Browsing by Author "Dong, J. J."
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- Entrainment and Unit Velocity: Surprises in an Accelerated Exclusion ProcessDong, J. J.; Klumpp, S.; Zia, Royce K. P. (American Physical Society, 2012-09-27)We introduce a class of distance-dependent interactions in an accelerated exclusion process inspired by the observation of transcribing RNA polymerase speeding up when "pushed" by a trailing one. On a ring, the accelerated exclusion process steady state displays a discontinuous transition, from being homogeneous (with augmented currents) to phase segregated. In the latter state, the holes appear loosely bound and move together, much like a train. Surprisingly, the current-density relation is simply J = 1 - rho, signifying that the "hole train" travels with unit velocity.
- Inhomogeneous exclusion processes with extended objects: The effect of defect locationsDong, J. J.; Schmittmann, Beate; Zia, Royce K. P. (American Physical Society, 2007-11)We study the effects of local inhomogeneities, i.e., slow sites of hopping rate q < 1, in a totally asymmetric simple exclusion process for particles of size l >= 1 (in units of the lattice spacing). We compare the simulation results of l=1 and l>1 and notice that the existence of local defects has qualitatively similar effects on the steady state. We focus on the stationary current as well as the density profiles. If there is only a single slow site in the system, we observe a significant dependence of the current on the location of the slow site for both l=1 and l>1 cases. When two slow sites are introduced, more intriguing phenomena emerge, e.g., dramatic decreases in the current when the two are close together. In addition, we study the asymptotic behavior when q -> 0. We also explore the associated density profiles and compare our findings to an earlier study using a simple mean-field theory. We then outline the biological significance of these effects.