Pareto optimal fronts of kinetic proofreading
Biological processes such as DNA replication, RNA transcription, and protein translation operate with remarkable speed and accuracy in selecting the right substrate from pools of chemically identical molecules. This result is obtained by non-equilibrium reactions that dissipate chemical energy. It i...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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IOP Publishing
2023-01-01
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| Series: | New Journal of Physics |
| Subjects: | |
| Online Access: | https://doi.org/10.1088/1367-2630/acc757 |
| _version_ | 1797748722131533824 |
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| author | Davide Chiuchiu Shrabani Mondal Simone Pigolotti |
| author_facet | Davide Chiuchiu Shrabani Mondal Simone Pigolotti |
| author_sort | Davide Chiuchiu |
| collection | DOAJ |
| description | Biological processes such as DNA replication, RNA transcription, and protein translation operate with remarkable speed and accuracy in selecting the right substrate from pools of chemically identical molecules. This result is obtained by non-equilibrium reactions that dissipate chemical energy. It is widely recognized that there must be a trade-off between speed, error, and dissipation characterizing these systems. In this paper, we quantify this trade-off using tools from mathematical optimization theory. We characterize the Pareto optimal front for a generalized version of Hopfield’s kinetic proofreading model, which is a paradigmatic example of biological error correction. We find that models with more proofreading steps are characterized by better trade-offs. Furthermore, we numerically study scaling relations between speed, accuracy, and dissipation on the Pareto front. |
| first_indexed | 2024-03-12T16:08:53Z |
| format | Article |
| id | doaj.art-c8db9bf4f0334027ade1f7d4b88a73ba |
| institution | Directory Open Access Journal |
| issn | 1367-2630 |
| language | English |
| last_indexed | 2024-03-12T16:08:53Z |
| publishDate | 2023-01-01 |
| publisher | IOP Publishing |
| record_format | Article |
| series | New Journal of Physics |
| spelling | doaj.art-c8db9bf4f0334027ade1f7d4b88a73ba2023-08-09T14:14:17ZengIOP PublishingNew Journal of Physics1367-26302023-01-0125404300710.1088/1367-2630/acc757Pareto optimal fronts of kinetic proofreadingDavide Chiuchiu0Shrabani Mondal1https://orcid.org/0000-0002-6011-1066Simone Pigolotti2https://orcid.org/0000-0002-6157-6906Biological Complexity Unit, Okinawa Institute of Science and Technology Graduate University , Onna, Okinawa 904-0495, JapanBiological Complexity Unit, Okinawa Institute of Science and Technology Graduate University , Onna, Okinawa 904-0495, Japan; Department of Chemistry, Physical Chemistry Section, Jadavpur University , Kolkata 700032, IndiaBiological Complexity Unit, Okinawa Institute of Science and Technology Graduate University , Onna, Okinawa 904-0495, JapanBiological processes such as DNA replication, RNA transcription, and protein translation operate with remarkable speed and accuracy in selecting the right substrate from pools of chemically identical molecules. This result is obtained by non-equilibrium reactions that dissipate chemical energy. It is widely recognized that there must be a trade-off between speed, error, and dissipation characterizing these systems. In this paper, we quantify this trade-off using tools from mathematical optimization theory. We characterize the Pareto optimal front for a generalized version of Hopfield’s kinetic proofreading model, which is a paradigmatic example of biological error correction. We find that models with more proofreading steps are characterized by better trade-offs. Furthermore, we numerically study scaling relations between speed, accuracy, and dissipation on the Pareto front.https://doi.org/10.1088/1367-2630/acc757error correctionthermodynamic tradeoffspeed-error tradeoffnon-equilibrium thermodynamics |
| spellingShingle | Davide Chiuchiu Shrabani Mondal Simone Pigolotti Pareto optimal fronts of kinetic proofreading New Journal of Physics error correction thermodynamic tradeoff speed-error tradeoff non-equilibrium thermodynamics |
| title | Pareto optimal fronts of kinetic proofreading |
| title_full | Pareto optimal fronts of kinetic proofreading |
| title_fullStr | Pareto optimal fronts of kinetic proofreading |
| title_full_unstemmed | Pareto optimal fronts of kinetic proofreading |
| title_short | Pareto optimal fronts of kinetic proofreading |
| title_sort | pareto optimal fronts of kinetic proofreading |
| topic | error correction thermodynamic tradeoff speed-error tradeoff non-equilibrium thermodynamics |
| url | https://doi.org/10.1088/1367-2630/acc757 |
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