Trade-offs and thermodynamics of energy-relay proofreading
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arXiv
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| Format: | Preprint |
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2024
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| _version_ | 1866929732966154240 |
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| author | Berx, Jonas Proesmans, Karel |
| author_facet | Berx, Jonas Proesmans, Karel |
| contents | Biological processes that are able to discriminate between different molecules consume energy and dissipate heat. They operate at different levels of fidelity and speed, and as a consequence there exist fundamental trade-offs between these quantities and the entropy production rate. Usually, the energy source required to operate in a high-fidelity regime comes from the consumption of external energetic molecules, e.g., GTP hydrolysis in protein translation . In this work, we study trade-offs between several kinetic and thermodynamic observables for Hopfield's energy-relay mechanism, which does not consume external molecules and is able to operate in depleted regions, at the cost of a higher error rate. The trade-offs are obtained both analytically and numerically via Pareto optimal fronts. We find that the scheme is able to operate in three distinct regimes: an energy relay regime, a mixed relay-Michaelis-Menten regime, and a Michaelis-Menten regime, depending on the kinetic and energetic parameters that tune transitions between states. The mixed regime features a dynamical phase transition in the error-entropy production Pareto trade-off, while the pure energy relay regime contains a region where this type of proofreading energetically outperforms standard kinetic proofreading. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2403_07626 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Trade-offs and thermodynamics of energy-relay proofreading Berx, Jonas Proesmans, Karel Statistical Mechanics Biological Physics Biological processes that are able to discriminate between different molecules consume energy and dissipate heat. They operate at different levels of fidelity and speed, and as a consequence there exist fundamental trade-offs between these quantities and the entropy production rate. Usually, the energy source required to operate in a high-fidelity regime comes from the consumption of external energetic molecules, e.g., GTP hydrolysis in protein translation . In this work, we study trade-offs between several kinetic and thermodynamic observables for Hopfield's energy-relay mechanism, which does not consume external molecules and is able to operate in depleted regions, at the cost of a higher error rate. The trade-offs are obtained both analytically and numerically via Pareto optimal fronts. We find that the scheme is able to operate in three distinct regimes: an energy relay regime, a mixed relay-Michaelis-Menten regime, and a Michaelis-Menten regime, depending on the kinetic and energetic parameters that tune transitions between states. The mixed regime features a dynamical phase transition in the error-entropy production Pareto trade-off, while the pure energy relay regime contains a region where this type of proofreading energetically outperforms standard kinetic proofreading. |
| title | Trade-offs and thermodynamics of energy-relay proofreading |
| topic | Statistical Mechanics Biological Physics |
| url | https://arxiv.org/abs/2403.07626 |