{
  "id": "2009.11145",
  "version": "v1",
  "published": "2020-09-23T13:43:44.000Z",
  "updated": "2020-09-23T13:43:44.000Z",
  "title": "Emergence of effective temperatures in an out-of-equilibrium model of RNA folding",
  "authors": [
    "Marco Ancona",
    "Alessandro Bentivoglio",
    "Michele Caraglio",
    "Giuseppe Gonnella",
    "Alessandro Pelizzola"
  ],
  "comment": "13 pages, 7 figures",
  "categories": [
    "cond-mat.stat-mech",
    "cond-mat.soft",
    "physics.bio-ph"
  ],
  "abstract": "We investigate the possibility of extending the notion of temperature in a stochastic model for the RNA/protein folding driven out of equilibrium. We simulate the dynamics of a small RNA hairpin subject to an external pulling force, which is time-dependent. First, we consider a fluctuation-dissipation relation (FDR), that extends the fluctuation-dissipation theorem in nonequilibrium contexts. We verify that various effective temperatures values can be obtained in a range of parameters and for different observables, only when the slowest intrinsic relaxation timescale of the system regulates the dynamics of the system. Then, we introduce a different nonequilibrium temperature, which is defined from the rate of heat exchanged with a weakly-interacting thermal bath. Notably, this `kinetic' temperature can be defined for any frequency of the external switching force. We also discuss and compare the behavior of these two emerging parameters, by discriminating the time-delayed nature of the FDR temperature from the instantaneous character of the kinetic temperature.",
  "revisions": [
    {
      "version": "v1",
      "updated": "2020-09-23T13:43:44.000Z"
    }
  ],
  "analyses": {
    "keywords": [
      "effective temperatures",
      "out-of-equilibrium model",
      "rna folding",
      "slowest intrinsic relaxation timescale",
      "small rna hairpin subject"
    ],
    "note": {
      "typesetting": "TeX",
      "pages": 13,
      "language": "en",
      "license": "arXiv",
      "status": "editable"
    }
  }
}