{
  "annotation_id": "f9e04012-435f-45b3-9f41-699ac9b3a68a",
  "date_created": "2026-03-02T18:01:35.619000Z",
  "date_modified": "2026-03-02T18:01:35.619000Z",
  "file_hash": "7a2a60d876c758eab32ace55d8c97f2df1a9c0360c6434f5579599dbcddb2227",
  "private": false,
  "record": {
    "abstract": "In the process of translation, ribosomes read the genetic code on an mRNA and\nassemble the corresponding polypeptide chain. The ribosomes perform discrete\ndirected motion which is well modeled by a totally asymmetric simple exclusion\nprocess (TASEP) with open boundaries. Using Monte Carlo simulations and a\nsimple mean-field theory, we discuss the effect of one or two ``bottlenecks\u0027\u0027\n(i.e., slow codons) on the production rate of the final protein. Confirming and\nextending previous work by Chou and Lakatos, we find that the location and\nspacing of the slow codons can affect the production rate quite dramatically.\nIn particular, we observe a novel ``edge\u0027\u0027 effect, i.e., an interaction of a\nsingle slow codon with the system boundary. We focus in detail on ribosome\ndensity profiles and provide a simple explanation for the length scale which\ncontrols the range of these interactions.",
    "arxiv_id": "q-bio/0602024",
    "authors": [
      "J. J. Dong",
      "B. Schmittmann",
      "R. K. P. Zia"
    ],
    "categories": [
      "q-bio.BM",
      "cond-mat.stat-mech",
      "physics.bio-ph"
    ],
    "doi": "10.1007/s10955-006-9134-7",
    "journal_ref": "Journal of Statistical Physics, Volume 128, Numbers 1-2 / July,\n  2007",
    "title": "Towards a model for protein production rates",
    "url": "https://arxiv.org/abs/q-bio/0602024"
  },
  "schema_id": "dorsal/arxiv",
  "source": {
    "execution_id": "50bbe611-f6d3-43bc-b7ec-25a144e9b8de",
    "id": "arXiv Dataset IDs",
    "type": "Model",
    "variant": "snapshot-2026-03-01",
    "version": "0.1.0"
  },
  "user_id": 1000002
}