dorsal/arxiv
View SchemaDynamics of RNA Translocation through a Nanopore
| Authors | J. B. Lucks, Y. Kafri |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0703028 |
| URL | https://arxiv.org/abs/q-bio/0703028 |
Abstract
We present a simplified model of the dynamics of translocation of RNA through a nanopore which only allows the passage of unbound nucleotides. In particular, we consider the disorder averaged translocation dynamics of random, two-component, single-stranded nucleotides, by reducing the dynamics to the motion of a random walker on a one-dimensional free energy landscape of translocation. These translocation landscapes are calculated from the folds of the RNA sequences and the voltage bias applied across the nanopore. We compute these landscapes for 1500 randomly drawn two-letter sequences of length 4000. Simulations of the dynamics on these landscapes display anomalous characteristics, similar to random forcing energy landscapes, where the translocation process proceeds slower than linearly in time for sufficiently small voltage biases across the nanopore, but moves linearly in time at large voltage biases. We argue that our simplified model provides an upper bound to the more realistic translocation dynamics, and thus we expect that all RNA translocation models will exhibit anomalous regimes.
{
"annotation_id": "5bf6664e-0aca-49a4-8662-68971ef2502a",
"date_created": "2026-03-02T18:01:35.094000Z",
"date_modified": "2026-03-02T18:01:35.094000Z",
"file_hash": "420e708f0ba220f13e953fcb871c51c3c919a80ad4e28d8c8397740485344411",
"private": false,
"record": {
"abstract": "We present a simplified model of the dynamics of translocation of RNA through\na nanopore which only allows the passage of unbound nucleotides. In particular,\nwe consider the disorder averaged translocation dynamics of random,\ntwo-component, single-stranded nucleotides, by reducing the dynamics to the\nmotion of a random walker on a one-dimensional free energy landscape of\ntranslocation. These translocation landscapes are calculated from the folds of\nthe RNA sequences and the voltage bias applied across the nanopore. We compute\nthese landscapes for 1500 randomly drawn two-letter sequences of length 4000.\nSimulations of the dynamics on these landscapes display anomalous\ncharacteristics, similar to random forcing energy landscapes, where the\ntranslocation process proceeds slower than linearly in time for sufficiently\nsmall voltage biases across the nanopore, but moves linearly in time at large\nvoltage biases. We argue that our simplified model provides an upper bound to\nthe more realistic translocation dynamics, and thus we expect that all RNA\ntranslocation models will exhibit anomalous regimes.",
"arxiv_id": "q-bio/0703028",
"authors": [
"J. B. Lucks",
"Y. Kafri"
],
"categories": [
"q-bio.BM",
"cond-mat.soft",
"q-bio.QM"
],
"title": "Dynamics of RNA Translocation through a Nanopore",
"url": "https://arxiv.org/abs/q-bio/0703028"
},
"schema_id": "dorsal/arxiv",
"source": {
"execution_id": "5f5064b8-9a49-4f7f-b48b-f5185d1c6327",
"id": "arXiv Dataset IDs",
"type": "Model",
"variant": "snapshot-2026-03-01",
"version": "0.1.0"
},
"user_id": 1000002
}