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Context in synthetic biology: Memory effects of environments with mono-molecular reactions

Falk, Johannes ; Bronstein, Leo ; Hanst, Maleen ; Drossel, Barbara ; Koeppl, Heinz (2025)
Context in synthetic biology: Memory effects of environments with mono-molecular reactions.
In: The Journal of Chemical Physics, 2019, 150 (2)
doi: 10.26083/tuprints-00028992
Article, Secondary publication, Publisher's Version

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Item Type: Article
Type of entry: Secondary publication
Title: Context in synthetic biology: Memory effects of environments with mono-molecular reactions
Language: English
Date: 15 January 2025
Place of Publication: Darmstadt
Year of primary publication: 14 January 2019
Place of primary publication: Melville, NY
Publisher: AIP Publishing
Journal or Publication Title: The Journal of Chemical Physics
Volume of the journal: 150
Issue Number: 2
Collation: 14 Seiten
DOI: 10.26083/tuprints-00028992
Corresponding Links:
Origin: Secondary publication service
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.

Uncontrolled Keywords: Reaction rate constants, Chemical reaction dynamics, Synthetic biology, Cellular noise, Markov processes, Random walks, Stochastic processes
Status: Publisher's Version
URN: urn:nbn:de:tuda-tuprints-289927
Classification DDC: 500 Science and mathematics > 570 Life sciences, biology
600 Technology, medicine, applied sciences > 621.3 Electrical engineering, electronics
Divisions: 18 Department of Electrical Engineering and Information Technology > Institute for Telecommunications > Bioinspired Communication Systems
18 Department of Electrical Engineering and Information Technology > Self-Organizing Systems Lab
Date Deposited: 15 Jan 2025 09:24
Last Modified: 15 Jan 2025 09:25
URI: https://tuprints.ulb.tu-darmstadt.de/id/eprint/28992
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