2011/05/18 by Chris A. Brackley, Brackley, Chris A., David S. Broomhead +6
Biochemistry, Genetics and Molecular Biology · Computer Science · Mathematics · #FOS: Biological sciences #FOS: Mathematics #Formal Methods in Verification #Gene Regulatory Network Analysis #Petri Nets in System Modeling #Quantitative Methods (q-bio.QM) #Rings and Algebras (math.RA) #math.RA #q-bio.QM
paper · pdf · doi:10.48550/arxiv.1105.3580
arxiv created 2011/05/18 · openalex publication_date 2011/05/18 · arxiv updated 2015/03/18 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
We examine the dynamics of the translation stage of cellular protein production, in which ribosomes move uni-directionally along mRNA strands building an amino acid chain as they go. We describe the system using a timed event graph - a class of Petri net useful for studying discrete events which take a finite time. We use max-plus algebra to describe a deterministic version of the model, calculating the protein production rate and density of ribosomes on the mRNA. We find exact agreement between these analytical results and numerical simulations of the deterministic case.