Abstract
This article describes some of the theoretical and simulation results on random entanglement, and give a few scientific applications. I will prove that, on the simple cubic lattice Z3, the probability that a randomly chosen n-edge polygon in Z3 is knotted goes to one exponentially rapidly with length n (Murphy’s Law of entanglement); in other words, all but exponentially few polygons of length n in Z3 are knotted. Measures of entanglement complexity of random knots and random arcs are discussed as well as application of random knotting to viral DNA packing.
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References
[Ax1] Alexander, J.W.: An Example of a Simply Connected Surface Bounding a Region which is not Simply Connected. Proceedings of the National Academy of Sciences USA, 10, 8–10 (1924).
[Ax2] Alexander, J.W.: On the Subdivision of 3-Space by a Polyhedron. Proceedings of the National Academy of Sciences USA, 10, 6–8 (1924).
[Sv] Silver, D.S.: Knot Theory's Odd Origins. American Scientist, 94, 58–66 (2006).
[Mof] Moffatt, H.K.: Knots and Fluid Dynamics. In Ideal Knots, Series on Knots and Everything, eds. Stasiak, A., Katritch, V., Kauffman, L.H. (World Scientific, Singapore), Vol. 19, 223–233 (1999).
[Ric1] Ricca, R.L.: New Developments in Topological Fluid Mechanics: From Kelvin's Vortex Knots to Magnetic Knots. In Ideal Knots, Series on Knots and Everything, eds. Stasiak, A., Katritch, V., Kauffman, L.H. (World Scientific, Singapore), Vol. 19, 255–273 (1999).
[Ric2] Ricca, R.L.: Tropicity and Complexity Measures for Vortex Tangles, Lecture Notes in Physics v. 571. Springer, Berlin Heidelberg New York, 366–372 (2001).
[LZC] Liu, Z, Zechiedrich, E.L., Chan, H.S.: Inferring global topology from local juxta-position geometry: interlinking polymer rings and ramifications for topoisomerase action. Biophys. J., 90, 2344–2355 (2006).
[BZ] Buck, G, Zechiedrich, E.L.: DNA disentangling by type-2 topoisomerases. J. Mol Biol. Jul 23; 340(5): 933–9 (2004).
[FW] Frisch, H.L., Wasserman, E.: Chemical Topology. J. Am. Chem. Soc. 83, 3789–3795 (1961).
[Was] Wasserman, E.: Chemical Topology. Scientific American 207, 94–102 (1962)
[Del] Delbruck, M: in Mathematical Problems in the Biological Sciences, Proceedings of Symposia in Applied Mathematics 14, 327– (1962).
[VLF] Vologodskii, A.V., Lukashin, A.V., Frank-Kemenetkii, M.D., Anshelevich, V.V.: The Knot Problem in Statistical Mechanics of Polymer Chains. Sov. Phys.-JETP 39, 1059– (1974).
[CM] des Cloizeaux, J., Mehta, M.L.: J. de Physique 40, 665– (1979).
[MW] Michels, J.P.J., Wiegel, F.W.: Probability of Knots in a Polymer Ring. Phys. Lett. 90A, 381–384 (1984).
[SW] Sumners, D.W., Whittington, S.G.: Knots in Self-Avoiding Walks. J. Phys. A: Math. Gen. 21, 1689–1694 (1988).
[Kes] Kesten, H.: On the Number of Self-Avoiding Walks. J. Math. Phys. 4, 960–969 (1963).
[Pip] Pippenger, N.: Knots in Random Walks. Discrete Appl. Math. 25, 273–278 (1989).
[Adm] Adams, C.C.: The Knot Book. W.H. Freeman and Co., New York (1991).
[RSW] van Rensburg, E.J.J., Sumners, D.W., Wasserman, E., Whittington, S.G.: Entanglement Complexity of Self-Avoiding Walks. J. Phys. A.: Math. Gen. 25, 6557–6566 (1992).
[RBHS] Lacher R.C., Bryant J.L., Howard L., Sumners D.W. Linking phenomena in the amorphous phase of semicrystalline polymers. Macromolecules 19, 2639–2643 (1986).
[DNS] Diao, Y.,Nardo, J.C., Sun Y.: Global Knotting in Equilateral Polygons. J. of Knot Theory and Its Ramifications 10, 597–607 (2001).
[Do2] Diao, Y.: The Knotting of Equilateral Polygons in R 3. J. of Knot Theory and Its Ramifications 4, 189–196 (1995).
[DPS] Diao, Y., Pippenger, N., Sumners, D.W.: On Random Knots. J. of Knot Theory and Its Ramifications 3, 419–424 (1994).
[Do1] Diao, Y.: Minimal Knotted Polygons on the Simple Cubic Lattice. J. of Knot Theory and Its Ramifications 2, 413–425 (1993).
[RW] van Rensburg, E.J.J., Whittington, S.G.: The Knot Probability in Lattice Polygons. J. Phys. A.: Math. Gen. 23, 3573–3590 (1990).
[SSW] Soteros C., Sumners D.W., Whittington S.G.: Entanglement complexity of graphs in Z 3, Math. Proc Camb. Phil. Soc. 111, 75–91 (1992).
[Jun] Jungreis, D.: Gaussian Random Polygons are Globally Knotted. J. of Knot Theory and Its Ramifications 4, 455–464 (1994).
[Ken] Kendall:The knotting of brownian motion in 3-space. J. Lon. Math. Soc. 19, 378–(1979).
[DT1] Deguchi, T., Tsurasaki, K.: Universality of Random Knotting. Phys. Rev. E. 55, 6245–6248 (1997).
[Nak] Nakanishi, Y.: A Note on Unknotting Number. Math. Sem. Notes Kobe Univ. 9, 99–108 (1981).
[Ful] Fuller, B.: The Writhing Number of a Space Curve. Proc. Nat. Acad. Sci. USA 68, 815–819 (1971).C
[LS] Lacher, R.C., Sumners D.W.: Data structures and algorithms for computation of topological invariants of entanglements: link, twist and writhe. In Computer Simulation of Polymers, Prentice-Hall, Roe, R.J., ed. Englewood Cliffs, NJ, 365–373 (1991).
[Cim] Cimasoni, D.: Computing the Writhe of a Knot. J. Knot Theory and Its Ramifications 10, 387–395 (2001).
[LaS] Laing, C, Sumners D.W.: Computing the Writhe on Lattices. J. Phys A, Math. Gen. 39, 3535–3543 (2006).
[ROS] van Rensburg, E.J.J., Orlandini, E., Sumners, D.W., Tesi. M.C., Whittington, S.G.: The writhe of a self-avoiding polygon. J. Phys. A Math. Gen. 26, L981–L986 (1993).
Burde, G., Zieschang, H.: Knots. De Gruyter, Berlin, New York (1985).
Rolfsen, D.: Knots and Links. Publish or Perish (1976).
[RCV] Rybenkov, V. V., Cozzarelli, N. R. & Vologodskii, A. V.: Probability of DNA Knotting and the Effective Diameter of the DNA Double Helix. Proc. Natl. Acad. Sci. USA 90, 5307–5311 (1993).
[ShW] Shaw, S. Y., Wang, J. C.: Knotting of a DNA chain during ring closure. Science 260, 533–536 (1993).
[WC] Wasserman, S. A., Cozzarelli, N. R.: Biochemical topology: applications to DNA recombination and replication. Science 232, 951–960 (1986).
[SBS] Stark, W.M., Boocock, M.R., Sherratt, D. J.: Site-specific recombination by Tn3 resolvase. Trends Genet. 5, 304–309 (1989).
[FLA] Frank-Kamenetskii, M.D., Lukashin, A.V., Anshelevich, V.V., Vologodskii, A.V.: Torsional and bending rigidity of the double helix from data on small DNA rings. J. Biomol. Struct. Dyn. 2, 1005–1012 (1985).
[ES] Ernst, C., Sumners, D. W.: A Calculus for Rational Tangles: Applications to DNA Recombination. Math. Proc. Camb. Phil. Soc. 108, 489–515 (1990).
[SKI] Shishido, K., Komiyama, N., Ikawa, S.: Increased production of a knotted form of plasmid pBR322 DNA in Escherichia coli DNA topoisomerase mutants. J. Mol. Biol. 195, 215–218 (1987).
[LDC] Liu, L. F., Davis, J. L., Calendar, R.: Novel topologically knotted DNA from bacteriophage P4 capsids: studies with DNA topoisomerases. Nucleic Acids Res. 9, 3979–3989 (1981).
[LPC] Liu, L. F., Perkocha, L., Calendar, R.. Wang, J. C.: Knotted DNA from Bacteriophage Capsids. Proc. Natl. Acad. Sci. USA 78, 5498–5502 (1981).
[MML] Menissier, J., de Murcia, G., Lebeurier, G., Hirth, L.: Electron microscopic studies of the different topological forms of the cauliflower mosaic virus DNA: knotted encapsidated DNA and nuclear minichromosome. EMBO J. 2, 1067–1071 (1983).
[Man] Mansfield, M. L.: Knots in Hamilton Cycles. Macromolecules 27, 5924–5926 (1994).
[TRO] Tesi, M. C., van Resburg, J.J.E., Orlandini, E., Whittington, S. G.: Knot probability for lattice polygons in confined geometries. J. Phys. A: Math. Gen 27, 347–360 (1994).
[MMO] C. Micheletti, C, Marenduzzo, D., Orlandini, E., Sumners, D.W.: Knotting of Random Ring Polymers in Confined Spaces. J. Chem. Phys. 124, 064903 (2006).
[TAV] Trigueros, S, Arsuaga, J., Vazquez, M.E., Sumners, D.W., Roca, J.: Novel display of knotted DNA molecules by two-dimensional gel electrophoresis. Nucleic Acids Research 29, 67–71 (2001).
[AVT] J. Arsuaga, M. Vazquez, S. Trigueros, D.W. Sumners and J. Roca, Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids, Proc. National Academy of Sciences USA 99, 5373–5377 (2002).
[ArT]Arsuaga, J., R. Tan, K-Z, Vazquez, M.E., Sumners, D.W., Harvey, S.C.: Investigation of viral DNA packing using molecular mechanics models. Biophysical Chemistry 101–102, 475–484 (2002).
[AVM] Arsuaga, J., Vazquez, M.E., McGuirk, P., Sumners, D.W., Roca, J.: DNA Knots Reveal Chiral Organization of DNA in Phage Capsids. Proc. National Academy of Sciences USA 102, 9165–9169 (2005).
[EC] Earnshaw, W. C., Casjens, S. R.: DNA packaging by the double-stranded DNA bacteriophages. Cell 21, 319–331 (1980).
[RHA] Rishov, S., Holzenburg, A., Johansen, B.V., Lindqvist, B.H.: Bacteriophage P2 and P4 Morphogenesis: Structure and Function of the Connector. Virology 245, 11–17 (1998).
[STS] Smith, D.E., Tans, S.J., Smith, S.B., Grimes S., Anderson, D.L., Bustamante, C.: The bacteriophage ϕ29 portal motor can package DNA against a large internal force. Nature 413, 748–752 (2001).
[KCS] Kellenberger, E., Carlemalm, E., Sechaud, J., Ryter, A., Haller, G.: Considerations on the condensation and the degree of compactness in non-eukaryotic DNA: in Bacterial Chromatin, eds. Gualerzi, C. & Pon, C. L. (Springer, Berlin), p. 11 (1986).
[SB] San Martin, C., Burnett, R.: Structural studies on adenoviruses. Curr. Top. Microbiol. Immunol. 272, 57–94 (2003).
[SDD] Schmutz, M., Durand, D., Debin, A., Palvadeau, Y., Eitienne, E.R., Thierry, A. R.: DNA packing in stable lipid complexes designed for gene transfer imitates DNA compaction in bacteriophage. Proc. Natl. Acad. Sci. USA 96, 12293–12298 (1999).
[ACT] Aubrey, K., Casjens, S., Thomas, G.: Secondary structure and interactions of the packaged dsDNA genome of bacteriophage P22 investigated by Raman difference spectroscopy. Biochemistry 31, 11835–11842 (1992).
[EH] Earnshaw, W. C., Harrison, S.: DNA arrangement in isometric phage heads. Nature 268, 598–602 (1977).
[LDB] Lepault, J., Dubochet, J., Baschong, W., Kellenberger, E.: Organization of double-stranded DNA in bacteriophages: a study by cryo-electron microscopy of vitrified samples. EMBO J. 6, 1507–1512 (1987).
[HMC] Hass, R., Murphy, R.F., Cantor, C.R.: Testing models of the arrangement of DNA inside bacteriophage λ by crosslinking the packaged DNA. J. Mol. Biol. 159, 71–92 (1982).
[Ser] Serwer, P.: Arrangement of double-stranded DNA packaged in bacteriophage capsids : An alternative model. J. Mol. Biol. 190, 509–512 (1986).
[RWC] Richards, K., Williams, R., Calendar, R.: Mode of DNA packing within bacteriophage heads. J. Mol. Biol. 78, 255–259 (1973).
[CCR] Cerritelli, M., Cheng, N., Rosenberg, A., McPherson, C., Booy, F., Steven, A.. Encapsidated Conformation of Bacteriophage T7 DNA. Cell 91, 271–280 (1997).
[BNB] Black, L., Newcomb, W., Boring, J., Brown, J.: Ion Etching of Bacteriophage T4: Support for a Spiral-Fold Model of Packaged DNA. Proc. Natl. Acad. Sci. USA 82, 7960–7964 (1985).
[Hud] Hud, N.: Double-stranded DNA organization in bacteriophage heads: an alternative toroid-based model. Biophys. J. 69, 1355–1362 (1995).
[JCJ] Jiang, W., Chang, J., Jakana, J., Weigele, P., King, J., Chiu, W.: Structure of epsilon15 bacteriophage reveals genome organization and DNA packaging/injection apparatus. Nature 439, 612–616 (2006).
[WMC] Wang, J.C., Martin, K.V., Calendar, R.: Sequence similarity of the cohesive ends of coliphage P4, P2, and 186 deoxyribonucleic acid. Biochemistry 12, 2119–2123 (1973).
[LDC] Liu, L.F., Davis, J.L., Calendar, R.: Novel topologically knotted DNA from bacteriophage P4 capsids: studies with DNA topoisomerases. Nucleic Acids Res. 9, 3979–3989 (1981).
[WMH] Wolfson, J.S., McHugh, G.L., Hooper, D.C., Swartz, M.N.: Knotting of DNA molecules isolated from deletion mutants of intact bacteriophage P4. Nucleic Acids Res. 13, 6695–6702 (1985).
[IJC] Isaken, M., Julien, B., Calendar, R., Lindgvist, B.H.: Isolation of knotted DNA from coliphage P4: in DNA Topoisomerase Protocols, DNA Topology, and Enzymes, eds. Bjornsti, M. A. & Osheroff, N. (Humana, Totowa, NJ), Vol. 94, pp. 69–74 (1999).
[RDM] Raimondi, A. Donghi, R., Montaguti, A., Pessina, A., Deho, G.: Analysis of spontaneous deletion mutants of satellite bacteriophage P4. J. Virol. 54, 233–235 (1985).
[RUV] Rybenkov, V.V., Ullsperger, C., Vologodskii, A.V., Cozarelli, N.R.: Simplification of DNA Topology Below Equilibrium Values by Type II Topoisomerases. Science 277, 690–693 (1997).
[MRR] Metropolis, N., Rosenbluth, A.W., Rosenbluth, M.N., Teller, A.H., Teller, E.: Equation of State Calculations by Fast Computing Machines. J. Chem. Phys. 21, 1087–1092 (1953).
[Mil] Millet, K.: Knotting of Regular Polygons in 3-Space. In Series of Knots and Everything, eds. Sumners D.W. & Millet K.C. (World Scientific, Singapore), Vol. 7, pp. 31–46 (1994).
[MS] Madras, N., Slade, G.: The Self-Avoiding Walk, Birkhauser, Boston (1993).
[DT2] Deguchi, T., Tsurusaki, K.: A Statistical Study of Random Knotting Using the Vassiliev Invariants. J. Knot Theor. Ramifications 3, 321–353 (1994).
[SKB] Stasiak, A., Katrich, V., Bednar, J., Michoud, D., Dubochet, J.: Electrophoretic mobility of DNA knots. Nature 384, 122 (1996).
[VCL] Vologodskii, A.V., Crisona, N.J., Laurie, B., Pieranski, P., Katritch, V., Dubochet, J., Stasiak, A.: Sedimentation and electrophoretic migration of DNA knots and catenanes. J. Mol. Biol. 278, 1–3 (1998).
[KKS] Kanaar, R., Klippel, A., Shekhtman, E., Dungan, J., Kahmann, R., Cozzarelli, N.R.: Processive recombination by the phage Mu Gin system: Implications for the mechanisms of DNA strand exchange, DNA site alignment, and enhancer action. Cell 62, 353–366 (1990).
[WSR] Weber, C., Stasiak, A., De Los Rios, P., Dietler, G.: Numerical Simulation of Gel Electrophoresis of DNA Knots in Weak and Strong Electric Fields. Biophys. J. 90, 3100–3105 (2006).
[RSW] van Rensburg, J., Sumners, D.W., Whittington, S.G.: The Writhe of Knots and Links, In Ideal Knots, Series on Knots and Everything, eds. Stasiak, A., Katritch, V., Kauffman, L.H. (World Scientific, Singapore), Vol. 19, 70–87 (1999).
[MM] Marenduzzo, D., Micheletti, C.: Thermodynamics of DNA packaging inside a viral capsid: The role of DNA intrinsic thickness. J. Mol. Biol. 330, 485–492 (2003).
[MMT] Maritan, A., Micheletti, C., Trovato, A., Banavar, J.: Optimal shapes of compact strings. Nature 406, 287–289 (2000).
[TK] Tzil, S., Kindt, J.T., Gelbart, W., Ben-Shaul, A.: Nucleic acid packaging of DNA viruses. Biophys. J. 84, 1616–1627 (2003).
[LL] LaMarque, J.C., Le, T.L., Harvey, S.C.: Packaging double-helical DNA into viral capsids. Biopolymers 73, 3480–355 (2004).
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Sumners, D. (2009). Random Knotting: Theorems, Simulations and Applications. In: Ricca, R. (eds) Lectures on Topological Fluid Mechanics. Lecture Notes in Mathematics(), vol 1973. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-00837-5_7
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