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Simulations of two-dimensional unbiased polymer translocation using the bond fluctuation model

机译:使用键涨落模型模拟二维无偏聚合物的移位

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摘要

We use the bond fluctuation model (BFM) to study the pore-blockade times of a translocating polymer of length N in two dimensions, in the absence of external forces on the polymer (i.e., unbiased translocation) and hydrodynamic interactions (i.e., the polymer is a Rouse polymer), through a narrow pore. Earlier studies using the BFM concluded that the pore-blockade time scales with polymer length as τd ∼ Nβ, with β = 1+2ν, whereas some recent studies using different polymer models produce results consistent with β = 2+ν, originally predicted by us. Here ν is the Flory exponent of the polymer; ν = 0.75 in 2D. In this paper we show that for the BFM if the simulations are extended to longer polymers, the purported scaling τd ∼ N1+2ν ceases to hold. We characterize the finite-size effects, and study the mobility of individual monomers in the BFM. In particular, we find that in the BFM, in the vicinity of the pore the individual monomeric mobilities are heavily suppressed in the direction perpendicular to the membrane. After a modification of the BFM which counters this suppression (but possibly introduces other artifacts in the dynamics), the apparent exponent β increases significantly. Our conclusion is that BFM simulations do not rule out our theoretical prediction for unbiased translocation, namely, β = 2+ν.
机译:我们使用键涨落模型(BFM)研究二维长度为N的易位聚合物在没有外力作用(即无偏位)和流体动力学相互作用(即聚合物)的情况下的孔堵塞时间是一种Rouse聚合物),通过一个狭窄的孔。早期使用BFM的研究得出结论,聚合物长度为τd〜Nβ,β= 1 +2ν的孔堵塞时间尺度,而最近使用不同聚合物模型进行的一些研究得出的结果与我们最初预测的β= 2 +ν一致。 。此处ν是聚合物的弗洛里指数; ν= 0.75 in 2D。在本文中,我们表明对于BFM,如果将模拟扩展到更长的聚合物,则声称的比例缩放τd〜N1 +2ν不再成立。我们表征有限大小的影响,并研究BFM中单个单体的迁移率。特别地,我们发现在BFM中,在孔附近,在垂直于膜的方向上严重抑制了各个单体迁移率。在对BFM进行修改以抵消这种抑制(但可能在动力学中引入其他伪像)之后,视在指数β显着增加。我们的结论是,BFM模拟不排除我们对无偏位的理论预测,即β= 2 +ν。

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    Panja, D.; Barkema, G.T.;

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  • 年度 2010
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  • 正文语种 en
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