A two-state ribosome and protein model can robustly capture the chemical reaction dynamics of gene expression: Difference between revisions
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{{Paper | {{Paper | ||
|Title=A two-state ribosome and protein model can robustly capture the chemical reaction dynamics of gene expression | |Title=A two-state ribosome and protein model can robustly capture the chemical reaction dynamics of gene expression | ||
|Authors=Ayush Pandey, Richard M Murray | |Authors=Ayush Pandey, Richard M. Murray | ||
|Source=2020 Winter q-bio | |Source=2020 Winter q-bio | ||
|Abstract=We derive phenomenological models of gene expression from a mechanistic description of chemical reactions using an automated model reduction method. Using this method, we get analytical descriptions and computational performance guarantees to compare the reduced dynamics with the full models. We develop a new two-state model with the dynamics of the available free ribosomes in the system and the protein concentration. We show that this new two-state model captures the detailed mass-action kinetics of the chemical reaction network under various biologically plausible conditions on model parameters. On comparing the performance of this model with the commonly used mRNA transcript-protein dynamical model for gene expression, we analytically show that the free ribosome and protein model has superior error and robustness performance. | |Abstract=We derive phenomenological models of gene expression from a mechanistic description of chemical reactions using an automated model reduction method. Using this method, we get analytical descriptions and computational performance guarantees to compare the reduced dynamics with the full models. We develop a new two-state model with the dynamics of the available free ribosomes in the system and the protein concentration. We show that this new two-state model captures the detailed mass-action kinetics of the chemical reaction network under various biologically plausible conditions on model parameters. On comparing the performance of this model with the commonly used mRNA transcript-protein dynamical model for gene expression, we analytically show that the free ribosome and protein model has superior error and robustness performance. | ||
Latest revision as of 18:20, 9 October 2022
| Title | A two-state ribosome and protein model can robustly capture the chemical reaction dynamics of gene expression |
|---|---|
| Authors | Ayush Pandey and Richard M. Murray |
| Source | 2020 Winter q-bio |
| Abstract | We derive phenomenological models of gene expression from a mechanistic description of chemical reactions using an automated model reduction method. Using this method, we get analytical descriptions and computational performance guarantees to compare the reduced dynamics with the full models. We develop a new two-state model with the dynamics of the available free ribosomes in the system and the protein concentration. We show that this new two-state model captures the detailed mass-action kinetics of the chemical reaction network under various biologically plausible conditions on model parameters. On comparing the performance of this model with the commonly used mRNA transcript-protein dynamical model for gene expression, we analytically show that the free ribosome and protein model has superior error and robustness performance. |
| Type | Conference paper |
| URL | https://www.biorxiv.org/content/biorxiv/early/2020/11/26/2020.11.25.399287.full.pdf |
| DOI | |
| Tag | PM21-wqbio |
| ID | 2020c |
| Funding | DARPA BioCon |
| Flags |
