We present a method to study the dynamics of long DNA molecules inside a cubic array of confining spheres, connected through narrow openings. Our method is based on the coarse-grained, lakes-straits model of Zimm and is therefore much faster than Brownian dynamics simulations. In contrast to Zimms approach, our method uses a standard stochastic kinetic simulation to account for the mass transfer through the narrow straits and the formation of new lakes. The different rates, or propensities, of the reactions are obtained using first-passage time statistics and a Monte Carlo sampling to compute the total free energy of the chain. The total free energy takes into account the self-avoiding nature of the chain as well as confinement effects from the impenetrable spheres. The mobilities of various chains agree with biased reptation theory at low and high fields. At moderate fields, confinement effects lead to a new regime of reptation where the mobility is a linear function of molecular weight and the dispersion is minimal.
|Original language||English (US)|
|Journal||Journal of Chemical Physics|
|State||Published - Dec 21 2010|
Bibliographical noteFunding Information:
This work was supported by the David and Lucile Packard Foundation and carried out in part using the computing resources at the University of Minnesota Supercomputing Institute. N.L. also acknowledges the support of a Doctoral Dissertation Fellowship from the University of Minnesota.
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