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Monte Carlo simulation on polymer translocation in crowded environment
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10.1063/1.3658047
/content/aip/journal/jcp/135/17/10.1063/1.3658047
http://aip.metastore.ingenta.com/content/aip/journal/jcp/135/17/10.1063/1.3658047
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

A 2D sketch of 3D SAW bond-fluctuation model on SC lattice. (a) Original configuration. There are three NN empty sites marked “A”, “B”, and “C” for the selected monomer 4. But only the site “B” is a “good” site as it satisfies: (1) empty site, (2) without bond crossing, and (3) bond length being allowed. On 2D SC lattice, bond length can be 1 or . (b) New configuration as monomer 4 moving to a new site. Here, the bond length is changeable.

Image of FIG. 2.
FIG. 2.

Semi-logarithmic plot of the translocation time τ vs the concentration of obstacle ϕ c at the cis side for polymer with length N = 100 at the chemical potential difference Δμ = 0 and Δμ = 0.5. Pure excluded volume effect of obstacles is considered. The inset presents τ vs the concentration of obstacle ϕ t at the trans side for polymer with length N = 100 at Δμ = 0.5.

Image of FIG. 3.
FIG. 3.

(a) Semi-logarithmic plot of the translocation time τ vs the polymer-obstacle interaction ɛ c at different concentrations of obstacle ϕ c at the cis side; (b) Plot of the translocation time τ vs the obstacle concentration ϕ c for the polymer-obstacle interaction ɛ c = 0.5, −0.3, −0.6, −0.8, and −1. Horizontal dashed line represents τ0 at ϕ c = 0, while the vertical one indicates the point . Other parameters are: chain length N = 100, chemical potential difference Δμ = 0.5, and obstacle concentration at the trans side ϕ t =0.

Image of FIG. 4.
FIG. 4.

Semi-logarithm plot of the translocation time τ vs the polymer-obstacle interaction ɛ t at different obstacle concentrations at the trans side. Other parameters are: N = 100, Δμ = 0.5, and ϕ c = 0.

Image of FIG. 5.
FIG. 5.

Sketches of free energy landscape of translocation at different obstacle concentrations. The free energy increases for ϕ c > 0 at cis side (a) and for ϕ t > 0 at trans side (b). The attractive interaction lowers the free energy. z is along the translocation direction of chain.

Image of FIG. 6.
FIG. 6.

Plot of the special interactions (open circle) and (solid triangle) versus the chemical potential difference Δμ.

Image of FIG. 7.
FIG. 7.

Log-log plot of the translocation time τ versus the polymer chain length for three cases: (1) ϕ c = 0.125 at = −0.2 (circle); (2) ϕ t = 0.125 at (cross); and (3) ϕ c = ϕ t = 0 (solid line) at different chemical potential difference Δμ = 0.2, 0.5, and 1.0. Dashed line has a slope 1.25.

Image of FIG. 8.
FIG. 8.

Configurational properties of chain during the translocation at ϕ c = ϕ t = 0.125. Mean square end-to-end distance 〈R 2〉 (a), mean square radius of gyration 〈S 2〉 (b), and segment-obstacle NN pair number N pair (c) at different chemical potential differences. Plot (d) shows N pair at different interaction ɛ and at Δμ = 0.5. Value m c(t) is the length of partial chain at cis (trans) side during the translocation. Chain length is =100. ɛ = 0 is used for plots (a)–(c).

Image of FIG. 9.
FIG. 9.

Log-log plot of the mean square displacement of center of mass 〈Δr 2〉 versus the simulation time t at different obstacle concentrations. Solid lines are the linear fit of the simulation data. The inset presents the exponent β at different obstacle concentrations. Other parameters are: chain length N = 100, polymer-obstacle interaction ɛ = 0, and system size L x = L y = L z = 80.

Image of FIG. 10.
FIG. 10.

Log-log plot of the mean square displacement of center of mass 〈Δr 2〉 versus the simulation time t at different polymer-obstacle interactions. The solid lines are guide for eyes. The inset presents the exponent β at different polymer-obstacle interactions. Concentration of obstacle is ϕ = 0.05 and chain length is N = 100.

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/content/aip/journal/jcp/135/17/10.1063/1.3658047
2011-11-02
2014-04-20
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Monte Carlo simulation on polymer translocation in crowded environment
http://aip.metastore.ingenta.com/content/aip/journal/jcp/135/17/10.1063/1.3658047
10.1063/1.3658047
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