title: Effective rates from thermodynamically consistent coarse-graining of models for molecular motors with probe particles.
abstract: Many single-molecule experiments for molecular motors comprise not only the motor but also large probe particles coupled to it. The theoretical analysis of these assays, however, often takes into account only the degrees of freedom representing the motor. We present a coarse-graining method that maps a model comprising two coupled degrees of freedom which represent motor and probe particle to such an effective one-particle model by eliminating the dynamics of the probe particle in a thermodynamically and dynamically consistent way. The coarse-grained rates obey a local detailed balance condition and reproduce the net currents. Moreover, the average entropy production as well as the thermodynamic efficiency is invariant under this coarse-graining procedure. Our analysis reveals that only by assuming unrealistically fast probe particles, the coarse-grained transition rates coincide with the transition rates of the traditionally used one-particle motor models. Additionally, we find that for multicyclic motors the stall force can depend on the probe size. We apply this coarse-graining method to specific case studies of the F(1)-ATPase and the kinesin motor.
authors.affiliation: II. Institut für Theoretische Physik, Universität Stuttgart, 70550 Stuttgart, Germany.
authors.forename: Eva
authors.initials: E
authors.lastname: Zimmermann
authors.affiliation: II. Institut für Theoretische Physik, Universität Stuttgart, 70550 Stuttgart, Germany.
authors.forename: Udo
authors.initials: U
authors.lastname: Seifert
mesh_terms: D000244:Adenosine Diphosphate / Q000737:chemistry; D000251:Adenosine Triphosphatases / Q000737:chemistry; D000255:Adenosine Triphosphate / Q000737:chemistry; D003198:Computer Simulation; D016547:Kinesins / Q000737:chemistry; D008958:Models, Molecular; D020409:Molecular Motor Proteins / Q000737:chemistry*; D013816:Thermodynamics; D013997:Time Factors
chemical_list: D020409:Molecular Motor Proteins; D000244:Adenosine Diphosphate; D000255:Adenosine Triphosphate; D000251:Adenosine Triphosphatases; D016547:Kinesins