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The growth of the mean average crossing number of equilateral polygons in confinement

J Arsuaga1,3, B Borgo1, Y Diao2,3 and R Scharein1

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The physical and biological properties of collapsed long polymer chains as well as of highly condensed biopolymers (such as DNA in all organisms) are known to be determined, at least in part, by their topological and geometrical properties. With this purpose of characterizing the topological properties of such condensed systems equilateral random polygons restricted to confined volumes are often used. However, very few analytical results are known. In this paper, we investigate the effect of volume confinement on the mean average crossing number (ACN) of equilateral random polygons. The mean ACN of knots and links under confinement provides a simple alternative measurement for the topological complexity of knots and links in the statistical sense. For an equilateral random polygon of n segments without any volume confinement constrain, it is known that its mean ACN langACNrang is of the order \frac{3}{16}n\ln n +O(n). Here we model the confining volume as a simple sphere of radius R. We provide an analytical argument which shows that langACNrang of an equilateral random polygon of n segments under extreme confinement (meaning R Lt n) grows as O(n2). We propose to model the growth of langACNrang as a(R)n2 + b(R)nln(n) under a less-extreme confinement condition, where a(R) and b(R) are functions of R with R being the radius of the confining sphere. Computer simulations performed show a fairly good fit using this model.


PACS

36.20.Fz Constitution (chains and sequences)

87.14.G- Nucleic acids

MSC

92D20 Protein sequences, DNA sequences

82D60 Polymers

51E12 Generalized quadrangles, generalized polygons

Subjects

Soft matter, liquids and polymers

Atomic and molecular physics

Biological physics

Dates

Issue 46 (20 November 2009)

Received 30 July 2009, in final form 25 September 2009

Published 22 October 2009



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