论文标题
双纳米孔系统中的拔河
Tug-of-War in a Double-Nanopore System
论文作者
论文摘要
我们通过双纳米孔（DNP）系统模拟了模型双链DNA螺纹的拔河（TOW）方案。同时在两个孔中捕获的DNA都受到两个相等和相反的力量$ - \ vec {f} _l = \ vec {f} _r $（tow），其中$ \ vec {f} _l $和$ \ \ \ \ \ \ vec {f} _r $是将部队应用于左和右孔的部队。 Even though the net force on the DNA polymer $Δ\vec{f}_{LR}=\vec{f}_L+ \vec{f}_R=0$, the mean first passage time (MFPT) $\langle τ\rangle$ depends on the magnitude of the TOW forces $ \left | f_l \ right | = \ left | f_r \ right | = f_ {lr} $。我们从定性地解释了$ \langleτ\ rangle $在$ f_ {lr} $上的$ \ langleτ\ rangle $从三孔共聚物的单孔易位中的$ f_ {lr} $。我们证明，单体的飞行时间（TOF）具有索引$ m $（$ \langleτ_{lr}（m）\ rangle $）从一个孔到另一个孔，展示了Quasi-periodic结构与毛孔之间的距离$ d_ {lr} $相称。最后，我们研究了$δ\ vec {f} _ {lr} = \ vec {f} _l+ \ vec {f} _r \ ne 0 $，并定性地重现了mfpt对$δ\ vec {f} _ {lr} $的实验结果。对于中等偏见，DNP系统的链长度$ n $的MFPT遵循与单个纳米孔相同的缩放ANSATZ，$ \ langleτ\ rangle = \ weft（an^{1 + q {1 + t} +η_{pore} +η_{pore} n \ right） $η_{孔} $是孔摩擦，它使我们能够估算长链的$ \langleτ\ rangle $。我们的布朗动力学仿真研究提供了有关从$ \langleτ_{lr}（m）\ rangle $获得的易位速度细节的基本见解和有价值的信息，以及在时间域中获得的数据转换到基因组距离单位中获得的数据的准确性。
We simulate a tug-of-war (TOW) scenario for a model double-stranded DNA threading through a double nanopore (DNP) system. The DNA, simultaneously captured at both pores is subject to two equal and opposite forces $-\vec{f}_L= \vec{f}_R$ (TOW), where $\vec{f}_L$ and $\vec{f}_R$ are the forces applied to the left and the right pore respectively. Even though the net force on the DNA polymer $Δ\vec{f}_{LR}=\vec{f}_L+ \vec{f}_R=0$, the mean first passage time (MFPT) $\langle τ\rangle$ depends on the magnitude of the TOW forces $ \left | f_L \right | = \left |f_R \right | = f_{LR}$. We qualitatively explain this dependence of $\langle τ\rangle$ on $f_{LR}$ from the known results for the single-pore translocation of a triblock copolymer. We demonstrate that the time of flight (TOF) of a monomer with index $m$ ($\langle τ_{LR}(m) \rangle$) from one pore to the other exhibits quasi-periodic structure commensurate with the distance between the pores $d_{LR}$. Finally, we study the case $Δ\vec{f}_{LR}=\vec{f}_L+ \vec{f}_R \ne 0$, and qualitatively reproduce the experimental result of the dependence of the MFPT on $Δ\vec{f}_{LR}$. For a moderate bias, the MFPT for the DNP system for a chain length $N$ follows the same scaling ansatz as that of for the single nanopore, $\langle τ\rangle = \left( AN^{1+ν} + η_{pore}N \right) \left(Δf_{LR}\right)^{-1}$, where $η_{pore}$ is the pore friction, which enables us to estimate $\langle τ\rangle $ for a long chain. Our Brownian dynamics simulation studies provide fundamental insights and valuable information about the details of the translocation speed obtained from $\langle τ_{LR}(m) \rangle$, and accuracy of the translation of the data obtained in the time-domain to units of genomic distances.
