Time-dependent information transmission in a model regulatory circuit

Mancini, Francesca; Wiggins, Chris H.; Marsili, Matteo; Walczak, Aleksandra M.

doi:10.1103/physreve.88.022708

Cited by 14 publications

(34 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For l = 0 the constraint on the dissipated energy does not enter the optimization and one recovers the results found without imposing energetic constraints (σ = σ = ∞) [38]. In this limit the system is driven out of equilibrium and at least one of the rates vanishes.…”

Section: Information Transmission With Energy Dissipationmentioning

confidence: 58%

“…We know from our work in the infinite dissipation limit [38], that the optimal solutions cycle irreversibly through the four states. The symmetry between + and − states corresponds to a degeneracy between cycling clockwise and counterclockwise and by picking this parametrization of the network we are restricting ourselves to clockwise cycles without any loss of generality.…”

Section: B Feedbackmentioning

confidence: 99%

“…This means the output changes on faster timescales than the input and the smallest eigenvalue is λ = 2u. More precisely, as in the dissipation-less case [38], the optimal rate is u * = 0 at τ = 0. To find s * , we substitute the parametrization in Eq.…”

Section: Limit τ =mentioning

confidence: 99%

“…Inspired by these observations, we previously studied the optimal circuits for transmitting information between an input and output read out with a fixed delay, in and out of steady state [38]. Delayed readouts are natural to most biochemical circuits, since sensing a signal requires production of the response, which takes time.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Trade-Offs in Delayed Information Transmission in Biochemical Networks

2015

Self Cite

View full text Add to dashboard Cite

In order to transmit biochemical signals, biological regulatory systems dissipate energy with concomitant entropy production. Additionally, signaling often takes place in challenging environmental conditions. In a simple model regulatory circuit given by an input and a delayed output, we explore the trade-offs between information transmission and the system's energetic efficiency. We determine the maximally informative network, given a fixed amount of entropy production and delayed response, exploring both the case with and without feedback. We find that feedback allows the circuit to overcome energy constraints and transmit close to the maximum available information even in the dissipationless limit. Negative feedback loops, characteristic of shock responses, are optimal at high dissipation. Close to equilibrium positive feedback loops, known for their stability, become more informative. Asking how the signaling network should be constructed to best function in the worst possible environment, rather than an optimally tuned one or in steady state, we discover that at large dissipation the same universal motif is optimal in all of these conditions.

show abstract

Section: Information Transmission With Energy Dissipationmentioning

confidence: 58%

Section: B Feedbackmentioning

confidence: 99%

Section: Limit τ =mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Trade-Offs in Delayed Information Transmission in Biochemical Networks

2015

Self Cite

View full text Add to dashboard Cite

show abstract

“…However, this type of response is common in nature for cells that are responding under stress, such as yeast in 0 percent glucose, which we used as an example in this work. An obvious limitation of our calculation is that we have studied gene regulatory networks in the steady state, and hence, the dynamic features of information processing are not included [36][37][38]. The cellular machinery consists of complex networks of motifs, and the effect on information processing of embedding simple genetic regulatory systems such as those studied here in large networks needs elucidation.…”

Section: Discussionmentioning

confidence: 99%

Mutual information and the fidelity of response of gene regulatory models

Tabbaa

Jayaprakash

2014

Phys. Biol.

View full text Add to dashboard Cite

We investigate cellular response to extracellular signals by using information theory techniques motivated by recent experiments. We present results for the steady state of the following gene regulatory models found in both prokaryotic and eukaryotic cells: a linear transcriptiontranslation model and a positive or negative auto-regulatory model. We calculate both the information capacity and the mutual information exactly for simple models and approximately for the full model. We find that (1) small changes in mutual information can lead to potentially important changes in cellular response and (2) there are diminishing returns in the fidelity of response as the mutual information increases. We calculate the information capacity using Gillespie simulations of a model for the TNF-α-NF-κ B network and find good agreement with the measured value for an experimental realization of this network. Our results provide a quantitative understanding of the differences in cellular response when comparing experimentally measured mutual information values of different gene regulatory models. Our calculations demonstrate that Gillespie simulations can be used to compute the mutual information of more complex gene regulatory models, providing a potentially useful tool in synthetic biology.

show abstract

Detecting Concentration Changes with Cooperative Receptors

Bò

Celani

2015

J Stat Phys

View full text Add to dashboard Cite

Cells constantly need to monitor the state of the environment to detect changes and timely respond. The detection of concentration changes of a ligand by a set of receptors can be cast as a problem of hypothesis testing, and the cell viewed as a Neyman-Pearson detector. Within this framework, we investigate the role of receptor cooperativity in improving the cell's ability to detect changes. We find that cooperativity decreases the probability of missing an occurred change. This becomes especially beneficial when difficult detections have to be made. Concerning the influence of cooperativity on how fast a desired detection power is achieved, we find in general that there is an optimal value at finite levels of cooperation, even though easy discrimination tasks can be performed more rapidly by noncooperative receptors.

show abstract

Time-dependent information transmission in a model regulatory circuit

Cited by 14 publications

References 31 publications

Trade-Offs in Delayed Information Transmission in Biochemical Networks

Trade-Offs in Delayed Information Transmission in Biochemical Networks

Mutual information and the fidelity of response of gene regulatory models

Detecting Concentration Changes with Cooperative Receptors

Contact Info

Product

Resources

About