title: Iso-flux tension propagation theory of driven polymer translocation: the role of initial configurations.
abstract: We investigate the dynamics of pore-driven polymer translocation by theoretical analysis and molecular dynamics (MD) simulations. Using the tension propagation theory within the constant flux approximation we derive an explicit equation of motion for the tension front. From this we derive a scaling relation for the average translocation time τ, which captures the asymptotic result τ∝N0(1+ν), where N0 is the chain length and ν is the Flory exponent. In addition, we derive the leading correction-to-scaling term to τ and show that all terms of order N0(2ν) exactly cancel out, leaving only a finite-chain length correction term due to the effective pore friction, which is linearly proportional to N0. We use the model to numerically include fluctuations in the initial configuration of the polymer chain in addition to thermal noise. We show that when the cis side fluctuations are properly accounted for, the model not only reproduces previously known results but also considerably improves the estimates of the monomer waiting time distribution and the time evolution of the translocation coordinate s(t), showing excellent agreement with MD simulations.
authors.affiliation: Department of Applied Physics and COMP Center of Excellence, Aalto University School of Science, P.O. Box 11000, FI-00076 Aalto, Espoo, Finland.
authors.forename: Jalal
authors.initials: J
authors.lastname: Sarabadani
authors.affiliation: Department of Applied Physics and COMP Center of Excellence, Aalto University School of Science, P.O. Box 11000, FI-00076 Aalto, Espoo, Finland.
authors.forename: Timo
authors.initials: T
authors.lastname: Ikonen
authors.affiliation: Department of Applied Physics and COMP Center of Excellence, Aalto University School of Science, P.O. Box 11000, FI-00076 Aalto, Espoo, Finland.
authors.forename: Tapio
authors.initials: T
authors.lastname: Ala-Nissila
mesh_terms: D017276:Friction; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D009038:Motion; D011108:Polymers / Q000737:chemistry*; D016062:Porosity
chemical_list: D011108:Polymers