Linear random knots and their scaling behavior

被引:97
作者
Millett, K
Dobay, A
Stasiak, A
机构
[1] Univ Lausanne, Lab Analyse Ultrastruct, CH-1015 Lausanne, Switzerland
[2] Univ Calif Santa Barbara, Dept Math, Santa Barbara, CA 93106 USA
[3] Univ Munich, Fak Phys, D-80333 Munich, Germany
关键词
D O I
10.1021/ma048779a
中图分类号
O63 [高分子化学(高聚物)];
学科分类号
070305 ; 080501 ; 081704 ;
摘要
We present here a nonbiased probabilistic method that allows us to consistently analyze knottedness of linear random walks with up to several hundred noncorrelated steps. The method consists of analyzing the spectrum of knots formed by multiple closures of the same open walk through random points on a sphere enclosing the walk. Knottedness of individual "frozen" configurations of linear chains is therefore defined by a characteristic spectrum of realizable knots. We show that in the great majority of cases this method clearly defines the dominant knot type of a walk, i.e., the strongest component of the spectrum. In such cases, direct end-to-end closure creates a knot that usually coincides with the knot type that dominates the random closure spectrum. Interestingly, in a very small proportion of linear random walks, the knot type is not clearly defined. Such walks can be considered as residing in a border zone of the configuration space of two or more knot types. We also characterize the scaling behavior of linear random knots.
引用
收藏
页码:601 / 606
页数:6
相关论文
共 40 条
[1]  
ADAMS CC, 1994, KNOT BOOK, P306
[2]  
[Anonymous], 1994, J KNOT THEOR RAMIF
[3]   Investigation of viral DNA packaging using molecular mechanics models [J].
Arsuaga, J ;
Tan, RKZ ;
Vazquez, M ;
Sumners, DW ;
Harvey, SC .
BIOPHYSICAL CHEMISTRY, 2002, 101 :475-484
[4]   Knotting probability of DNA molecules confined in restricted volumes:: DNA knotting in phage capsids [J].
Arsuaga, J ;
Vázquez, M ;
Trigueros, S ;
Sumners, D ;
Roca, J .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2002, 99 (08) :5373-5377
[5]   Dynamic patterns and self-knotting of a driven hanging chain [J].
Belmonte, A ;
Shelley, MJ ;
Eldakar, ST ;
Wiggins, CH .
PHYSICAL REVIEW LETTERS, 2001, 87 (11)
[6]   Knots and random walks in vibrated granular chains [J].
Ben-Naim, E ;
Daya, ZA ;
Vorobieff, P ;
Ecke, RE .
PHYSICAL REVIEW LETTERS, 2001, 86 (08) :1414-1417
[7]   Construction and electrophoretic migration of single-stranded DNA knots and catenanes [J].
Bucka, A ;
Stasiak, A .
NUCLEIC ACIDS RESEARCH, 2002, 30 (06) :e24
[8]   Rational tangle distances on knots and links [J].
Darcy, IK ;
Sumners, DW .
MATHEMATICAL PROCEEDINGS OF THE CAMBRIDGE PHILOSOPHICAL SOCIETY, 2000, 128 :497-510
[9]  
De Gennes PG., 1979, SCALING CONCEPTS POL
[10]   TIGHT KNOTS [J].
DEGENNES, PG .
MACROMOLECULES, 1984, 17 (04) :703-704