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 |
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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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