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Shaping Pulses to Control Bistable Biological Systems [article]

Aivar Sootla, Diego Oyarzun, David Angeli, Guy-Bart Stan
2015 arXiv   pre-print
In this paper we study how to shape temporal pulses to switch a bistable system between its stable steady states.  ...  Our motivation for pulse-based control comes from applications in synthetic biology, where it is generally difficult to implement real-time feedback control systems due to technical limitations in sensors  ...  For any small enough ε, our control strategy will induce oscillations. VII. CONCLUSION AND DISCUSSION In this paper we have presented a framework for shaping pulses to control bistable systems.  ... 
arXiv:1409.6150v3 fatcat:j3fwf2pmsnevvnnbynjtvgoory

Shaping pulses to control bistable biological systems

Aivar Sootla, Diego Oyarzun, David Angeli, Guy-Bart Stan
2015 2015 American Control Conference (ACC)  
In this paper we study how to shape temporal pulses to switch a bistable system between its stable steady states.  ...  Our motivation for pulse-based control comes from applications in synthetic biology, where it is generally difficult to implement real-time feedback control systems due to technical limitations in sensors  ...  For any small enough ε, our control strategy will induce oscillations. VII. CONCLUSION AND DISCUSSION In this paper we have presented a framework for shaping pulses to control bistable systems.  ... 
doi:10.1109/acc.2015.7171815 dblp:conf/amcc/SootlaOAS15 fatcat:ytzx6zzrq5h2jbvzsui6t5ucea

Frustrated bistability as a means to engineer oscillations in biological systems

S Krishna, S Semsey, M H Jensen
2009 Physical Biology  
Oscillations play an important physiological role in a variety of biological systems.  ...  addition of a negative feedback loop that destabilizes the bistable system.  ...  Varying the shape of oscillations Modifying the underlying bistable system Tinkering with the underlying bistable system is another way of changing the shape to the desired one.  ... 
doi:10.1088/1478-3975/6/3/036009 pmid:19461130 fatcat:kytrztwgbrbwtf56gcy4qib7gy

Pulse propagation sustained by noise in arrays of bistable electronic circuits

R. Báscones, J. García-Ojalvo, J. M. Sancho
2002 Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics  
As a result, propagating fronts become destabilized in the presence of noise, and the system self-organizes to allow the transmission of pulses.  ...  These external random fluctuations are applied to the parameter that controls the transition between bistable and monostable dynamics in the individual circuits.  ...  In a biological context, a similar response to periodic trains of pulses has been recently observed in experiments on thalamocortical neurons of cats, an observation that gives evidence of the generic  ... 
doi:10.1103/physreve.65.061108 pmid:12188704 fatcat:pfvsfttrjbf5hh2fupfjliyoaa

Feedback Loops Shape Cellular Signals in Space and Time

O. Brandman, T. Meyer
2008 Science  
We discuss core feedback motifs that have distinct roles in shaping signaling responses in space and time. We also discuss approaches to experimentally investigate feedback loops in signaling systems.  ...  Positive and negative feedback loops are common regulatory elements in biological signaling systems.  ...  Local Ca 2 + signaling pulses are useful to control cell functions such as secretion (33) .  ... 
doi:10.1126/science.1160617 pmid:18927383 pmcid:PMC2680159 fatcat:a525rjgl6vd5dhudzuyxvc3kqu

Stochastic induced dynamics in neuromorphic optoelectronic oscillators

Bruno Romeira, Ricardo Avó, Julien Javaloyes, Salvador Balle, Charles N. Ironside, José M. L. Figueiredo
2014 Optical and quantum electronics  
and coherence resonances-that are similar to that of biological systems such as neurons.  ...  pulsed signals exploiting either the monostable or the bistable operating conditions.  ...  pulse (whose shape is independent of the stimulus) followed by a lapse, called the refractory time, during which the system does not respond to new stimuli.  ... 
doi:10.1007/s11082-014-9905-3 fatcat:vvdnfhiel5covorl66gq6g3434

Neuromorphic Control [article]

Luka Ribar, Rodolphe Sepulchre
2021 arXiv   pre-print
Neuromorphic engineering is a rapidly developing field that aims to take inspiration from the biological organization of neural systems to develop novel technology for computing, sensing, and actuating  ...  The interconnection structure endows the neuromorphic systems with a simple control methodology that reframes the neuronal control as an input-output shaping problem.  ...  By introducing a slow negative feedback current with a low activation to the bistable system of Figure 7 , the system exhibits a robust transient spiking response to a prolonged negative input pulse in  ... 
arXiv:2011.04441v2 fatcat:rkfaulzaijamzfwi3v4fqwscfi

Biexcitability and Bursting Mechanisms in Neural and Genetic Circuits

Peyman Gifani, Jorge Goncalves
2014 IFAC Proceedings Volumes  
Neurons generate bursts followed by refractory periods controlled by ion channels in the membrane.  ...  In particular, a special bi-excitable architecture which embeds two excitable states are compared in these systems.      ...  The strength and frequency of the triggering pulses (red lines on the time axis in Fig. 4 ) and the current state of the system are involved in shaping burst patterns.  ... 
doi:10.3182/20140824-6-za-1003.02630 fatcat:khef3h2m3na4zmxwcjmh7z5xem

Dissipative structures in biological systems: bistability, oscillations, spatial patterns and waves

Albert Goldbeter
2018 Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences  
One contribution of 11 to a theme issue 'Dissipative structures in matter out of equilibrium: from chemistry, photonics and biology (part 1)'.  ...  I wish to thank Geneviève Dupont, Jean-Christophe Leloup, Didier Gonze and Claude Gérard, as well as former members of the Unit of Theoretical Chronobiology at ULB for fruitful discussions.  ...  control the operation of biological systems at all levels, from cells to tissues, organs and animal populations.  ... 
doi:10.1098/rsta.2017.0376 pmid:29891498 fatcat:5hqz7jffzzgejok2xtrtijq2ba

Spatial resonator solitons

V. B. Taranenko, G. Slekys, C. O. Weiss
2003 Chaos  
These spatial resonator solitons are bistable and due to their mobility suggest schemes of information processing not possible with the fixed bistable elements forming the basic ingredient of traditional  ...  Many links appear to exist to fields different from optics, such as fluids, phase transitions or particle physics.  ...  (c) shows that by short positive (negative) pulses the resonator can be switched from one branch of bistability loop to the other.  ... 
doi:10.1063/1.1576971 pmid:12777142 fatcat:76ocutlwmzbxblghrb2s4tt3su

Shaping Pulses to Control Bistable Monotone Systems Using Koopman Operator

Aivar Sootla, Alexandre Mauroy, Jorge Goncalves
2016 IFAC-PapersOnLine  
In this paper, we further develop a recently proposed control method to switch a bistable system between its steady states using temporal pulses.  ...  The motivation for using pulses comes from biomedical and biological applications (e.g. synthetic biology), where it is generally difficult to build feedback control systems due to technical limitations  ...  One can also verify that there exist pulse control signals u that switch the system from the state x * to the state x • .  ... 
doi:10.1016/j.ifacol.2016.10.247 fatcat:6sfocc62v5ddfofpiwqnfbrxpa

The combination of positive and negative feedback loops confers exquisite flexibility to biochemical switches

Benjamin Pfeuty, Kunihiko Kaneko
2009 Physical Biology  
Taken together, our results suggest an efficient mechanism by which positive and negative feedback loops cooperate to drive the flexible and multifaceted switching behaviors arising in biological systems  ...  This specific type of bistability is found to allow for separate and flexible control of switch-on and switch-off events, for example (i) to combine fast and reversible transitions, (ii) to enable transient  ...  Theoretical analysis of chemical or biochemical systems combining positive and negative feedback has shown that transitions from bistability to oscillations represented by a typical cross-shaped phase  ... 
doi:10.1088/1478-3975/6/4/046013 pmid:19910671 fatcat:wasbvf5sgjh5xg42z5ehnvgtfu

Fronts and pulses in an enzymatic reaction catalyzed by glucose oxidase

D. G. Miguez, V. K. Vanag, I. R. Epstein
2007 Proceedings of the National Academy of Sciences of the United States of America  
Waves and pulses in simple, artificially designed enzymatic systems may shed new light on natural waves and patterns in biological systems.  ...  We performed simulations only for parameters close to the bistability region because, in our experimental system, we found only bistability. Zero-flux boundary conditions were used.  ... 
doi:10.1073/pnas.0611438104 pmid:17420460 pmcid:PMC1855356 fatcat:kz7l6qmes5c2pj5maggoidio7m

Linear Population Allocation by Bistable Switches in Response to Transient Stimulation

Jaydeep K. Srimani, Guang Yao, John Neu, Yu Tanouchi, Tae Jun Lee, Lingchong You, Peter Csermely
2014 PLoS ONE  
We find that bistable systems exhibit a common property: for input signals with short durations, the fraction of switching cells increases linearly with the signal duration, allowing the population to  ...  Many cellular decision processes, including proliferation, differentiation, and phenotypic switching, are controlled by bistable signaling networks.  ...  To this end, the bistable system that controls the T3SS expression may coordinate the population distribution (T3SS+ vs. T3SS2) based on the favorability of environmental conditions.  ... 
doi:10.1371/journal.pone.0105408 pmid:25141235 pmcid:PMC4139379 fatcat:zbka4cvko5eo5o2coaifuraxku

Synaptic Depression Mediates Bistability in Neuronal Networks with Recurrent Inhibitory Connectivity

Yair Manor, Farzan Nadim
2001 Journal of Neuroscience  
We show that across a wide range of parameter values this network shows robust bistability of the oscillation mode and that it is possible to switch the network from one mode to the other by injection  ...  of a brief current pulse in either neuron.  ...  The artificial synapses were modeled to mimic the time courses and depression properties measured in the biological system (Manor et al., 1997) .  ... 
doi:10.1523/jneurosci.21-23-09460.2001 pmid:11717380 fatcat:keqe3hmnffe5vjvuglgqxdwc5e
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