Effects of noise in excitable systems

Lindner, Benjamin; García‐Ojalvo, Jordi; Neiman, Alexander; Schimansky‐Geier, Lutz

doi:10.1016/j.physrep.2003.10.015

Cited by 1,359 publications

(868 citation statements)

References 374 publications

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“…the case of the Elowitz lab, the emerging research program focusing on noise led to new collaborations of which the most important was the cooperation with physicist Jordi Garcia-Ojalvo, who had studied excitable systems in the context of complex systems (Lindner et al, 2004). By perceiving biological systems as complex systems, scientists in the basic science-oriented branch of synthetic biology draw analogies to such systems as neurons, lasers, and coupled oscillatory systems.…”

Section: ) Epistemic Importance Of Negative Analogiesmentioning

confidence: 99%

Varieties of noise: Analogical reasoning in synthetic biology

Knuuttila

Loettgers

2014

Studies in History and Philosophy of Science Part A

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Abstract:The picture of synthetic biology as a kind of engineering science has largely created the public understanding of this novel field, covering both its promises and risks. In this paper, we will argue that the actual situation is more nuanced and complex. Synthetic biology is a highly interdisciplinary field of research located at the interface of physics, chemistry, biology, and computational science. All of these fields provide concepts, metaphors, mathematical tools, and models, which are typically utilized by synthetic biologists by drawing analogies between the different fields of inquiry. We will study analogical reasoning in synthetic biology through the emergence of the functional meaning of noise, which marks an important shift in how engineering concepts are employed in this field. The notion of noise serves also to highlight the differences between the two branches of synthetic biology: the basic science-oriented branch and the engineering-oriented branch, which differ from each other in the way they draw analogies to various other fields of study. Moreover, we show that fixing the mapping between a source domain and the target domain seems not to be the goal of analogical reasoning in actual scientific practice.

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Section: ) Epistemic Importance Of Negative Analogiesmentioning

confidence: 99%

Varieties of noise: Analogical reasoning in synthetic biology

Knuuttila

Loettgers

2014

Studies in History and Philosophy of Science Part A

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“…They can appear similar to regular oscillations under certain conditions. Such phenomena and its characterizations have been subject of many research efforts in recent time (Lindner et al, 2004). This consequence of diffusion in biochemical systems is also of great importance for the Ca 2+ system.…”

Section: Accepted Manuscriptmentioning

confidence: 99%

Dynamics of excitable elements with time-delayed coupling

Rüdiger

Schimansky‐Geier

2009

Journal of Theoretical Biology

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Motivated by recent experiments on intracellular calcium release we study the effects of different types of coupling on the dynamics of arrays of excitable elements. We intend to find a mechanism, which produces a sustained activity of the elements following a spike. While instantaneous diffusive coupling does not exhibit this property, we show that, for a coupling term with temporal delay, signals from adjacent elements can serve as mutual excitations and thus prolong the duration of the signal. We propose that time delayed coupling is generated by diffusion between isolated clusters of calcium channels. Our model could thus provide an explanation for two different release modes observed in the Ca 2+ system.

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“…Rodriguez and Tuckwell (1996) make a similar assumption in their analysis of the role of noise in the Fitzhugh-Nagumo equations. This approach applied to differential equations is reviewed in Lindner et al (2004). Here we follow their methods applied to maps.…”

Section: Appendixmentioning

confidence: 99%

Phase resetting and coupling of noisy neural oscillators

Ermentrout

Saunders

2006

J Comput Neurosci

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A number of experimental groups have recently computed Phase Response Curves (PRCs) for neurons. There is a great deal of noise in the data. We apply methods from stochastic nonlinear dynamics to coupled noisy phaseresetting maps and obtain the invariant density of phase distributions. By exploiting the special structure of PRCs, we obtain some approximations for the invariant distributions. Comparisons to Monte-Carlo simulations are made. We show how phase-dependence of the noise can move the peak of the invariant density away from the peak expected from the analysis of the deterministic system and thus lead to noise-induced bifurcations.

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Effects of noise in excitable systems

Cited by 1,359 publications

References 374 publications

Varieties of noise: Analogical reasoning in synthetic biology

Varieties of noise: Analogical reasoning in synthetic biology

Dynamics of excitable elements with time-delayed coupling

Phase resetting and coupling of noisy neural oscillators

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