-
2
-
-
0037117517
-
Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids
-
Arsuaga J, Vazquez M, Trigueros S, Sumners D W and Roca J 2002 Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids Proc. Natl Acad. Sci. USA 99 5373-7
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, Issue.8
, pp. 5373-5377
-
-
Arsuaga, J.1
Vazquez, M.2
Trigueros, S.3
Sumners, D.W.4
Roca, J.5
-
3
-
-
35748962418
-
The linking of uniform random polygons in confined spaces
-
Arsuaga J, Blackstone T, Diao Y, Karadayi E and Saito M 2007a The linking of uniform random polygons in confined spaces J. Phys. A: Math. Theor. 40 1925-36
-
(2007)
J. Phys. A: Math. Theor.
, vol.40
, Issue.9
, pp. 1925-1936
-
-
Arsuaga, J.1
Blackstone, T.2
Diao, Y.3
Karadayi, E.4
Saito, M.5
-
4
-
-
35748939381
-
Sampling large random knots in a confined space
-
Arsuaga J, Blackstone T, Diao Y, Hinson K, Karadayi E and Saito M 2007b Sampling large random knots in a confined space J. Phys. A: Math. Theor. 40 11697-711
-
(2007)
J. Phys. A: Math. Theor.
, vol.40
, Issue.39
, pp. 11697-11711
-
-
Arsuaga, J.1
Blackstone, T.2
Diao, Y.3
Hinson, K.4
Karadayi, E.5
Saito, M.6
-
5
-
-
75849161744
-
Mathematical methods in DNA topology: Applications to chromosome organization and site-specific recombination
-
Arsuaga J, Diao Y and Vazquez M 2009 Mathematical methods in DNA topology: applications to chromosome organization and site-specific recombination Mathematics of DNA Structure, Function and Interactions ed C J Benham, S Harvey, W K Olson, D W Sumners and D Swigon (New York: Springer Science + Business Media) pp 7-36
-
(2009)
Mathematics of DNA Structure, Function and Interactions
, vol.150
, pp. 7-36
-
-
Arsuaga, J.1
Diao, Y.2
Vazquez, M.3
-
6
-
-
72449153557
-
The growth of the mean average crossing number of equilateral polygons in confinement
-
Arsuaga J, Borgo B, Diao Y and Sharein R 2009 The growth of the mean average crossing number of equilateral polygons in confinement J. Phys. A: Math. Theor. 42 465202-11
-
(2009)
J. Phys. A: Math. Theor.
, vol.42
, Issue.46
, pp. 465202-465211
-
-
Arsuaga, J.1
Borgo, B.2
Diao, Y.3
Sharein, R.4
-
7
-
-
0005267391
-
Self-similarity in entanglement complexity along the backbones of compact proteins
-
Arteca G A 1997 Self-similarity in entanglement complexity along the backbones of compact proteins Phys Rev. E 56 4516-20
-
(1997)
Phys Rev.
, vol.56
, Issue.4
, pp. 4516-4520
-
-
Arteca, G.A.1
-
8
-
-
0034322247
-
Relative measure of geometrical entanglement to study folding-unfolding transitions
-
Arteca G and Tapia O 2000 Relative measure of geometrical entanglement to study folding-unfolding transitions Int. J. Quantum Chem. 80 848-55
-
(2000)
Int. J. Quantum Chem.
, vol.80
, Issue.4-5
, pp. 848-855
-
-
Arteca, G.1
Tapia, O.2
-
9
-
-
0001972054
-
Self linking numbers of space polygons
-
Banchoff T 1976 Self linking numbers of space polygons Indiana Univ. Math. J. 25 1171-88
-
(1976)
Indiana Univ. Math. J.
, vol.25
, Issue.12
, pp. 1171-1188
-
-
Banchoff, T.1
-
10
-
-
41349087453
-
How does the chromatin fiber deal with topological constraints
-
Barbi M, Mozziconacci J and Victor J 2005 How does the chromatin fiber deal with topological constraints Phys. Rev. E 71 031910
-
(2005)
Phys. Rev.
, vol.71
, Issue.3
, pp. 031910
-
-
Barbi, M.1
Mozziconacci, J.2
Victor, J.3
-
12
-
-
33745309555
-
The writhe of open and closed curves
-
Berger M A and Prior C 2006 The writhe of open and closed curves J. Phys. A: Math. Gen. 39 8321-48
-
(2006)
J. Phys. A: Math. Gen.
, vol.39
, Issue.26
, pp. 8321-8348
-
-
Berger, M.A.1
Prior, C.2
-
13
-
-
38649099051
-
Accessibility and occlusion of biopolymers, ray tracing of radiating tubes and the temperature of a tangle
-
Buck G, Scharein R G, Schnick J and Simon J 2008 Accessibility and occlusion of biopolymers, ray tracing of radiating tubes and the temperature of a tangle Phys. Rev. E 77 011803-6
-
(2008)
Phys. Rev.
, vol.77
, Issue.1
, pp. 011803-011806
-
-
Buck, G.1
Scharein, R.G.2
Schnick, J.3
Simon, J.4
-
14
-
-
0001443491
-
Sur les classes d'isotopie des noeuds tridimensionnels et leurs invariants
-
Calugreanu G 1961 Sur les classes d'isotopie des noeuds tridimensionnels et leurs invariants Czech. Math. J. 11 588-625
-
(1961)
Czech. Math. J.
, vol.11
, pp. 588-625
-
-
Calugreanu, G.1
-
16
-
-
3042564838
-
Linking numbers and nucleosomes
-
Crick F H 1976 Linking numbers and nucleosomes Proc. Natl Acad. Sci. USA 73 2639-43
-
(1976)
Proc. Natl Acad. Sci. USA
, vol.73
, Issue.8
, pp. 2639-2643
-
-
Crick, F.H.1
-
19
-
-
0344321734
-
The knotting of equilateral polygons in
-
Diao Y 1995 The knotting of equilateral polygons in J. Knot Theory Ramif. 4 189-96
-
(1995)
J. Knot Theory Ramif.
, vol.4
, Issue.2
, pp. 189-196
-
-
Diao, Y.1
-
20
-
-
0345356915
-
The average crossing number of equilateral random polygons
-
Diao Y, Dobay A, Kushner R B, Millett K and Stasiak A 2003 The average crossing number of equilateral random polygons J. Phys. A: Math. Gen. 36 11561-74
-
(2003)
J. Phys. A: Math. Gen.
, vol.36
, Issue.46
, pp. 11561-11574
-
-
Diao, Y.1
Dobay, A.2
Kushner, R.B.3
Millett, K.4
Stasiak, A.5
-
21
-
-
24144484773
-
The average inter-crossing number of equilateral random walks and polygons
-
Diao Y, Dobay A and Stasiak A 2005 The average inter-crossing number of equilateral random walks and polygons J. Phys. A: Math. Gen. 38 7601-16
-
(2005)
J. Phys. A: Math. Gen.
, vol.38
, Issue.35
, pp. 7601-7616
-
-
Diao, Y.1
Dobay, A.2
Stasiak, A.3
-
22
-
-
0038286173
-
Scaling behavior of random knots
-
Dobay A, Dubochet J, Millett K, Sottas P and Stasiak A 2003 Scaling behavior of random knots Proc. Natl Acad. Sci. USA 100 5611-15
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, Issue.10
, pp. 5611-5615
-
-
Dobay, A.1
Dubochet, J.2
Millett, K.3
Sottas, P.4
Stasiak, A.5
-
23
-
-
0033646965
-
Variations in molecular compactness and chain entanglement during the compression of grafted polymers
-
Edvinsson T, Elvingson C and Arteca G 2000 Variations in molecular compactness and chain entanglement during the compression of grafted polymers Macromol. Theory Simul. 9 398-406
-
(2000)
Macromol. Theory Simul.
, vol.9
, Issue.7
, pp. 398-406
-
-
Edvinsson, T.1
Elvingson, C.2
Arteca, G.3
-
24
-
-
2142699012
-
Statistical mechanics with topological constraints: I
-
Edwards F 1967 Statistical mechanics with topological constraints: I Proc. Phys. Soc. 91 513-9
-
(1967)
Proc. Phys. Soc.
, vol.91
, Issue.3
, pp. 513-519
-
-
Edwards, F.1
-
25
-
-
0000792391
-
Statistical mechanics with topological constraints: II
-
Edwards F 1968 Statistical mechanics with topological constraints: II J. Phys. A: Gen. Phys. 1 15-28
-
(1968)
J. Phys. A: Gen. Phys.
, vol.1
, Issue.1
, pp. 15-28
-
-
Edwards, F.1
-
28
-
-
84968473981
-
A new polynomial invariant for knots and links
-
Freyd P, Yetter D, Hoste J, Lickorish W, Millett K and Ocneanu A 1985 A new polynomial invariant for knots and links Bull. Am. Math. Soc. 12 239-46
-
(1985)
Bull. Am. Math. Soc.
, vol.12
, Issue.2
, pp. 239-246
-
-
Freyd, P.1
Yetter, D.2
Hoste, J.3
Lickorish, W.4
Millett, K.5
Ocneanu, A.6
-
29
-
-
0017886919
-
Decomposition of the linking number of a closed ribbon: A problem from Molecular biology
-
Fuller B 1978 Decomposition of the linking number of a closed ribbon: a problem from Molecular biology Proc. Natl Acad. Sci. USA 75 3557-61
-
(1978)
Proc. Natl Acad. Sci. USA
, vol.75
, Issue.8
, pp. 3557-3561
-
-
Fuller, B.1
-
31
-
-
0035976886
-
Opacity and entanglement of polymer chains
-
Grassberger P 2001 Opacity and entanglement of polymer chains J. Phys. A: Math. Gen. 34 99959-63
-
(2001)
J. Phys. A: Math. Gen.
, vol.34
, pp. 99959-99963
-
-
Grassberger, P.1
-
32
-
-
47249163351
-
Total curvature and total torsion of a freely jointed circular polymer with n ≫ 1 segments
-
Grosberg Y 2008 Total curvature and total torsion of a freely jointed circular polymer with n ≫ 1 segments Macromolecules 41 4524-7
-
(2008)
Macromolecules
, vol.41
, Issue.12
, pp. 4524-4527
-
-
Grosberg, Y.1
-
33
-
-
0032329340
-
Knots and Physics: Old wine in new bottles
-
Hirshfeld A C 1997 Knots and Physics: old wine in new bottles Am. J. Phys. 66 1060-6
-
(1997)
Am. J. Phys.
, vol.66
, Issue.12
, pp. 1060-1066
-
-
Hirshfeld, A.C.1
-
34
-
-
1642334642
-
Quantization of energy and writhe in self-repelling knots
-
Hoidn P, Kusner R B and Stasiak A 2002 Quantization of energy and writhe in self-repelling knots New J. Phys. 4 20.1-11
-
(2002)
New J. Phys.
, vol.4
, pp. 201-11
-
-
Hoidn, P.1
Kusner, R.B.2
Stasiak, A.3
-
35
-
-
0034652329
-
Closing the ring: Links between SMC proteins and chromosome partitioning, condensation and supercoiling
-
Holmes V and Cozzarelli N R 2000 Closing the ring: links between SMC proteins and chromosome partitioning, condensation and supercoiling Proc. Natl Acad. Sci. USA 97 1322-4
-
(2000)
Proc. Natl Acad. Sci. USA
, vol.97
, Issue.4
, pp. 1322-1324
-
-
Holmes, V.1
Cozzarelli, N.R.2
-
36
-
-
36549101558
-
New model of polymer entanglement: Localized Gauss integral model
-
Iwata K and Edwards S F 1989 New model of polymer entanglement: localized Gauss integral model J. Chem. Phys. 90 084567-15
-
(1989)
J. Chem. Phys.
, vol.90
, pp. 084567-084515
-
-
Iwata, K.1
Edwards, S.F.2
-
37
-
-
21144473069
-
The writhe of a self-avoiding polygon
-
Janse van Rensburg E J, Orlandini E, Sumners D W, Tesi M C and Whittington S G 1993 The writhe of a self-avoiding polygon J. Phys. A: Math. Gen. 26 L981-6
-
(1993)
J. Phys. A: Math. Gen.
, vol.26
, Issue.19
-
-
Janse Van Rensburg, E.J.1
Orlandini, E.2
Sumners, D.W.3
Tesi, M.C.4
Whittington, S.G.5
-
38
-
-
84968518084
-
A polynomial invariant of knots via von Neumann algebras
-
Jones V F R 1985 A polynomial invariant of knots via von Neumann algebras Bull. Am. Math. Soc. 12 103-12
-
(1985)
Bull. Am. Math. Soc.
, vol.12
, Issue.1
, pp. 103-112
-
-
Jones, V.F.R.1
-
39
-
-
0029906723
-
Geometry and Physics of knots
-
Katritch V, Bednar J, Michoud D, Scharein R G, Dubochet J and Stasiak A 1996 Geometry and Physics of knots Nature 384 142-5
-
(1996)
Nature
, vol.384
, Issue.6605
, pp. 142-145
-
-
Katritch, V.1
Bednar, J.2
Michoud, D.3
Scharein, R.G.4
Dubochet, J.5
Stasiak, A.6
-
41
-
-
0034668195
-
Computation of writhe in modelling of supercoiled DNA
-
Klenin K and Langowski J 2000 Computation of writhe in modelling of supercoiled DNA Biopolymers 54 307-17
-
(2000)
Biopolymers
, vol.54
, Issue.5
, pp. 307-317
-
-
Klenin, K.1
Langowski, J.2
-
42
-
-
0242350926
-
Topological constraints at the Theta-point: Closed loops at two loops
-
Kung W and Kamien R D 2003 Topological constraints at the Theta-point: closed loops at two loops Europhys. Lett. 64 323-9
-
(2003)
Europhys. Lett.
, vol.64
, Issue.3
, pp. 323-329
-
-
Kung, W.1
Kamien, R.D.2
-
44
-
-
33645155026
-
Computing the writhe on lattices
-
Laing C and Sumners D W 2006 Computing the writhe on lattices J. Phys. A: Math. Gen. 39 3535-43
-
(2006)
J. Phys. A: Math. Gen.
, vol.39
, Issue.14
, pp. 3535-3543
-
-
Laing, C.1
Sumners, D.W.2
-
46
-
-
42349088217
-
Efficient chain moves for Monte Carlo simulations of a wormlike DNA model
-
Liu Z and Chan H S 2008 Efficient chain moves for Monte Carlo simulations of a wormlike DNA model J. Chem. Phys. 128 145104-31
-
(2008)
J. Chem. Phys.
, vol.128
, Issue.14
, pp. 145104-145131
-
-
Liu, Z.1
Chan, H.S.2
-
47
-
-
0028494840
-
Knots in Hamilton cycles
-
Mansfield M L 1994 Knots in Hamilton cycles Macromolecules 27 5924-6
-
(1994)
Macromolecules
, vol.27
, Issue.20
, pp. 5924-5926
-
-
Mansfield, M.L.1
-
48
-
-
69849112239
-
Interplay of DNA supercoiling and catenation during the segregation of sister duplexes
-
Martinez-Robles M L, Witz G, Hernandez P, Schvartzman J B, Stasiak A and Krimer D B 2009 Interplay of DNA supercoiling and catenation during the segregation of sister duplexes Nucl. Acids Res. 37 5126-37
-
(2009)
Nucl. Acids Res.
, vol.37
, Issue.15
, pp. 5126-5137
-
-
Martinez-Robles, M.L.1
Witz, G.2
Hernandez, P.3
Schvartzman, J.B.4
Stasiak, A.5
Krimer, D.B.6
-
49
-
-
0038441296
-
Tendril perversion in intrinsically curved rods
-
McMillen T and Goriely A 2002 Tendril perversion in intrinsically curved rods J. Nonlinear Sci. 12 241-81
-
(2002)
J. Nonlinear Sci.
, vol.12
, Issue.3
, pp. 241-281
-
-
McMillen, T.1
Goriely, A.2
-
52
-
-
13244258252
-
Linear random knots and their scaling behavior
-
Millett K, Dobay A and Stasiak A 2004 Linear random knots and their scaling behavior Macromolecules 38 601-6
-
(2004)
Macromolecules
, vol.38
, Issue.2
, pp. 601-606
-
-
Millett, K.1
Dobay, A.2
Stasiak, A.3
-
54
-
-
34247342665
-
Statistical topology of closed curves: Some applications in polymer physics
-
Orlandini E and Whittington S G 2007 Statistical topology of closed curves: some applications in polymer physics Rev. Mod. Phys. 79 611-42
-
(2007)
Rev. Mod. Phys.
, vol.79
, Issue.2
, pp. 611-642
-
-
Orlandini, E.1
Whittington, S.G.2
-
55
-
-
21344497453
-
The writhe of a self-avoiding walk
-
Orlandini E, Tesi M C, Whittington S G, Sumners D W and Janse van Resburg E J 1994 The writhe of a self-avoiding walk J. Phys. A: Math. Gen. 27 L333-8
-
(1994)
J. Phys. A: Math. Gen.
, vol.27
, Issue.10
-
-
Orlandini, E.1
Tesi, M.C.2
Whittington, S.G.3
Sumners, D.W.4
Janse Van Resburg, E.J.5
-
57
-
-
11044224120
-
Entangled polymers in condensed phases
-
Orlandini E and Whittington S G 2004 Entangled polymers in condensed phases J. Chem. Phys. 121 12094-99
-
(2004)
J. Chem. Phys.
, vol.121
, Issue.23
, pp. 12094-12099
-
-
Orlandini, E.1
Whittington, S.G.2
-
58
-
-
0039023668
-
Knots in random walks
-
Pippenger N 1989 Knots in random walks Discrete Appl. Math. 25 273-8
-
(1989)
Discrete Appl. Math.
, vol.25
, Issue.3
, pp. 273-278
-
-
Pippenger, N.1
-
59
-
-
34249734712
-
Total curvature and total torsion of knotted polymers
-
Plunkett P, Piatek M, Dobay A, Kern J, Millett K, Stasiak A and Rawdon E 2007 Total curvature and total torsion of knotted polymers Macromolecules 40 3860-67
-
(2007)
Macromolecules
, vol.40
, Issue.10
, pp. 3860-3867
-
-
Plunkett, P.1
Piatek, M.2
Dobay, A.3
Kern, J.4
Millett, K.5
Stasiak, A.6
Rawdon, E.7
-
60
-
-
84968468326
-
Conway algebras and skein equivalence of links
-
Przytycki J and Traczyk P 1987 Conway algebras and skein equivalence of links Proc. Am. Math. Soc. 100 744-48
-
(1987)
Proc. Am. Math. Soc.
, vol.100
, Issue.4
, pp. 744-748
-
-
Przytycki, J.1
Traczyk, P.2
-
62
-
-
0000019149
-
Conformation spaces of molecular rings
-
Randell R 1988b Conformation spaces of molecular rings Studies in Physical and Theoretical Chemistry vol 54 ed R C Lacher (Amsterdam: Elsevier) pp 141-56
-
(1988)
Studies in Physical and Theoretical Chemistry
, vol.54
, pp. 141-156
-
-
Randell, R.1
-
64
-
-
0036037457
-
Proteins in vacuo: A connection between mean overcrossing number and orientationally averaged collision cross section
-
Reimann G T, Arteca G and Tapia O 2002 Proteins in vacuo: a connection between mean overcrossing number and orientationally averaged collision cross section J. Chem. Phys. 4 4058-64
-
(2002)
J. Chem. Phys.
, vol.4
, Issue.16
, pp. 4058-4064
-
-
Reimann, G.T.1
Arteca, G.2
Tapia, O.3
-
65
-
-
0037422619
-
Automatic classification of protein structure by using Gauss integrals
-
Rogen P and Fain B 2003 Automatic classification of protein structure by using Gauss integrals Proc. Natl Acad. Sci. 100 119-24
-
(2003)
Proc. Natl Acad. Sci.
, vol.100
, Issue.1
, pp. 119-124
-
-
Rogen, P.1
Fain, B.2
-
67
-
-
0037162233
-
The mobility and diffusivity of a knotted polymer: Topological deformation effect
-
Sheng Y-J and Tsao H-K 2002 The mobility and diffusivity of a knotted polymer: topological deformation effect J. Chem. Phys. 116 10523-8
-
(2002)
J. Chem. Phys.
, vol.116
, Issue.23
, pp. 10523-10528
-
-
Sheng, Y.-J.1
Tsao, H.-K.2
-
71
-
-
33746760081
-
The writhing of circular cross-section rods: Undersea cables to DNA supercoils
-
Stump D, Fraser W and Gates K 1998 The writhing of circular cross-section rods: undersea cables to DNA supercoils Proc. R. Soc. Lond. A 454 2123-56
-
(1998)
Proc. R. Soc. Lond.
, vol.454
, Issue.1976
, pp. 2123-2156
-
-
Stump, D.1
Fraser, W.2
Gates, K.3
-
74
-
-
33746366787
-
Topological analysis of linear polymer melts: A statistical approach
-
Tzoumanekas C and Theodorou D 2006 Topological analysis of linear polymer melts: a statistical approach Macromolecules 39 4592-604
-
(2006)
Macromolecules
, vol.39
, Issue.13
, pp. 4592-4604
-
-
Tzoumanekas, C.1
Theodorou, D.2
-
75
-
-
0027171352
-
Monte Carlo analysis of the conformation of DNA catenanes
-
Vologodskii A V and Cozzarelli N R 1993 Monte Carlo analysis of the conformation of DNA catenanes J. Mol. Biol. 232 1130-40
-
(1993)
J. Mol. Biol.
, vol.232
, Issue.4
, pp. 1130-1140
-
-
Vologodskii, A.V.1
Cozzarelli, N.R.2
-
77
-
-
33646124238
-
Gel electrophoresis of DNA knots in weak and strong electric fields
-
Weber C, Stasiak A, Fleurant M, De Los Rios P and Dietler G 2006 Gel electrophoresis of DNA knots in weak and strong electric fields Biophys. J. 90 3100-5
-
(2006)
Biophys. J.
, vol.90
, Issue.9
, pp. 3100-3105
-
-
Weber, C.1
Stasiak, A.2
Fleurant, M.3
De Los Rios, P.4
Dietler, G.5
-
78
-
-
0000751914
-
Self-linking and the Gauss integral in higher dimensions
-
White J H and Bauer W R 1969 Self-linking and the Gauss integral in higher dimensions Am. J. Math. 91 693-728
-
(1969)
Am. J. Math.
, vol.91
, Issue.3
, pp. 693-728
-
-
White, J.H.1
Bauer, W.R.2
|