{
  "id": "0906.4988",
  "version": "v1",
  "published": "2009-06-26T18:30:17.000Z",
  "updated": "2009-06-26T18:30:17.000Z",
  "title": "A Random Force is a Force, of Course, of Coarse: Decomposing Complex Enzyme Kinetics with Surrogate Models",
  "authors": [
    "Christopher P. Calderon"
  ],
  "comment": "11 pages / 6 figures",
  "doi": "10.1103/PhysRevE.80.061118",
  "categories": [
    "cond-mat.stat-mech",
    "physics.bio-ph"
  ],
  "abstract": "The temporal autocorrelation (AC) function associated with monitoring order parameters characterizing conformational fluctuations of an enzyme is analyzed using a collection of surrogate models. The surrogates considered are phenomenological stochastic differential equation (SDE) models. It is demonstrated how an ensemble of such surrogate models, each surrogate being calibrated from a single trajectory, indirectly contains information about unresolved conformational degrees of freedom. This ensemble can be used to construct complex temporal ACs associated with a \"non-Markovian\" process. The ensemble of surrogates approach allows researchers to consider models more flexible than a mixture of exponentials to describe relaxation times and at the same time gain physical information about the system. The relevance of this type of analysis to matching single-molecule experiments to computer simulations and how more complex stochastic processes can emerge from a mixture of simpler processes is also discussed. The ideas are illustrated on a toy SDE model and on molecular dynamics simulations of the enzyme dihydrofolate reductase.",
  "revisions": [
    {
      "version": "v1",
      "updated": "2009-06-26T18:30:17.000Z"
    }
  ],
  "analyses": {
    "subjects": [
      "02.50.-r",
      "82.39.Fk",
      "87.15.Vv",
      "87.10.Mn"
    ],
    "keywords": [
      "decomposing complex enzyme kinetics",
      "surrogate models",
      "random force",
      "complex temporal acs",
      "order parameters characterizing conformational fluctuations"
    ],
    "tags": [
      "journal article"
    ],
    "publication": {
      "publisher": "APS",
      "journal": "Physical Review E",
      "year": 2009,
      "month": "Dec",
      "volume": 80,
      "number": 6,
      "pages": "061118"
    },
    "note": {
      "typesetting": "TeX",
      "pages": 11,
      "language": "en",
      "license": "arXiv",
      "status": "editable",
      "adsabs": "2009PhRvE..80f1118C"
    }
  }
}