ArticleScientific reports2017
Optimal Translation Along a Circular mRNA.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- On the gain of entrainment in theJournal of the Royal Society, Interface · 2023Article
- A theoretical framework to analyse the flow of particles in a dynamical system with stochastic transition rates and site capacities.Royal Society open science · 2022Article
- Maximizing average throughput in oscillatory biochemical synthesis systems: an optimal control approach.Royal Society open science · 2021Article
- Synthetic protein quality control to enhance full-length translation in bacteria.Nature chemical biology · 2021Article
- Variability in mRNA translation: a random matrix theory approach.Scientific reports · 2021Article
- Networks of ribosome flow models for modeling and analyzing intracellular traffic.Scientific reports · 2019Article
- Analytical and simulation studies of driven diffusive system with asymmetric heterogeneous interactions.Scientific reports · 2018Article
- A deterministic mathematical model for bidirectional excluded flow with Langmuir kinetics.PloS one · 2017Article
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3 authors.
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Abstract
The ribosome flow model on a ring (RFMR) is a deterministic model for ribosome flow along a circularized mRNA. We derive a new spectral representation for the optimal steady-state production rate and the corresponding optimal steady-state ribosomal density in the RFMR. This representation has several important advantages. First, it provides a simple and numerically stable algorithm for determining the optimal values even in very long rings. Second, it enables efficient computation of the sensitivity of the optimal production rate to small changes in the transition rates along the mRNA. Third, it implies that the optimal steady-state production rate is a strictly concave function of the transition rates. Maximizing the optimal steady-state production rate with respect to the rates under an affine constraint on the rates thus becomes a convex optimization problem that admits a unique solution. This solution can be determined numerically using highly efficient algorithms. This optimization problem is important, for example, when re-engineering heterologous genes in a host organism. We describe the implications of our results to this and other aspects of translation.
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