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Simulations of the untying of molecular friction knots between individual polymer strands
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10.1063/1.2835605
/content/aip/journal/jcp/128/9/10.1063/1.2835605
http://aip.metastore.ingenta.com/content/aip/journal/jcp/128/9/10.1063/1.2835605
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

The square knot and the granny knot.

Image of FIG. 2.
FIG. 2.

Snapshots of two polymer strands joined by the square knot and subsequently pulled apart, as observed in a Langevin dynamics simulation. The time increases from top to bottom. The snapshots were generated with the help of the PYMOL software (Ref. 17).

Image of FIG. 3.
FIG. 3.

Effect of the polymer sequence and of the knot type on the untying time. The mean time for the untying of the square and the granny knots as a function of the force pulling the polymer strands apart for different polymer chains and different knots at . Three types of polymers were used, described by the sequences , , and , as indicated. The time is normalized by the polymer contour length because different sequences have different .

Image of FIG. 4.
FIG. 4.

Effect of temperature on the knot untying time. The mean time for the untying of the square knot between two strands as a function of the force pulling the polymer strands apart at different temperatures.

Image of FIG. 5.
FIG. 5.

The tilted periodic potential model. Periodic potential tilted by a force , . The dashed lines correspond to and the solid lines correspond to .

Image of FIG. 6.
FIG. 6.

Separation of two strands tied into the square knot. Interaction between two polymer strands within the square knot slows down their separation by a factor , which is plotted here as a function of for different temperatures. The data used are the same as that for Fig. 4. The solid line is a fit of the data obtained by using Eq. (2), where and .

Image of FIG. 7.
FIG. 7.

Separation of two strands tied into the granny knot. plotted as a function of for different temperatures. The solid line is a fit of the data obtained by using Eq. (2), where and .

Image of FIG. 8.
FIG. 8.

Separation of two strands tied into the square knot. is close to 1 except at low forces.

Image of FIG. 9.
FIG. 9.

Separation of two strands tied into the square knot. is close to 1 except at low forces.

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/content/aip/journal/jcp/128/9/10.1063/1.2835605
2008-03-03
2014-04-25
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Simulations of the untying of molecular friction knots between individual polymer strands
http://aip.metastore.ingenta.com/content/aip/journal/jcp/128/9/10.1063/1.2835605
10.1063/1.2835605
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