The importance of introducing a waiting time for Lattice Monte Carlo simulations of a polymer translocation process |
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Authors: | Hendrick W de Haan Michel G Gauthier Mykyta V Chubynsky Gary W Slater |
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Affiliation: | aDepartment of Physics, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, Canada, K1N 6N5;bDepartment of Physics, Simon Fraser University, 8888 University Dr., Burnaby, British Columbia, Canada, V5A 1S6 |
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Abstract: | For a standard Lattice Monte Carlo (LMC) simulation of a random walker subject to a bias, it is impossible to obtain both a correct mean velocity and diffusion coefficient. To correct this, a modified LMC algorithm has been developed where the introduction of a probability of remaining in the current state allows for a distribution of intervals between jumps. In this paper, we demonstrate the impact of this modification for a first-passage problem: the translocation of a polymer through a nanopore. We find that while either approach yields the correct mean first-passage time, the incorporation of a waiting time is necessary to obtain the correct spread of times. |
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Keywords: | Monte Carlo Simulations Translocation Polymer Nanopore |
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