    Malaria is still a major burden that causes approximately one million deaths annually worldwide. Its eradication supposes a great challenge to the humanity and to the scientific community, in particular. In vitro cultivation of the parasite is essential for the development of new drugs. Current culture methods are based on heuristics and demand for specific improvements.The present thesis is a theoretical approach to in vitro cultivation of the protozoan parasite Plasmodium falciparum infecting human red blood cells. It mainly focuses on the process of building a model of appropriate complexity to deal with the specific demands above mentioned, but it also includes the formulation and implementation of algorithms, and the design and execution of experimental trials.This kind of work requires multidisciplinary collaboration: the insight of the experts in malaria research is complemented with modeling and simulation, which allows for checking settled assumptions, increasing the understanding on the system and improving the current culturing methods.The use of tools for building, analyzing and sharing models is an imperative to this end. In this thesis, Pattern-oriented Modeling (PoM) has been adopted as the most appropriate way for raising of models and the ODD protocol (Objectives, Design Concepts and Details) has been proposed as the standard tool for communicating them.Individual-based Modeling (IbM) has been used to tackle malaria culture systems. IbMs define a set of rules governing each cell, its interactions with others and with its immediate surroundings. From this set of rules, and taking into account diversity within the population and a certain degree of randomness in the individual processes, IbMs explicitly show the emerging behavior of the system as a whole. Methods from statistical thermodynamics have been applied to understand the emergence of macroscopic patterns from the population structure (e.g. distribution of infection stages among infected red blood cells).The research resulted in the development of the model and simulator INDISIM-RBC, which has proved to be a good tool to improve understanding of the cultures under study. It is a mechanistically rich individual-based model and it quantitatively reproduces and predicts several patterns observed in real cultures at different levels of description.We demonstrated that INDISIM-RBC can be used to study in detail several aspects of malaria cultivation that remained unclear, as well as to perform virtual experiments. Consequently, it can be used to open novel lines of research and to examine potential experimental techniques. INDISIM-RBC has also been used to improve the current experimental culturing protocols in static cultivation by obtaining the optimal geometry of the hematocrit layer and subcultivation periods in the continuous cultures.This study on malaria has been compared to the research carried out by the group regarding other microbial communities. Thereby studying general emerging properties of microbial systems in general, with regard to the effect of cell individuality, heterogeneity and diversity, the local nature of interactions; and biological and spatial complexity. In doing so, the acquired holistic view has been used to develop tools that allow for a better characterization and study of the infection process, in particular.

  • NOISE IN LIFE 2010

     Garcia Ojalvo, Jorge
    Participation in a competitive project

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