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Search Results: 1 - 10 of 13477 matches for " Jordi Garcia-Ojalvo "
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Physical approaches to the dynamics of genetic circuits: A tutorial
Jordi Garcia-Ojalvo
Physics , 2011, DOI: 10.1080/00107514.2011.588432
Abstract: Cellular behavior is governed by gene regulatory processes that are intrinsically dynamic and nonlinear, and are subject to non-negligible amounts of random fluctuations. Such conditions are ubiquitous in physical systems, where they have been studied for decades using the tools of statistical and nonlinear physics. The goal of this review is to show how approaches traditionally used in physics can help in reaching a systems-level understanding of living cells. To that end, we present an overview of the dynamical phenomena exhibited by genetic circuits and their functional significance. We also describe the theoretical and experimental approaches that are being used to unravel the relationship between circuit structure and function in dynamical cellular processes under the influence of noise, both at the single-cell level and in cellular populations, where intercellular coupling plays an important role.
Colored noise in Spatially-Extended Systems
Jordi Garcia-Ojalvo,Jose M. Sancho
Physics , 1993, DOI: 10.1103/PhysRevE.49.2769
Abstract: We study the effects of time and space correlations of an external additive colored noise on the steady-state behavior of a Time-Dependent Ginzburg-Landau model. Simulations show the existence of nonequilibrium phase transitions controlled by both the correlation time and length of the noise. A Fokker-Planck equation and the steady probability density of the process are obtained by means of a theoretical approximation.
A neural mechanism for binaural pitch perception via ghost stochastic resonance
Pablo Balenzuela,Jordi Garcia-Ojalvo
Physics , 2004, DOI: 10.1063/1.1871612
Abstract: We present a physiologically plausible binaural mechanism for the perception of the pitch of complex sounds via ghost stochastic resonance. In this scheme, two neurons are driven by noise and different periodic signal each (with frequencies f1=kf0 and f2=(k+1)f0, where k>1), and their outputs (plus noise) are applied synaptically to a third neuron. Our numerical results, using the Morris-Lecar neuron model with chemical synapses explicity considered, show that intermediate noise levels enhance the response of the third neuron at frequencies close to f0, as in the cases previously described of ghost resonance. For the case of inharmonic combinations of inputs (both frequencies shifted by the same amount Df) noise is also seen to enhance the response of the third neuron at a frequency fr with also shift linearly with Df. In addition, we show that similar resonances can be observed as a function of the synaptic time constant. The suggested ghost-resonance-based stochastic mechanism can thus arise either at the peripheral level or at a higher level of neural processing in the perception of the pitch
On the role of chemical synapses in coupled neurons with noise
Pablo Balenzuela Jordi Garcia-Ojalvo
Physics , 2005, DOI: 10.1103/PhysRevE.72.021901
Abstract: We examine the behavior in the presence of noise of an array of Morris-Lecar neurons coupled via chemical synapses. Special attention is devoted to comparing this behavior with the better known case of electrical coupling arising via gap junctions. In particular, our numerical simulations show that chemical synapses are more efficient than gap junctions in enhancing coherence at an optimal noise (what is known as array-enhanced coherence resonance): in the case of (nonlinear) chemical coupling, we observe a substantial increase in the stochastic coherence of the system, in comparison with (linear) electrical coupling. We interpret this qualitative difference between both types of coupling as arising from the fact that chemical synapses only act while the presynaptic neuron is spiking, whereas gap junctions connect the voltage of the two neurons at all times. This leads in the electrical coupling case to larger correlations during interspike time intervals which are detrimental to the array-enhanced coherence effect. Finally, we report on the existence of a system-size coherence resonance in this locally coupled system, exhibited by the average membrane potential of the array.
Gene circuit designs for noisy excitable dynamics
Pau Rué,Jordi Garcia-Ojalvo
Quantitative Biology , 2011, DOI: 10.1016/j.mbs.2011.02.013
Abstract: Certain cellular processes take the form of activity pulses that can be interpreted in terms of noise-driven excitable dynamics. Here we present an overview of different gene circuit architectures that exhibit excitable pulses of protein expression, when subject to molecular noise. Different types of excitable dynamics can occur depending on the bifurcation structure leading to the specific excitable phase-space topology. The bifurcation structure is not, however, linked to a particular circuit architecture. Thus a given gene circuit design can sustain different classes of excitable dynamics depending on the system parameters.
Dynamical Consequences of Bandpass Feedback Loops in a Bacterial Phosphorelay
Shaunak Sen,Jordi Garcia-Ojalvo,Michael B. Elowitz
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0025102
Abstract: Under conditions of nutrient limitation, Bacillus subtilis cells terminally differentiate into a dormant spore state. Progression to sporulation is controlled by a genetic circuit consisting of a phosphorelay embedded in multiple transcriptional feedback loops, which is used to activate the master regulator Spo0A by phosphorylation. These transcriptional regulatory interactions are “bandpass”-like, in the sense that activation occurs within a limited band of Spo0A~P concentrations. Additionally, recent results show that the phosphorelay activation occurs in pulses, in a cell-cycle dependent fashion. However, the impact of these pulsed bandpass interactions on the circuit dynamics preceding sporulation remains unclear. In order to address this question, we measured key features of the bandpass interactions at the single-cell level and analyzed them in the context of a simple mathematical model. The model predicted the emergence of a delayed phase shift between the pulsing activity of the different sporulation genes, as well as the existence of a stable state, with elevated Spo0A activity but no sporulation, embedded within the dynamical structure of the system. To test the model, we used time-lapse fluorescence microscopy to measure dynamics of single cells initiating sporulation. We observed the delayed phase shift emerging during the progression to sporulation, while a re-engineering of the sporulation circuit revealed behavior resembling the predicted additional state. These results show that periodically-driven bandpass feedback loops can give rise to complex dynamics in the progression towards sporulation.
Phase-Coherence Transitions and Communication in the Gamma Range between Delay-Coupled Neuronal Populations
Alessandro Barardi,Belen Sancristóbal,Jordi Garcia-Ojalvo
PLOS Computational Biology , 2014, DOI: doi/10.1371/journal.pcbi.1003723
Abstract: Synchronization between neuronal populations plays an important role in information transmission between brain areas. In particular, collective oscillations emerging from the synchronized activity of thousands of neurons can increase the functional connectivity between neural assemblies by coherently coordinating their phases. This synchrony of neuronal activity can take place within a cortical patch or between different cortical regions. While short-range interactions between neurons involve just a few milliseconds, communication through long-range projections between different regions could take up to tens of milliseconds. How these heterogeneous transmission delays affect communication between neuronal populations is not well known. To address this question, we have studied the dynamics of two bidirectionally delayed-coupled neuronal populations using conductance-based spiking models, examining how different synaptic delays give rise to in-phase/anti-phase transitions at particular frequencies within the gamma range, and how this behavior is related to the phase coherence between the two populations at different frequencies. We have used spectral analysis and information theory to quantify the information exchanged between the two networks. For different transmission delays between the two coupled populations, we analyze how the local field potential and multi-unit activity calculated from one population convey information in response to a set of external inputs applied to the other population. The results confirm that zero-lag synchronization maximizes information transmission, although out-of-phase synchronization allows for efficient communication provided the coupling delay, the phase lag between the populations, and the frequency of the oscillations are properly matched.
Synchronization in semiconductor laser rings
Javier M. Buldu,M. C. Torrent,Jordi Garcia-Ojalvo
Physics , 2006, DOI: 10.1109/JLT.2007.895555
Abstract: We examine the dynamics of semiconductor lasers coupled in a ring configuration. The lasers, which have stable output intensity when isolated, behave chaotically when coupled unidirectionally in a closed chain. In this way, we show that neither feedback nor bidirectional coupling is necessary to induce chaotic dynamics at the laser output. We study the synchronization phenomena arising in this particular coupling architecture, and discuss its possible application to chaos-based communications. Next, we extend the study to bidirectional coupling and propose an appropriate technique to optical chaos encryption/decryption in closed chains of mutually coupled semiconductor lasers.
Crowd synchrony and quorum sensing in delay-coupled lasers
Jordi Zamora-Munt,C. Masoller,Jordi Garcia-Ojalvo,Rajarshi Roy
Physics , 2010, DOI: 10.1103/PhysRevLett.105.264101
Abstract: Crowd synchrony and quorum sensing arise when a large number of dynamical elements communicate with each other via a common information pool. Previous evidence in different fields, including chemistry, biology and civil engineering, has shown that this type of coupling leads to synchronization, when coupling is instantaneous and the number of coupled elements is large enough. Here we consider a situation in which the transmission of information between the system components and the coupling pool is not instantaneous. To that end, we model a system of semiconductor lasers optically coupled to a central laser with a delay. Our results show that, even though the lasers are non-identical due to their distinct optical frequencies, zero-lag synchronization arises. By changing a system parameter, we can switch between two different types of synchronization transition. The dependence of the transition with respect to the delay-coupling parameters is studied.
Reversible and Noisy Progression towards a Commitment Point Enables Adaptable and Reliable Cellular Decision-Making
Anna Kuchina ,Lorena Espinar ,Jordi Garcia-Ojalvo,Gürol M. Süel
PLOS Computational Biology , 2011, DOI: 10.1371/journal.pcbi.1002273
Abstract: Cells must make reliable decisions under fluctuating extracellular conditions, but also be flexible enough to adapt to such changes. How cells reconcile these seemingly contradictory requirements through the dynamics of cellular decision-making is poorly understood. To study this issue we quantitatively measured gene expression and protein localization in single cells of the model organism Bacillus subtilis during the progression to spore formation. We found that sporulation proceeded through noisy and reversible steps towards an irreversible, all-or-none commitment point. Specifically, we observed cell-autonomous and spontaneous bursts of gene expression and transient protein localization events during sporulation. Based on these measurements we developed mathematical population models to investigate how the degree of reversibility affects cellular decision-making. In particular, we evaluated the effect of reversibility on the 1) reliability in the progression to sporulation, and 2) adaptability under changing extracellular stress conditions. Results show that reversible progression allows cells to remain responsive to long-term environmental fluctuations. In contrast, the irreversible commitment point supports reliable execution of cell fate choice that is robust against short-term reductions in stress. This combination of opposite dynamic behaviors (reversible and irreversible) thus maximizes both adaptable and reliable decision-making over a broad range of changes in environmental conditions. These results suggest that decision-making systems might employ a general hybrid strategy to cope with unpredictably fluctuating environmental conditions.
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