Engelmann, Nicolai ; Schwarz, Tobias ; Kubaczka, Erik ; Hochberger, Christian ; Koeppl, Heinz (2023)
Context-Aware Technology Mapping in Genetic Design Automation.
In: ACS Synthetic Biology, 12 (2)
doi: 10.1021/acssynbio.2c00361
Artikel, Bibliographie
Dies ist die neueste Version dieses Eintrags.
Kurzbeschreibung (Abstract)
Genetic design automation (GDA) tools hold promise to speed-up circuit design in synthetic biology. Their widespread adoption is hampered by their limited predictive power, resulting in frequent deviations between the in silico and in vivo performance of a genetic circuit. Context effects, i.e., the change in overall circuit functioning, due to the intracellular environment of the host and due to cross-talk among circuits components are believed to be a major source for the aforementioned deviations. Incorporating these effects in computational models of GDA tools is challenging but is expected to boost their predictive power and hence their deployment. Using fine-grained thermodynamic models of promoter activity, we show in this work how to account for two major components of cellular context effects: (i) crosstalk due to limited specificity of used regulators and (ii) titration of circuit regulators to off-target binding sites on the host genome. We show how we can compensate the incurred increase in computational complexity through dedicated branch-and-bound techniques during the technology mapping process. Using the synthesis of several combinational logic circuits based on Cello’s device library as a case study, we analyze the effect of different intensities and distributions of crosstalk on circuit performance and on the usability of a given device library.
| Typ des Eintrags: | Artikel |
|---|---|
| Erschienen: | 2023 |
| Autor(en): | Engelmann, Nicolai ; Schwarz, Tobias ; Kubaczka, Erik ; Hochberger, Christian ; Koeppl, Heinz |
| Art des Eintrags: | Bibliographie |
| Titel: | Context-Aware Technology Mapping in Genetic Design Automation |
| Sprache: | Englisch |
| Publikationsjahr: | 17 Februar 2023 |
| Verlag: | ACS Publications |
| Titel der Zeitschrift, Zeitung oder Schriftenreihe: | ACS Synthetic Biology |
| Jahrgang/Volume einer Zeitschrift: | 12 |
| (Heft-)Nummer: | 2 |
| Kollation: | 14 Seiten |
| DOI: | 10.1021/acssynbio.2c00361 |
| Zugehörige Links: | |
| Kurzbeschreibung (Abstract): | Genetic design automation (GDA) tools hold promise to speed-up circuit design in synthetic biology. Their widespread adoption is hampered by their limited predictive power, resulting in frequent deviations between the in silico and in vivo performance of a genetic circuit. Context effects, i.e., the change in overall circuit functioning, due to the intracellular environment of the host and due to cross-talk among circuits components are believed to be a major source for the aforementioned deviations. Incorporating these effects in computational models of GDA tools is challenging but is expected to boost their predictive power and hence their deployment. Using fine-grained thermodynamic models of promoter activity, we show in this work how to account for two major components of cellular context effects: (i) crosstalk due to limited specificity of used regulators and (ii) titration of circuit regulators to off-target binding sites on the host genome. We show how we can compensate the incurred increase in computational complexity through dedicated branch-and-bound techniques during the technology mapping process. Using the synthesis of several combinational logic circuits based on Cello’s device library as a case study, we analyze the effect of different intensities and distributions of crosstalk on circuit performance and on the usability of a given device library. |
| Freie Schlagworte: | genetic design automation, equilibrium thermodynamics, branch and bound, technology mapping, context effects, crosstalk |
| ID-Nummer: | pmid:36693176 |
| Zusätzliche Informationen: | Erstveröffentlichung |
| Fachbereich(e)/-gebiet(e): | 18 Fachbereich Elektrotechnik und Informationstechnik 18 Fachbereich Elektrotechnik und Informationstechnik > Institut für Nachrichtentechnik > Bioinspirierte Kommunikationssysteme 18 Fachbereich Elektrotechnik und Informationstechnik > Institut für Datentechnik 18 Fachbereich Elektrotechnik und Informationstechnik > Institut für Nachrichtentechnik 18 Fachbereich Elektrotechnik und Informationstechnik > Institut für Datentechnik > Rechnersysteme 18 Fachbereich Elektrotechnik und Informationstechnik > Self-Organizing Systems Lab Interdisziplinäre Forschungsprojekte Interdisziplinäre Forschungsprojekte > Centre for Synthetic Biology |
| Hinterlegungsdatum: | 27 Feb 2023 15:38 |
| Letzte Änderung: | 11 Okt 2024 14:52 |
| PPN: | 507273400 |
| Export: | |
| Suche nach Titel in: | TUfind oder in Google |
Verfügbare Versionen dieses Eintrags
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Context-Aware Technology Mapping in Genetic Design Automation. (deposited 30 Sep 2024 09:53)
- Context-Aware Technology Mapping in Genetic Design Automation. (deposited 27 Feb 2023 15:38) [Gegenwärtig angezeigt]
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