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Context in Synthetic Biology: Memory Effets of Environments with Mono-molecular Reactions

Falk, J. and Bronstein, L. and Hanst, M. and Drossel, B. and Koeppl, H. (2019):
Context in Synthetic Biology: Memory Effets of Environments with Mono-molecular Reactions.
In: The Journal of Chemical Physics, American Institute of Physics, 150, (2), ISSN 0021-9606, DOI: 10.1063/1.5053816, [Online-Edition: https://aip.scitation.org/doi/10.1063/1.5053816],
[Article]

Abstract

Synthetic biology aims at designing modular genetic circuits that can be assembled according to the desired function. When embedded in a cell, a circuit module becomes a small subnetwork within a larger environmental network, and its dynamics is therefore affected by potentially unknown interactions with the environment. It is well-known that the presence of the environment not only causes extrinsic noise but also memory effects, which means that the dynamics of the subnetwork is affected by its past states via a memory function that is characteristic of the environment. We study several generic scenarios for the coupling between a small module and a larger environment, with the environment consisting of a chain of mono-molecular reactions. By mapping the dynamics of this coupled system onto random walks, we are able to give exact analytical expressions for the arising memory functions. Hence, our results give insights into the possible types of memory functions and thereby help to better predict subnetwork dynamics.

Item Type: Article
Erschienen: 2019
Creators: Falk, J. and Bronstein, L. and Hanst, M. and Drossel, B. and Koeppl, H.
Title: Context in Synthetic Biology: Memory Effets of Environments with Mono-molecular Reactions
Language: English
Abstract:

Synthetic biology aims at designing modular genetic circuits that can be assembled according to the desired function. When embedded in a cell, a circuit module becomes a small subnetwork within a larger environmental network, and its dynamics is therefore affected by potentially unknown interactions with the environment. It is well-known that the presence of the environment not only causes extrinsic noise but also memory effects, which means that the dynamics of the subnetwork is affected by its past states via a memory function that is characteristic of the environment. We study several generic scenarios for the coupling between a small module and a larger environment, with the environment consisting of a chain of mono-molecular reactions. By mapping the dynamics of this coupled system onto random walks, we are able to give exact analytical expressions for the arising memory functions. Hence, our results give insights into the possible types of memory functions and thereby help to better predict subnetwork dynamics.

Journal or Publication Title: The Journal of Chemical Physics
Volume: 150
Number: 2
Publisher: American Institute of Physics
Divisions: 18 Department of Electrical Engineering and Information Technology
18 Department of Electrical Engineering and Information Technology > Institute for Telecommunications > Bioinspired Communication Systems
18 Department of Electrical Engineering and Information Technology > Institute for Telecommunications
05 Department of Physics
05 Department of Physics > Institute for condensed matter physics
05 Department of Physics > Institute for condensed matter physics > Statistische Physik und komplexe Systeme
Date Deposited: 22 Jan 2019 11:39
DOI: 10.1063/1.5053816
Official URL: https://aip.scitation.org/doi/10.1063/1.5053816
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