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تسجيل مستخدم جديدActive translocation of a semiflexible polymer assisted by an ATP-based molecular motor
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In this work we study the assisted translocation of a polymer across a membrane nanopore, inside which a molecular motor exerts a force fuelled by the hydrolysis of ATP molecules. In our model the motor switches to its active state for a fixed amount of time, while it waits for an ATP molecule binding and triggering the impulse, during an exponentially distributed time lapse. The polymer is modelled as a beads-springs chain with both excluded volume and bending contributions, and moves in a stochastic three dimensional environment modelled with a Langevin dynamics at fixed temperature. The resulting dynamics shows a Michaelis-Menten translocation velocity that depends on the chain flexibility. The scaling behavior of the mean translocation time with the polymer length for different bending values is also investigated.
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We present a Brownian dynamics model of driven polymer translocation, in which non-equilibrium memory effects arising from tension propagation (TP) along the cis side subchain are incorporated as a time-dependent friction. To solve the effective fric
tion, we develop a finite chain length TP formalism, expanding on the work of Sakaue [Sakaue, PRE 76, 021803 (2007)]. The model, solved numerically, yields results in excellent agreement with molecular dynamics simulations in a wide range of parameters. Our results show that non-equilibrium TP along the cis side subchain dominates the dynamics of driven translocation. In addition, the model explains the different scaling of translocation time w.r.t chain length observed both in experiments and simulations as a combined effect of finite chain length and pore-polymer interactions.
Using Langevin dynamics simulations, we investigate the dynamics of chaperone-assisted translocation of a flexible polymer through a nanopore. We find that increasing the binding energy $epsilon$ between the chaperone and the chain and the chaperone
concentration $N_c$ can greatly improve the translocation probability. Particularly, with increasing the chaperone concentration a maximum translocation probability is observed for weak binding. For a fixed chaperone concentration, the histogram of translocation time $tau$ has a transition from long-tailed distribution to Gaussian distribution with increasing $epsilon$. $tau$ rapidly decreases and then almost saturates with increasing binding energy for short chain, however, it has a minimum for longer chains at lower chaperone concentration. We also show that $tau$ has a minimum as a function of the chaperone concentration. For different $epsilon$, a nonuniversal dependence of $tau$ on the chain length $N$ is also observed. These results can be interpreted by characteristic entropic effects for flexible polymers induced by either crowding effect from high chaperone concentration or the intersegmental binding for the high binding energy.
Using Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a circular nanocontainer through a nanopore under a driving force $F$. We observe that the translocation probability initially increases and then saturates
with increasing $F$, independent of $phi$, which is the average density of the whole chain in the nanocontainer. The translocation time distribution undergoes a transition from a Gaussian distribution to an asymmetric distribution with increasing $phi$. Moreover, we find a nonuniversal scaling exponent of the translocation time as chain length, depending on $phi$ and $F$. These results are interpreted by the conformation of the translocated chain in the nanocontainer and the time of an individual segment passing through the pore during translocation.
Two phase picture is a simple and effective methodology to capture the nonequilibrium dynamics of polymer associated with tension propagation. When applying it to the driven translocation process, there is a point to be noted, as briefly discussed in
our recent article [Phys. Rev. E 85, 061803 (2012)]. In this article, we address this issue in detail and modify our previous prediction [Euro. Phys. J. E 34, 135 (2011)] by adopting an alternative steady-state ansatz. The modified scaling prediction turns out to be the same as that of the iso-flux model recently proposed by Rowghanian and Grosberg [J. Phys. Chem. B 115, 14127-14135 (2011)].
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