dorsal/arxiv
View SchemaCan one predict DNA Transcription Start Sites by studying bubbles?
| Authors | Titus S. van Erp, Santiago Cuesta-Lopez, Johannes-Geert Hagmann, Michel Peyrard |
|---|---|
| Categories | |
| ArXiv ID | physics/0508094 |
| URL | https://arxiv.org/abs/physics/0508094 |
| DOI | 10.1103/PhysRevLett.95.218104 |
Abstract
It has been speculated that bubble formation of several base-pairs due to thermal fluctuations is indicatory for biological active sites. Recent evidence, based on experiments and molecular dynamics (MD) simulations using the Peyrard-Bishop-Dauxois model, seems to point in this direction. However, sufficiently large bubbles appear only seldom which makes an accurate calculation difficult even for minimal models. In this letter, we introduce a new method that is orders of magnitude faster than MD. Using this method we show that the present evidence is unsubstantiated.
{
"annotation_id": "9d9c399f-9aa0-49b4-92ec-5a717bf6377a",
"date_created": "2026-03-02T18:01:00.768000Z",
"date_modified": "2026-03-02T18:01:00.768000Z",
"file_hash": "3c1d1967375414d330e32add0add2200599b7f92427962a786209e6f467d6c25",
"private": false,
"record": {
"abstract": "It has been speculated that bubble formation of several base-pairs due to\nthermal fluctuations is indicatory for biological active sites. Recent\nevidence, based on experiments and molecular dynamics (MD) simulations using\nthe Peyrard-Bishop-Dauxois model, seems to point in this direction. However,\nsufficiently large bubbles appear only seldom which makes an accurate\ncalculation difficult even for minimal models. In this letter, we introduce a\nnew method that is orders of magnitude faster than MD. Using this method we\nshow that the present evidence is unsubstantiated.",
"arxiv_id": "physics/0508094",
"authors": [
"Titus S. van Erp",
"Santiago Cuesta-Lopez",
"Johannes-Geert Hagmann",
"Michel Peyrard"
],
"categories": [
"physics.bio-ph",
"physics.comp-ph"
],
"doi": "10.1103/PhysRevLett.95.218104",
"title": "Can one predict DNA Transcription Start Sites by studying bubbles?",
"url": "https://arxiv.org/abs/physics/0508094"
},
"schema_id": "dorsal/arxiv",
"source": {
"execution_id": "a7267d72-9b18-4b42-9542-cbadca6c5966",
"id": "arXiv Dataset IDs",
"type": "Model",
"variant": "snapshot-2026-03-01",
"version": "0.1.0"
},
"user_id": 1000002
}