Kubaczka, Erik ; Gehringer, Maximilian ; Marlhens, Jérémie J. M. ; Schwarz, Tobias ; Molderings, Maik ; Engelmann, Nicolai ; Garcia, Hernan G. ; Hochberger, Christian ; Koeppl, Heinz (2024)
Energy Aware Technology Mapping of Genetic Logic Circuits.
In: ACS Synthetic Biology, 13 (10)
doi: 10.1021/acssynbio.4c00395
Artikel, Bibliographie
Dies ist die neueste Version dieses Eintrags.
Kurzbeschreibung (Abstract)
Energy and its dissipation are fundamental to all living systems, including cells. Insufficient abundance of energy carriers─as caused by the additional burden of artificial genetic circuits─shifts a cell’s priority to survival, also impairing the functionality of the genetic circuit. Moreover, recent works have shown the importance of energy expenditure in information transmission. Despite living organisms being non-equilibrium systems, non-equilibrium models capable of accounting for energy dissipation and non-equilibrium response curves are not yet employed in genetic design automation (GDA) software. To this end, we introduce Energy Aware Technology Mapping, the automated design of genetic logic circuits with respect to energy efficiency and functionality. The basis for this is an energy aware non-equilibrium steady state model of gene expression, capturing characteristics like energy dissipation─which we link to the entropy production rate─and transcriptional bursting, relevant to eukaryotes as well as prokaryotes. Our evaluation shows that a genetic logic circuit’s functional performance and energy efficiency are disjoint optimization goals. For our benchmark, energy efficiency improves by 37.2% on average when comparing to functionally optimized variants. We discover a linear increase in energy expenditure and overall protein expression with the circuit size, where Energy Aware Technology Mapping allows for designing genetic logic circuits with the energetic costs of circuits that are one to two gates smaller. Structural variants improve this further, while results show the Pareto dominance among structures of a single Boolean function. By incorporating energy demand into the design, Energy Aware Technology Mapping enables energy efficiency by design. This extends current GDA tools and complements approaches coping with burden in vivo.
| Typ des Eintrags: | Artikel |
|---|---|
| Erschienen: | 2024 |
| Autor(en): | Kubaczka, Erik ; Gehringer, Maximilian ; Marlhens, Jérémie J. M. ; Schwarz, Tobias ; Molderings, Maik ; Engelmann, Nicolai ; Garcia, Hernan G. ; Hochberger, Christian ; Koeppl, Heinz |
| Art des Eintrags: | Bibliographie |
| Titel: | Energy Aware Technology Mapping of Genetic Logic Circuits |
| Sprache: | Englisch |
| Publikationsjahr: | 8 Oktober 2024 |
| Verlag: | ACS Publ. |
| Titel der Zeitschrift, Zeitung oder Schriftenreihe: | ACS Synthetic Biology |
| Jahrgang/Volume einer Zeitschrift: | 13 |
| (Heft-)Nummer: | 10 |
| DOI: | 10.1021/acssynbio.4c00395 |
| Zugehörige Links: | |
| Kurzbeschreibung (Abstract): | Energy and its dissipation are fundamental to all living systems, including cells. Insufficient abundance of energy carriers─as caused by the additional burden of artificial genetic circuits─shifts a cell’s priority to survival, also impairing the functionality of the genetic circuit. Moreover, recent works have shown the importance of energy expenditure in information transmission. Despite living organisms being non-equilibrium systems, non-equilibrium models capable of accounting for energy dissipation and non-equilibrium response curves are not yet employed in genetic design automation (GDA) software. To this end, we introduce Energy Aware Technology Mapping, the automated design of genetic logic circuits with respect to energy efficiency and functionality. The basis for this is an energy aware non-equilibrium steady state model of gene expression, capturing characteristics like energy dissipation─which we link to the entropy production rate─and transcriptional bursting, relevant to eukaryotes as well as prokaryotes. Our evaluation shows that a genetic logic circuit’s functional performance and energy efficiency are disjoint optimization goals. For our benchmark, energy efficiency improves by 37.2% on average when comparing to functionally optimized variants. We discover a linear increase in energy expenditure and overall protein expression with the circuit size, where Energy Aware Technology Mapping allows for designing genetic logic circuits with the energetic costs of circuits that are one to two gates smaller. Structural variants improve this further, while results show the Pareto dominance among structures of a single Boolean function. By incorporating energy demand into the design, Energy Aware Technology Mapping enables energy efficiency by design. This extends current GDA tools and complements approaches coping with burden in vivo. |
| Freie Schlagworte: | genetic design automation, energy, non-equilibrium, thermodynamics, synthetic biology, gene-expression, technology mapping, metabolic burden, computer aided design, entropy production rate |
| Zusätzliche Informationen: | Erstveröffentlichung |
| Sachgruppe der Dewey Dezimalklassifikatin (DDC): | 600 Technik, Medizin, angewandte Wissenschaften > 621.3 Elektrotechnik, Elektronik |
| Fachbereich(e)/-gebiet(e): | 18 Fachbereich Elektrotechnik und Informationstechnik 18 Fachbereich Elektrotechnik und Informationstechnik > Self-Organizing Systems Lab Interdisziplinäre Forschungsprojekte Interdisziplinäre Forschungsprojekte > Centre for Synthetic Biology |
| Hinterlegungsdatum: | 28 Nov 2024 09:42 |
| Letzte Änderung: | 28 Nov 2024 09:42 |
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| Suche nach Titel in: | TUfind oder in Google |
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Energy Aware Technology Mapping of Genetic Logic Circuits. (deposited 25 Nov 2024 10:38)
- Energy Aware Technology Mapping of Genetic Logic Circuits. (deposited 28 Nov 2024 09:42) [Gegenwärtig angezeigt]
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