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Gaussian fluctuations in tethered DNA chains
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10.1063/1.3548887
/content/aip/journal/jcp/134/6/10.1063/1.3548887
http://aip.metastore.ingenta.com/content/aip/journal/jcp/134/6/10.1063/1.3548887
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

Differential fluorescence intensity −dα(E)/dE vs electric field E for three short ssDNAs. From left to right the lines are corresponding to ssDNA chains with 90, 80, and 60 nucleotides.

Image of FIG. 2.
FIG. 2.

Schematic representation of (a) grafted Gaussian chain and (b) semigrafted Gaussian chain. In both cases, the Gaussian chain is constrained in z > 0 half space with one end fixed at (0, 0, z 0) (for grafted chain) or anchored through a harmonic spring (for semigrafted chain). The planar wall is located at z = 0.

Image of FIG. 3.
FIG. 3.

Confinement free energy per segment for a grafted Gaussian chain in terms of chain length N. The solid line, the dashed-dotted line, and the dotted line correspond to z 0/a = 1, 2, and 3, respectively.

Image of FIG. 4.
FIG. 4.

Surface force for a grafted Gaussian chain in terms of chain length N. The solid line, the dashed-dotted line, and the dotted line correspond to z 0/a = 1, 2 and 3, respectively.

Image of FIG. 5.
FIG. 5.

Confinement free energy per segment for a semigrafted Gaussian chain as a function of chain length N. (a) spring constant kβa 2 = 1 and natural length l 0/a = 1 (solid line), 2 (dashed-dotted line), and 3 (dotted line); (b) l 0/a = 1 and kβa 2 = 1 (solid line), 2 (dashed-dotted line), and 3 (dotted line).

Image of FIG. 6.
FIG. 6.

The mean fluctuation force for a semigrafted Gaussian chain as a function of the chain length N. (a) spring constant kβa 2 = 1 and natural length l 0/a = 1 (solid line), 2 (dashed-dotted line), and 3 (dotted line); (b) l 0/a = 1 and kβa 2 = 1 (solid line), 2 (dashed-dotted line), and 3 (dotted line).

Image of FIG. 7.
FIG. 7.

The probability density of the fluctuation force for N = 90 predicted with three sets of spring parameters.

Image of FIG. 8.
FIG. 8.

Distribution of Nqρ(f t NqE) in terms of electric filed E: (a) Here the spring parameters are kβa 2 = 2, l 0/a = 1, and f t = 9/βa; the chain lengths are N = 60 (dotted blue line), 80 (dashed-dotted red line), and 90 (solid black line). (b) The chain length is fixed at N = 80, while the reduced rigidity and the natural spring length (kβa 2, l 0/a) are (1, 1), (2, 1), and (2, 2) for the solid line, the dashed-dotted line, and dotted line, respectively. The parameter f t remains the same as in (a).

Image of FIG. 9.
FIG. 9.

Dependence of on the chain length for four ssDNA chains studied in experiment. Solid triangle is the data from Fig. 1, while the squared solid triangle is from supplementary experiment data in Ref. 3. The dotted line connects the first point (N = 60) and the last point (N = 90).

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/content/aip/journal/jcp/134/6/10.1063/1.3548887
2011-02-09
2014-04-18
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Gaussian fluctuations in tethered DNA chains
http://aip.metastore.ingenta.com/content/aip/journal/jcp/134/6/10.1063/1.3548887
10.1063/1.3548887
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