ترغب بنشر مسار تعليمي؟ اضغط هنا

Nonequilibrium dynamics of polymer translocation: a mean-field model

157   0   0.0 ( 0 )
 نشر من قبل Chiu Fan Lee
 تاريخ النشر 2007
  مجال البحث فيزياء
والبحث باللغة English
 تأليف Chiu Fan Lee




اسأل ChatGPT حول البحث

We analyse the dynamics of polymer translocation in the strong force regime by recasting the problem into solving a differential equation with a moving absorbing boundary. For the total translocation time, $tau_{rm tr}$, our simple mean-field model predicts that $tau_{rm tr}sim$ (number of monomers)$^{1.5}$, which is in agreement with the exponent found in previous simulation results. Our model also predicts intricate dependencies of $tau_{rm tr}$ on the variations of the pulling force and of the temperature.



قيم البحث

اقرأ أيضاً

Using Langevin dynamics simulations, we investigate the influence of polymer-pore interactions on the dynamics of biopolymer translocation through nanopores. We find that an attractive interaction can significantly change the translocation dynamics. This can be understood by examining the three components of the total translocation time $tau approx tau_1+tau_2+tau_3$ corresponding to the initial filling of the pore, transfer of polymer from the textit{cis} side to the textit{trans} side, and emptying of the pore, respectively. We find that the dynamics for the last process of emptying of the pore changes from non-activated to activated in nature as the strength of the attractive interaction increases, and $tau_3$ becomes the dominant contribution to the total translocation time for strong attraction. This leads to a new dependence of $tau$ as a function of driving force and chain length. Our results are in good agreement with recent experimental findings, and provide a possible explanation for the different scaling behavior observed in solid state nanopores {it vs.} that for the natural $alpha$-hemolysin channel.
218 - Kehong Zhang , Kaifu Luo 2012
Using Langevin dynamics simulations, we investigate the dynamics of a flexible polymer translocation into a confined area under a driving force through a nanopore. We choose an ellipsoidal shape for the confinement and consider the dependence of the asymmetry of the ellipsoid measured by the aspect ratio on the translocation time. Compared with an isotropic confinement (sphere), an anisotropic confinement (ellipsoid) with the same volume slows down the translocation, and the translocation time increases with increasing the aspect ratio of the ellipsoid. We further find that it takes different time for polymer translocation into the same ellipsoid through major-axis and minor-axis directions, depending on the average density of the whole chain in the ellipsoid, $phi$. For $phi$ lower than a critical value $phi_c$, the translocation through minor axis is faster, and vice versa. These complicated behaviors are interpreted by the degree of the confinement and anisotropic confinement induced folding of the translocated chain.
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.
146 - Kehong Zhang , Kaifu Luo 2012
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.
159 - Wancheng Yu , Kaifu Luo 2011
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.
التعليقات
جاري جلب التعليقات جاري جلب التعليقات
سجل دخول لتتمكن من متابعة معايير البحث التي قمت باختيارها
mircosoft-partner

هل ترغب بارسال اشعارات عن اخر التحديثات في شمرا-اكاديميا