-
1
-
-
0020719315
-
A new Monte Carlo approach to the critical properties of self-avoiding random walks
-
Arãgao de Carvalho C., and Caracciolo S. A new Monte Carlo approach to the critical properties of self-avoiding random walks. J. Phys. (Paris) 44 (1983) 323-331
-
(1983)
J. Phys. (Paris)
, vol.44
, pp. 323-331
-
-
Arãgao de Carvalho, C.1
Caracciolo, S.2
-
3
-
-
0037117517
-
Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids
-
Arsuaga J., Vazquez M., Trigueros S., de Sumners W., and Roca J. Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids. Proc. Natl. Acad. Sci. USA 99 (2002) 5373-5377
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 5373-5377
-
-
Arsuaga, J.1
Vazquez, M.2
Trigueros, S.3
de Sumners, W.4
Roca, J.5
-
4
-
-
0000935544
-
Random paths and random surfaces on a digital computer
-
Berg B., and Foerster D. Random paths and random surfaces on a digital computer. Phys. Lett. B 106 4 (1981) 323-326
-
(1981)
Phys. Lett. B
, vol.106
, Issue.4
, pp. 323-326
-
-
Berg, B.1
Foerster, D.2
-
6
-
-
0029911698
-
Recent developments in DNA topoisomerase II structure and mechanism
-
Berger J.M., and Wang J.C. Recent developments in DNA topoisomerase II structure and mechanism. Curr. Opin. Struct. Biol. 6 (1996) 84-90
-
(1996)
Curr. Opin. Struct. Biol.
, vol.6
, pp. 84-90
-
-
Berger, J.M.1
Wang, J.C.2
-
7
-
-
3242754359
-
DNA disentangling by type-2 topoisomerases
-
Buck G.R., and Zechiedrich E.L. DNA disentangling by type-2 topoisomerases. J. Mol. Biol. 340 (2004) 933-939
-
(2004)
J. Mol. Biol.
, vol.340
, pp. 933-939
-
-
Buck, G.R.1
Zechiedrich, E.L.2
-
9
-
-
4243636725
-
A general limitation on Monte Carlo algorithms of Metropolis type
-
Caracciolo S., Pelissetto A., and Sokal A.D. A general limitation on Monte Carlo algorithms of Metropolis type. Phys. Rev. Lett. 72 2 (1994) 179-182
-
(1994)
Phys. Rev. Lett.
, vol.72
, Issue.2
, pp. 179-182
-
-
Caracciolo, S.1
Pelissetto, A.2
Sokal, A.D.3
-
10
-
-
0034923502
-
DNA topoisomerases: structures, function, and mechanism
-
Champloux J.J. DNA topoisomerases: structures, function, and mechanism. Annu. Rev. Biochem. 70 (2001) 369-413
-
(2001)
Annu. Rev. Biochem.
, vol.70
, pp. 369-413
-
-
Champloux, J.J.1
-
11
-
-
23044520009
-
Rational tangle distances on knots and links
-
Darcy I. Rational tangle distances on knots and links. Math. Proc. Cambridge Philos. Soc. 128 (2000) 497-510
-
(2000)
Math. Proc. Cambridge Philos. Soc.
, vol.128
, pp. 497-510
-
-
Darcy, I.1
-
12
-
-
0035627462
-
Biological distances on DNA knots and links: applications to XER recombination
-
Knots in Hellas 2, 1998, Delphi
-
Darcy I. Biological distances on DNA knots and links: applications to XER recombination. Knots in Hellas 2, 1998, Delphi. J. Knot Theory Ramifications 10 2 (2001) 269-294
-
(2001)
J. Knot Theory Ramifications
, vol.10
, Issue.2
, pp. 269-294
-
-
Darcy, I.1
-
13
-
-
0001321818
-
A statistical study of random knotting using the Vassiliev invariants, random knotting and linking
-
Deguchi T., and Tsurasaki K. A statistical study of random knotting using the Vassiliev invariants, random knotting and linking. J. Knot Theory Ramifications 3 (1994) 321-353
-
(1994)
J. Knot Theory Ramifications
, vol.3
, pp. 321-353
-
-
Deguchi, T.1
Tsurasaki, K.2
-
14
-
-
0035868644
-
Topoisomerase IV, alone, unknots DNA in E. Coli
-
Deibler R.W., Rahmati S., and Zechiedrich E.L. Topoisomerase IV, alone, unknots DNA in E. Coli. Genes Dev. 15 (2001) 748-761
-
(2001)
Genes Dev.
, vol.15
, pp. 748-761
-
-
Deibler, R.W.1
Rahmati, S.2
Zechiedrich, E.L.3
-
16
-
-
84972274704
-
A calculus for rational tangles: applications to DNA recombination
-
Ernst C., and Sumners D.W. A calculus for rational tangles: applications to DNA recombination. Math. Proc. Cambridge Philos. Soc. 108 3 (1990) 489-515
-
(1990)
Math. Proc. Cambridge Philos. Soc.
, vol.108
, Issue.3
, pp. 489-515
-
-
Ernst, C.1
Sumners, D.W.2
-
17
-
-
0042682250
-
-
Ewing B., and Millett K.C. (Eds), Hermann, Paris
-
In: Ewing B., and Millett K.C. (Eds). Computational Algorithms and the Complexity of Link Polynomials. Progress in Knot Theory and Related Topics. Travaux en Cours vol. 56 (1997), Hermann, Paris
-
(1997)
Progress in Knot Theory and Related Topics. Travaux en Cours
, vol.56
-
-
-
18
-
-
13244285443
-
Simulations of action of DNA topoisomerases to investigate boundaries and shapes of spaces of knots
-
Flammini A., Maritan A., and Stasiak A. Simulations of action of DNA topoisomerases to investigate boundaries and shapes of spaces of knots. Biophys. J. 87 (2004) 2968-2975
-
(2004)
Biophys. J.
, vol.87
, pp. 2968-2975
-
-
Flammini, A.1
Maritan, A.2
Stasiak, A.3
-
20
-
-
84968473981
-
A new polynomial invariant of knots and links
-
Freyd P., Yetter D., Hoste J., Lickorish W.B.R., Millett K., and Oceanu A. A new polynomial invariant of knots and links. Bull. Amer. Math. Soc. 12 (1985) 239-246
-
(1985)
Bull. Amer. Math. Soc.
, vol.12
, pp. 239-246
-
-
Freyd, P.1
Yetter, D.2
Hoste, J.3
Lickorish, W.B.R.4
Millett, K.5
Oceanu, A.6
-
21
-
-
0346906092
-
Computer evaluation of Homfly polynomials by using Gauss codes, with a skein-template algorithm
-
Gouesbet G., Meunier-Guttin-Cluzel S., and Letellier C. Computer evaluation of Homfly polynomials by using Gauss codes, with a skein-template algorithm. Appl. Math. Comput. 105 2-3 (1999) 271-289
-
(1999)
Appl. Math. Comput.
, vol.105
, Issue.2-3
, pp. 271-289
-
-
Gouesbet, G.1
Meunier-Guttin-Cluzel, S.2
Letellier, C.3
-
24
-
-
0021099687
-
Knotting of the circular duplex DNA by type II DNA topoisomerase from Drosophilla melanogaster
-
Hsieh T. Knotting of the circular duplex DNA by type II DNA topoisomerase from Drosophilla melanogaster. J. Biol. Chem. 258 (1983) 8413-8420
-
(1983)
J. Biol. Chem.
, vol.258
, pp. 8413-8420
-
-
Hsieh, T.1
-
25
-
-
0024021097
-
Effect of excluded volume on topological properties of circular DNA
-
Klenin K.V., Vologodskii A.V., Anshelevich V.V., Dykhne A.M., and Frank-Kamenetskii M.D. Effect of excluded volume on topological properties of circular DNA. J. Biomol. Struct. Dyn. (5) 5 (1988) 1173-1185
-
(1988)
J. Biomol. Struct. Dyn. (5)
, vol.5
, pp. 1173-1185
-
-
Klenin, K.V.1
Vologodskii, A.V.2
Anshelevich, V.V.3
Dykhne, A.M.4
Frank-Kamenetskii, M.D.5
-
26
-
-
0019517763
-
Novel topologically knotted DNA from bacteriophage P4 capsids: studies with DNA topoisomerases
-
Liu L.F., Davis J.L., and Calendar R. Novel topologically knotted DNA from bacteriophage P4 capsids: studies with DNA topoisomerases. Nucleic Acids Res. 9 (1981) 3979-3989
-
(1981)
Nucleic Acids Res.
, vol.9
, pp. 3979-3989
-
-
Liu, L.F.1
Davis, J.L.2
Calendar, R.3
-
28
-
-
0030458354
-
T7 RNA polymerase cannot transcribe through a highly knotted DNA template
-
Portugal J., and Rodriguez-Campos A. T7 RNA polymerase cannot transcribe through a highly knotted DNA template. Nucleic Acids Res. 24 (1996) 4890-4894
-
(1996)
Nucleic Acids Res.
, vol.24
, pp. 4890-4894
-
-
Portugal, J.1
Rodriguez-Campos, A.2
-
29
-
-
0039793489
-
The writhe of knots in the cubic lattice
-
van Rensburg E.J., Orlandini E., Sumners D.W., Tesi M.C., and Whittington S.G. The writhe of knots in the cubic lattice. J. Knot Theory Ramifications 6 (1997) 31-44
-
(1997)
J. Knot Theory Ramifications
, vol.6
, pp. 31-44
-
-
van Rensburg, E.J.1
Orlandini, E.2
Sumners, D.W.3
Tesi, M.C.4
Whittington, S.G.5
-
31
-
-
27844543323
-
Minimal Lattice Knots
-
World Scientific, Singapore
-
van Rensburg E.J. Minimal Lattice Knots. Ideal Knots vol. 19 (1998), World Scientific, Singapore
-
(1998)
Ideal Knots
, vol.19
-
-
van Rensburg, E.J.1
-
33
-
-
0028949206
-
The mechanisms of DNA topoisomerases
-
Roca J. The mechanisms of DNA topoisomerases. Trends Biochem. Sci. 20 (1995) 156-160
-
(1995)
Trends Biochem. Sci.
, vol.20
, pp. 156-160
-
-
Roca, J.1
-
34
-
-
0035910283
-
Varying levels of positive and negative supercoiling differently affect the efficiency with which topoisomerase II catenates and decatenates DNA
-
Roca J. Varying levels of positive and negative supercoiling differently affect the efficiency with which topoisomerase II catenates and decatenates DNA. J. Mol. Biol. 305 (2001) 441-450
-
(2001)
J. Mol. Biol.
, vol.305
, pp. 441-450
-
-
Roca, J.1
-
35
-
-
0029961651
-
DNA transport by a type II topoisomerase: direct evidence for a two-gate mechanism
-
Roca J., Berger J.M., Harrison S.C., and Wang J.C. DNA transport by a type II topoisomerase: direct evidence for a two-gate mechanism. Proc. Natl. Acad. Sci. USA 93 (1996) 4057-4062
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
, pp. 4057-4062
-
-
Roca, J.1
Berger, J.M.2
Harrison, S.C.3
Wang, J.C.4
-
36
-
-
17544380168
-
DNA knotting abolishes in vitro chromatin assembly
-
Rodriguez-Campos A. DNA knotting abolishes in vitro chromatin assembly. J. Biol. Chem. 271 (1996) 14150-14155
-
(1996)
J. Biol. Chem.
, vol.271
, pp. 14150-14155
-
-
Rodriguez-Campos, A.1
-
38
-
-
0027279063
-
Probability of DNA knotting and the effective diameter of the DNA double helix
-
Rybenkov V.V., Cozzarelli N.R., and Vologodskii A.V. Probability of DNA knotting and the effective diameter of the DNA double helix. Proc. Natl. Acad. Sci. USA 90 (1993) 5307-5311
-
(1993)
Proc. Natl. Acad. Sci. USA
, vol.90
, pp. 5307-5311
-
-
Rybenkov, V.V.1
Cozzarelli, N.R.2
Vologodskii, A.V.3
-
39
-
-
0030758268
-
Simplification of DNA topology below equilibrium values by type II topoisomerases
-
Rybenkov V.V., Ullsperger C., Vologodskii A.V., and Cozzarelli N.R. Simplification of DNA topology below equilibrium values by type II topoisomerases. Science 277 (1997) 690-693
-
(1997)
Science
, vol.277
, pp. 690-693
-
-
Rybenkov, V.V.1
Ullsperger, C.2
Vologodskii, A.V.3
Cozzarelli, N.R.4
-
41
-
-
0027200062
-
Knotting of a DNA chain during ring closure
-
Shaw S.Y., and Wang J.C. Knotting of a DNA chain during ring closure. Science 260 (1993) 533-536
-
(1993)
Science
, vol.260
, pp. 533-536
-
-
Shaw, S.Y.1
Wang, J.C.2
-
42
-
-
0024791187
-
The presence of the region on pBR322 that encodes resistance to tetracycline is responsible for high levels of plasmid DNA knotting in Escherichia coli DNA topoisomerase I deletion mutant
-
Shishido K., Ishii S., and Komiyama N. The presence of the region on pBR322 that encodes resistance to tetracycline is responsible for high levels of plasmid DNA knotting in Escherichia coli DNA topoisomerase I deletion mutant. Nucleic Acids Res. 17 (1989) 9749-9759
-
(1989)
Nucleic Acids Res.
, vol.17
, pp. 9749-9759
-
-
Shishido, K.1
Ishii, S.2
Komiyama, N.3
-
44
-
-
0024364817
-
Site-specific recombination by Tn3 resolvase: topological changes in the forward and reverse reactions
-
Stark W.M., Sherratt D.J., and Boocock M.R. Site-specific recombination by Tn3 resolvase: topological changes in the forward and reverse reactions. Cell 58 (1989) 779-790
-
(1989)
Cell
, vol.58
, pp. 779-790
-
-
Stark, W.M.1
Sherratt, D.J.2
Boocock, M.R.3
-
45
-
-
0034644125
-
DNA topology: feeling the pulse of a topoisomerase
-
Stasiak A. DNA topology: feeling the pulse of a topoisomerase. Curr. Biol. 10 (2000) 526-528
-
(2000)
Curr. Biol.
, vol.10
, pp. 526-528
-
-
Stasiak, A.1
-
46
-
-
0041306000
-
Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases
-
Stone M.D., Bryant Z., Crisona N.J., Smith S.B., Vologodskii A., Bustamante C., and Cozzarelli N.R. Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases. Proc. Natl. Acad. Sci. USA 100 15 (2003) 8654-8659
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, Issue.15
, pp. 8654-8659
-
-
Stone, M.D.1
Bryant, Z.2
Crisona, N.J.3
Smith, S.B.4
Vologodskii, A.5
Bustamante, C.6
Cozzarelli, N.R.7
-
48
-
-
33847757436
-
-
M. Szafron, Monte Carlo simulations of strand-passage in unknotted self-avoiding polygons, Masters thesis, University of Saskatoon, 2000
-
-
-
-
49
-
-
1542501878
-
Asymmetric removal of supercoils suggests how topoisomerase II simplifies DNA topology
-
Trigueros S., Salceda J., Bermudez I., Fernandez X., and Roca J. Asymmetric removal of supercoils suggests how topoisomerase II simplifies DNA topology. J. Mol. Biol. 335 (2004) 723-731
-
(2004)
J. Mol. Biol.
, vol.335
, pp. 723-731
-
-
Trigueros, S.1
Salceda, J.2
Bermudez, I.3
Fernandez, X.4
Roca, J.5
-
51
-
-
2542521543
-
Tangle analysis of Gin site-specific recombination
-
Vazquez M., and Sumners D.W. Tangle analysis of Gin site-specific recombination. Math. Proc. Cambridge Philos. Soc. 136 3 (2004) 565-582
-
(2004)
Math. Proc. Cambridge Philos. Soc.
, vol.136
, Issue.3
, pp. 565-582
-
-
Vazquez, M.1
Sumners, D.W.2
-
52
-
-
0018579392
-
Statistical mechanics of supercoils and the torsional stiffness of the DNA double helix
-
Vologodskii A.V., Anshelevich V.V., Lukashin A.V., and Frank-Kamenetskii M.D. Statistical mechanics of supercoils and the torsional stiffness of the DNA double helix. Nature 280 (1979) 294-298
-
(1979)
Nature
, vol.280
, pp. 294-298
-
-
Vologodskii, A.V.1
Anshelevich, V.V.2
Lukashin, A.V.3
Frank-Kamenetskii, M.D.4
-
53
-
-
0027171352
-
Monte Carlo analysis of the conformation of DNA catenates
-
Vologodskii A.V., and Cozzarelli N.R. Monte Carlo analysis of the conformation of DNA catenates. J. Mol. Biol. 232 (1993) 1130-1140
-
(1993)
J. Mol. Biol.
, vol.232
, pp. 1130-1140
-
-
Vologodskii, A.V.1
Cozzarelli, N.R.2
-
55
-
-
0026489194
-
Conformational and thermodynamic properties of supercoiled DNA
-
Vologodskii A.V., Levene S.D., Klenin K., Frank-Kamenetskii M.D., and Cozzarelli N.R. Conformational and thermodynamic properties of supercoiled DNA. J. Mol. Biol. 227 (1992) 1224-1243
-
(1992)
J. Mol. Biol.
, vol.227
, pp. 1224-1243
-
-
Vologodskii, A.V.1
Levene, S.D.2
Klenin, K.3
Frank-Kamenetskii, M.D.4
Cozzarelli, N.R.5
-
56
-
-
0035853134
-
Mechanism of topology simplification by type II DNA topoisomerases
-
Vologodskii A.V., Zhang W., Rybenkov V.V., Podtelezhnikov A.A., Subramanian D., Griffith J.D., and Cozzarelli N.R. Mechanism of topology simplification by type II DNA topoisomerases. Proc. Natl. Acad. Sci. USA 98 (2001) 3045-3049
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 3045-3049
-
-
Vologodskii, A.V.1
Zhang, W.2
Rybenkov, V.V.3
Podtelezhnikov, A.A.4
Subramanian, D.5
Griffith, J.D.6
Cozzarelli, N.R.7
-
57
-
-
0022518195
-
Biochemical topology: applications to DNA recombination and replication
-
Wasserman S.R., and Cozzarelli N.R. Biochemical topology: applications to DNA recombination and replication. Science 232 (1986) 951-960
-
(1986)
Science
, vol.232
, pp. 951-960
-
-
Wasserman, S.R.1
Cozzarelli, N.R.2
-
58
-
-
0033613387
-
A kinetic proofreading mechanism for disentanglement of DNA by topoisomerases
-
Yan J., Magnasco M.O., and Marko J.F. A kinetic proofreading mechanism for disentanglement of DNA by topoisomerases. Nature 401 (1999) 932-935
-
(1999)
Nature
, vol.401
, pp. 932-935
-
-
Yan, J.1
Magnasco, M.O.2
Marko, J.F.3
-
59
-
-
0030771373
-
Topoisomerase IV, not gyrase, decatenates products of site-specific recombination in Escherichia coli
-
Zechiedrich E.L., Khodursky A.B., and Cozzarelli N.R. Topoisomerase IV, not gyrase, decatenates products of site-specific recombination in Escherichia coli. Genes Dev. 11 (1997) 2580-2592
-
(1997)
Genes Dev.
, vol.11
, pp. 2580-2592
-
-
Zechiedrich, E.L.1
Khodursky, A.B.2
Cozzarelli, N.R.3
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