title: Slow sites in an exclusion process with limited resources.
abstract: We introduce slow bottleneck sites into a recent extension of the totally asymmetric exclusion process where hopping rates are allowed to vary dynamically with the availability of resources. In the context of messenger RNA (mRNA) translation in biology, this refers to the availability of amino acid-transfer-RNA (aa-tRNA) complexes which act as the source of amino acids for protein production. We study a simple designer mRNA with a single defect codon in the center. As well as the familiar queuing behavior we also observe a regime within the queuing phase where the queue becomes less severe as the aa-tRNAs become depleted.
authors.affiliation: Institute for Complex Systems and Mathematical Biology, SUPA, University of Aberdeen, Aberdeen AB24 3UE, United Kingdom.
authors.forename: Chris A
authors.initials: CA
authors.lastname: Brackley
authors.forename: M Carmen
authors.initials: MC
authors.lastname: Romano
authors.forename: Marco
authors.initials: M
authors.lastname: Thiel
mesh_terms: D003062:Codon / Q000235:genetics; D007700:Kinetics; D008957:Models, Genetic; D009010:Monte Carlo Method; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000235:genetics; D012345:RNA, Transfer, Amino Acid-Specific / Q000235:genetics; D012270:Ribosomes / Q000235:genetics
chemical_list: D003062:Codon; D012333:RNA, Messenger; D012345:RNA, Transfer, Amino Acid-Specific