First passage times and asymmetry of DNA translocation

Details First passage times and asymmetry of DNA translocation First passage times and asymmetry of DNA translocation

2005-08-10

arxiv.org/abs/q-bio/0508010v2

Physical Review E 72, 061918 (2005); also in January 1, 2006 issue of Virtual Journal of Biological Physics Research

Biology

Quantitative Biology

Biomolecules

10 pages, 4 figures We incorporated reviewers' suggestions from Physical Review E. We reformulated a few paragraphs in the int

Scientific paper

10.1103/PhysRevE.72.061918

Motivated by experiments in which single-stranded DNA with a short hairpin loop at one end undergoes unforced diffusion through a narrow pore, we study the first passage times for a particle, executing one-dimensional brownian motion in an asymmetric sawtooth potential, to exit one of the boundaries. We consider the first passage times for the case of classical diffusion, characterized by a mean-square displacement of the form $< (\Delta x)^2> \sim t$, and for the case of anomalous diffusion or subdiffusion, characterized by a mean-square displacement of the form $< (\Delta x)^2> \sim t^{\gamma}$ with $0<\gamma<1$. In the context of classical diffusion, we obtain an expression for the mean first passage time and show that this quantity changes when the direction of the sawtooth is reversed or, equivalently, when the reflecting and absorbing boundaries are exchanged. We discuss at which numbers of `teeth' $N$ (or number of DNA nucleotides) and at which heights of the sawtooth potential this difference becomes significant. For large $N$, it is well known that the mean first passage time scales as $N^2$. In the context of subdiffusion, the mean first passage time does not exist. Therefore we obtain instead the distribution of first passage times in the limit of long times. We show that the prefactor in the power relation for this distribution is simply the expression for the mean first passage time in classical diffusion. We also describe a hypothetical experiment to calculate the average of the first passage times for a fraction of passage events that each end within some time $t^*$. We show that this average first passage time scales as $N^{2/\gamma}$ in subdiffusion.

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