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Translocation dynamics of a short polymer driven by an oscillating force
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10.1063/1.4789016
/content/aip/journal/jcp/138/5/10.1063/1.4789016
http://aip.metastore.ingenta.com/content/aip/journal/jcp/138/5/10.1063/1.4789016
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

3D-view of the phenomenological potential energy U Ext, which is included in our system to simulate the presence of a barrier to be surmounted by the polymer during the translocation dynamics. The inset shows the projection of U Ext on the z-x plane (solid line); dashed lines indicate the maximum and the minimum shape of the potential barrier caused by the presence of the oscillating forcing field.

Image of FIG. 2.
FIG. 2.

MFTT vs. frequency of the forcing field for seven different values of the number of monomers, namely, N = 15, 18, 20, 32, 40, 50, 60. The noise intensity is D = 1.0. The values of the potential energy parameters are: K r = K θ = 20, εLJ = 0.1, σ = 3, and d = 5, in arbitrary units (AU). The amplitude of the forcing field is A = 2 × 10−2 (AU).

Image of FIG. 3.
FIG. 3.

Mean first translocation time (MFTT) as a function of the number of monomers for three different values of the angular frequency of the forcing field, namely, ω = 0.0001, 0.01, 0.1. For polymer chain length N > 40, a monotonic increasing behavior of MFTT vs N is observed. All other parameter values are the same as those of Fig. 2 .

Image of FIG. 4.
FIG. 4.

Standard deviation (SD) of the first translocation time (FTT) as a function of the frequency of the oscillating field, for the same values of polymer length plotted in Fig. 2 , except for N = 60, whose curve essentially overlaps that with N = 50 and, for this reason, it was not plotted, and N = 24 which instead was added. (Inset) The SD of FTT versus the number of monomers for three different values of the frequency of the forcing field, namely, ω = 0.0001, 0.1, 1. All other parameter values are the same as those of Fig. 2 .

Image of FIG. 5.
FIG. 5.

Probability density function (PDF) of the first translocation time (FTT). Each panel shows three PDFs, each one characterized by a specific value of the number of monomers, namely, N = 15, 30, 60. The three panels differs for the frequency of the forcing field: (a) low frequency domain (ω = 0.0001); (b) resonant activation region (ω = 0.01); (c) high frequency domain (ω = 1.0). All other parameter values are the same as those of Fig. 2 .

Image of FIG. 6.
FIG. 6.

Mean first translocation time of polymers having constant length (N = 30) as a function of the frequency of the oscillating field, for three different values of the noise intensity, namely D = 0.25, 0.5, 1.0. The inset shows the standard deviation (SD) of the FTTs. All other parameter values are the same as those of Fig. 2 .

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/content/aip/journal/jcp/138/5/10.1063/1.4789016
2013-02-01
2014-04-17
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Translocation dynamics of a short polymer driven by an oscillating force
http://aip.metastore.ingenta.com/content/aip/journal/jcp/138/5/10.1063/1.4789016
10.1063/1.4789016
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