-
1
-
-
0035923664
-
DNA packaging and ejection forces in bacteriophage
-
Kindt, J., S. Tzlil, A. Ben-Shaul, and W. M. Gelbart. 2001. DNA packaging and ejection forces in bacteriophage. Proc. Natl. Acad. Sci. USA. 98:13671-13674.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 13671-13674
-
-
Kindt, J.1
Tzlil, S.2
Ben-Shaul, A.3
Gelbart, W.M.4
-
2
-
-
33646920317
-
Polymer packaging and ejection in viral capsids: Shape matters
-
Ali, I., D. Marenduzzo, and J. M. Yeomans. 2006. Polymer packaging and ejection in viral capsids: shape matters. Phys. Rev. Lett. 96:208102.
-
(2006)
Phys. Rev. Lett
, vol.96
, pp. 208102
-
-
Ali, I.1
Marenduzzo, D.2
Yeomans, J.M.3
-
3
-
-
33947325925
-
Forces controlling the rate of DNA ejection from phage lambda
-
Lof, D., K. Schillen, B. Jonsson, and A. Evilevitch. 2007. Forces controlling the rate of DNA ejection from phage lambda. J. Mol. Biol. 368:55-65.
-
(2007)
J. Mol. Biol
, vol.368
, pp. 55-65
-
-
Lof, D.1
Schillen, K.2
Jonsson, B.3
Evilevitch, A.4
-
4
-
-
44849102419
-
Ejection dynamics of polymeric chains from viral capsids: Effect of solvent quality
-
Ali, I., D. Marenduzzo, and J. M. Yeomans. 2008. Ejection dynamics of polymeric chains from viral capsids: effect of solvent quality. Biophys. J. 94:4159-4164.
-
(2008)
Biophys. J
, vol.94
, pp. 4159-4164
-
-
Ali, I.1
Marenduzzo, D.2
Yeomans, J.M.3
-
5
-
-
0037058959
-
Investigation of viral DNA packaging using molecular mechanics models
-
Arsuaga, J., R. K. Z. Tan, M. Vazquez, D. W. Sumners, and S. C. Harvey. 2002. Investigation of viral DNA packaging using molecular mechanics models. Biophys. Chem. 101:475-484.
-
(2002)
Biophys. Chem
, vol.101
, pp. 475-484
-
-
Arsuaga, J.1
Tan, R.K.Z.2
Vazquez, M.3
Sumners, D.W.4
Harvey, S.C.5
-
6
-
-
35148817067
-
The conformation of double-stranded DNA inside bacteriophages depends on capsid size and shape
-
Petrov, A. S., M. B. Doz, and S. C. Harvey. 2007. The conformation of double-stranded DNA inside bacteriophages depends on capsid size and shape. J. Struct. Biol. 160:241-248.
-
(2007)
J. Struct. Biol
, vol.160
, pp. 241-248
-
-
Petrov, A.S.1
Doz, M.B.2
Harvey, S.C.3
-
7
-
-
47749092360
-
Packaging double-helical DNA into viral capsids: Structures, forces and energetics
-
In press
-
Petrov, A. S., and S. C. Harvey. 2008. Packaging double-helical DNA into viral capsids: structures, forces and energetics. Biophys. J. In press.
-
(2008)
Biophys. J
-
-
Petrov, A.S.1
Harvey, S.C.2
-
9
-
-
0038385492
-
Thermodynamics of DNA packaging inside a viral capsid: The role of DNA intrinsic thickness
-
Marenduzzo, D., and C. Micheletti. 2003. Thermodynamics of DNA packaging inside a viral capsid: the role of DNA intrinsic thickness. J. Mol. Biol. 330:485-492.
-
(2003)
J. Mol. Biol
, vol.330
, pp. 485-492
-
-
Marenduzzo, D.1
Micheletti, C.2
-
11
-
-
0037117517
-
Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids
-
Arsuaga, J., M. Vazquez, S. Trigueros, D. W. Sumners, and J. Roca. 2002. Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids. Proc. Natl. Acad. Sci. USA. 99:5373-5377.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 5373-5377
-
-
Arsuaga, J.1
Vazquez, M.2
Trigueros, S.3
Sumners, D.W.4
Roca, J.5
-
12
-
-
21544474118
-
DNA knots reveal a chiral organization of DNA in phage capsids
-
Arsuaga, J., M. Vazquez, P. McGuirk, S. Trigueros, D. W. Sumners, and J. Roca. 2005. DNA knots reveal a chiral organization of DNA in phage capsids. Proc. Natl. Acad. Sci. USA. 102:9165-9169.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 9165-9169
-
-
Arsuaga, J.1
Vazquez, M.2
McGuirk, P.3
Trigueros, S.4
Sumners, D.W.5
Roca, J.6
-
13
-
-
0035408589
-
Novel display of knotted DNA molecules by two dimensional gel electrophoresis
-
Trigueros, S., J. Arsuaga, M. E. Vazquez, D. W. Sumners, and J. Roca. 2001. Novel display of knotted DNA molecules by two dimensional gel electrophoresis. Nucleic Acids Res. 29:e67.
-
(2001)
Nucleic Acids Res
, vol.29
-
-
Trigueros, S.1
Arsuaga, J.2
Vazquez, M.E.3
Sumners, D.W.4
Roca, J.5
-
14
-
-
33746253988
-
Topological information embodied in local juxtaposition geometry provides a statistical mechanical basis for unknotting by type-2 DNA topoisomerases
-
Liu, Z. R., J. K. Mann, E. L. Zechiedrich, and H. S. Chan. 2006. Topological information embodied in local juxtaposition geometry provides a statistical mechanical basis for unknotting by type-2 DNA topoisomerases. J. Mol. Biol. 361:268-285.
-
(2006)
J. Mol. Biol
, vol.361
, pp. 268-285
-
-
Liu, Z.R.1
Mann, J.K.2
Zechiedrich, E.L.3
Chan, H.S.4
-
15
-
-
41449113042
-
The role of DNA twist in the packaging of viral genomes
-
Rollins, G. C., A. S. Petrov, and S. C. Harvey. 2008. The role of DNA twist in the packaging of viral genomes. Biophys. J. 94:L38-L40.
-
(2008)
Biophys. J
, vol.94
-
-
Rollins, G.C.1
Petrov, A.S.2
Harvey, S.C.3
-
16
-
-
42349088217
-
Efficient chain moves for Monte Carlo simulations of a wormlike DNA model: Excluded volume, supercoils, site juxtapositions, knots, and comparisons with random-flight and lattice models
-
Liu, Z. R., and H. S. Chan. 2008. Efficient chain moves for Monte Carlo simulations of a wormlike DNA model: excluded volume, supercoils, site juxtapositions, knots, and comparisons with random-flight and lattice models. J. Chem. Phys. 128:145104.
-
(2008)
J. Chem. Phys
, vol.128
, pp. 145104
-
-
Liu, Z.R.1
Chan, H.S.2
-
17
-
-
0023044418
-
On the topology of a polymer ring
-
Michels, J. P. J., and F. W. Wiegel. 1986. On the topology of a polymer ring. Proc. Roy. Soc. A. 403:269-284.
-
(1986)
Proc. Roy. Soc. A
, vol.403
, pp. 269-284
-
-
Michels, J.P.J.1
Wiegel, F.W.2
-
18
-
-
35748939381
-
Sampling large random knots in a confined space
-
Arsuaga, J., T. Blackstone, Y. Diao, K. Hinson, E. Karadayi, and M. Saito. 2007. Sampling large random knots in a confined space. J. Phys. A Math. Theor. 40:11697-11711.
-
(2007)
J. Phys. A Math. Theor
, vol.40
, pp. 11697-11711
-
-
Arsuaga, J.1
Blackstone, T.2
Diao, Y.3
Hinson, K.4
Karadayi, E.5
Saito, M.6
-
19
-
-
33750478783
-
Knotting of random ring polymers in confined spaces
-
Micheletti, C., D. Marenduzzo, E. Orlandini, and D. W. Sumners. 2006. Knotting of random ring polymers in confined spaces. J. Chem. Phys. 124:064903.
-
(2006)
J. Chem. Phys
, vol.124
, pp. 064903
-
-
Micheletti, C.1
Marenduzzo, D.2
Orlandini, E.3
Sumners, D.W.4
-
20
-
-
21344493383
-
Knot probability for lattice polygons in confined geometries
-
Tesi, M. C., E. J. J. van Rensburg, E. Orlandini, and S. G. Whittington. 1994. Knot probability for lattice polygons in confined geometries. J. Phys. A. 27:347-360.
-
(1994)
J. Phys. A
, vol.27
, pp. 347-360
-
-
Tesi, M.C.1
van Rensburg, E.J.J.2
Orlandini, E.3
Whittington, S.G.4
-
21
-
-
0034183593
-
Tightness of random knotting
-
Katrich, V., W. K. Olson, A. V. Vologodskii, J. Dubochet, and A. Stasiak. 2000. Tightness of random knotting. Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics. 61:5545-5549.
-
(2000)
Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics
, vol.61
, pp. 5545-5549
-
-
Katrich, V.1
Olson, W.K.2
Vologodskii, A.V.3
Dubochet, J.4
Stasiak, A.5
-
22
-
-
0038286173
-
Scaling behavior of random knots
-
Dobay, A., J. Dubochet, K. Millett, P. E. Sottas, and A. Stasiak. 2003. Scaling behavior of random knots. Proc. Natl. Acad. Sci. USA. 100:5611-5615.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 5611-5615
-
-
Dobay, A.1
Dubochet, J.2
Millett, K.3
Sottas, P.E.4
Stasiak, A.5
-
23
-
-
0027279063
-
Probability of DNA knotting and the effective diameter of the DNA double helix
-
Rybenkov, V. V., N. R. Cozzarelli, and A. V. Vologodskii. 1993. Probability of DNA knotting and the effective diameter of the DNA double helix. Proc. Natl. Acad. Sci. USA. 90:5307-5311.
-
(1993)
Proc. Natl. Acad. Sci. USA
, vol.90
, pp. 5307-5311
-
-
Rybenkov, V.V.1
Cozzarelli, N.R.2
Vologodskii, A.V.3
-
24
-
-
0028071373
-
Entropic elasticity of λ-phage DNA
-
Marko, J. F., and E. D. Siggia. 1994. Entropic elasticity of λ-phage DNA. Science. 265:1599.
-
(1994)
Science
, vol.265
, pp. 1599
-
-
Marko, J.F.1
Siggia, E.D.2
-
25
-
-
0029159251
-
Modeling of longrange electrostatic interactions in DNA
-
Vologodskii, A. V., and N. R. Cozzarelli. 1995. Modeling of longrange electrostatic interactions in DNA. Biopolymers. 35:289-296.
-
(1995)
Biopolymers
, vol.35
, pp. 289-296
-
-
Vologodskii, A.V.1
Cozzarelli, N.R.2
-
26
-
-
0034714863
-
Characteristic length of random knotting for cylindrical self-avoiding polygons
-
Shimamura, M. K., and T. Deguchi. 2000. Characteristic length of random knotting for cylindrical self-avoiding polygons. Phys. Lett. A. 274:184-191.
-
(2000)
Phys. Lett. A
, vol.274
, pp. 184-191
-
-
Shimamura, M.K.1
Deguchi, T.2
-
28
-
-
0039924671
-
Monte Carlo study of the interacting self-avoiding walk model in three dimensions
-
Tesi, M. C., E. J. J. Janse van Rensburg, E. Orlandini, and S. G. Whittington. 1996. Monte Carlo study of the interacting self-avoiding walk model in three dimensions. J. Stat. Phys. 82:155-181.
-
(1996)
J. Stat. Phys
, vol.82
, pp. 155-181
-
-
Tesi, M.C.1
Janse van Rensburg, E.J.J.2
Orlandini, E.3
Whittington, S.G.4
-
29
-
-
33646987405
-
Optimized Monte Carlo data-analysis
-
Ferrenberg, A. M., and R. H. Swendsen. 1989. Optimized Monte Carlo data-analysis. Phys. Rev. Lett. 63:1195-1198.
-
(1989)
Phys. Rev. Lett
, vol.63
, pp. 1195-1198
-
-
Ferrenberg, A.M.1
Swendsen, R.H.2
-
30
-
-
85031364552
-
3
-
Calvo, J. A, K. C. Millett, and E. J. Rawdon, editors, AMS Special Session on Physical Knotting and Unknotting, Las Vegas, Nevada, April 21-22
-
3. AMS Special Session on Physical Knotting and Unknotting, Las Vegas, Nevada, April 21-22, 2001 (Contemporary Mathematics).
-
(2001)
Contemporary Mathematics
-
-
-
31
-
-
0004598743
-
Self-entanglement in ring polymers
-
Koniaris, K., and M. Muthukumar. 1991. Self-entanglement in ring polymers. J. Chem. Phys. 95:2873-2881.
-
(1991)
J. Chem. Phys
, vol.95
, pp. 2873-2881
-
-
Koniaris, K.1
Muthukumar, M.2
-
32
-
-
0034710671
-
A deeply knotted protein structure and how it might fold
-
Taylor, W. R. 2000. A deeply knotted protein structure and how it might fold. Nature. 406:916-919.
-
(2000)
Nature
, vol.406
, pp. 916-919
-
-
Taylor, W.R.1
-
34
-
-
85031350373
-
Knotfind routine
-
Software Package
-
Hoste, J., and M. Thistlethwaite. 1999. Knotfind routine. KnotScape 101 Software Package. www.math.utk.edu/morwen/knotscape.html.
-
(1999)
KnotScape
, vol.101
-
-
Hoste, J.1
Thistlethwaite, M.2
-
35
-
-
0004192246
-
-
W. H. Freeman and Company, New York
-
Adams, C. C. 1994. The Knot Book. W. H. Freeman and Company, New York.
-
(1994)
The Knot Book
-
-
Adams, C.C.1
-
36
-
-
0029906723
-
Geometry and physics of knots
-
Katrich, V., J. Bednar, D. Michoud, J. Dubochet, and A. Stasiak. 1996. Geometry and physics of knots. Nature. 384:142-145.
-
(1996)
Nature
, vol.384
, pp. 142-145
-
-
Katrich, V.1
Bednar, J.2
Michoud, D.3
Dubochet, J.4
Stasiak, A.5
-
37
-
-
0032562742
-
Sedimentation and electrophoretic migration of DNA knots and catenanes
-
Vologodskii, A. V., N. J. Crisona, B. Laurie, P. Pieranski, V. Katritch, J. Dubochet, and A. Stasiak. 2002. Sedimentation and electrophoretic migration of DNA knots and catenanes. J. Mol. Biol. 278:1-3.
-
(2002)
J. Mol. Biol
, vol.278
, pp. 1-3
-
-
Vologodskii, A.V.1
Crisona, N.J.2
Laurie, B.3
Pieranski, P.4
Katritch, V.5
Dubochet, J.6
Stasiak, A.7
-
38
-
-
0347345841
-
Crossing number and the braid index of links
-
Ohyama, Y. 1993. Crossing number and the braid index of links. Canad. J. Math. 45:117-131.
-
(1993)
Canad. J. Math
, vol.45
, pp. 117-131
-
-
Ohyama, Y.1
-
40
-
-
84974465975
-
Seifert circles and knot polynomials
-
Morton, H. R. 1986. Seifert circles and knot polynomials. Math. Proc. Cambridge Press Soc. 99:107-109.
-
(1986)
Math. Proc. Cambridge Press Soc
, vol.99
, pp. 107-109
-
-
Morton, H.R.1
-
41
-
-
0034636020
-
A topological invariant to predict the three-dimensional writhe of ideal configurations of knots and links
-
Cerf, C., and A. Stasiak. 2000. A topological invariant to predict the three-dimensional writhe of ideal configurations of knots and links. Proc. Natl. Acad. Sci. USA. 97:3795-3798.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 3795-3798
-
-
Cerf, C.1
Stasiak, A.2
-
42
-
-
33750448646
-
Depletion effects and loop formation in self-avoiding polymers
-
Toan, N. M., D. Marenduzzo, P. R. Cook, and C. Micheletti. 2006. Depletion effects and loop formation in self-avoiding polymers. Phys. Rev. Lett. 97:178302.
-
(2006)
Phys. Rev. Lett
, vol.97
, pp. 178302
-
-
Toan, N.M.1
Marenduzzo, D.2
Cook, P.R.3
Micheletti, C.4
-
43
-
-
33646868070
-
Helical structures from an isotropic homopolymer model
-
Magee, J. E., V. R. Vasquez, and L. Lue. 2006. Helical structures from an isotropic homopolymer model. Phys. Rev. Lett. 96:207802.
-
(2006)
Phys. Rev. Lett
, vol.96
, pp. 207802
-
-
Magee, J.E.1
Vasquez, V.R.2
Lue, L.3
-
44
-
-
0034691565
-
Optimal shapes of compact strings
-
Maritan, A., C. Micheletti, A. Trovato, and J. R. Banavar. 2000. Optimal shapes of compact strings. Nature. 406:287-290.
-
(2000)
Nature
, vol.406
, pp. 287-290
-
-
Maritan, A.1
Micheletti, C.2
Trovato, A.3
Banavar, J.R.4
-
45
-
-
0034691422
-
Mathematics - best packing in proteins and DNA
-
Stasiak, A., and J. H. Maddocks. 2000. Mathematics - best packing in proteins and DNA. Nature. 406:251-253.
-
(2000)
Nature
, vol.406
, pp. 251-253
-
-
Stasiak, A.1
Maddocks, J.H.2
-
46
-
-
15544372825
-
Physics of thick polymers
-
Marenduzzo, D., A. Flammini, A. Trovato, J. R. Banavar, and A. Maritan. 2005. Physics of thick polymers. J. Polym. Sci. [B]. 43:650-679.
-
(2005)
J. Polym. Sci. [B]
, vol.43
, pp. 650-679
-
-
Marenduzzo, D.1
Flammini, A.2
Trovato, A.3
Banavar, J.R.4
Maritan, A.5
-
47
-
-
36849079711
-
Structural motifs of biomolecules
-
Banavar, J. R., T. X. Hoang, J. H. Maddocks, A. Maritan, C. Poletto, A. Stasiak, and A. Trovato. 2007. Structural motifs of biomolecules. Proc. Natl. Acad. Sci. USA. 104:17283-17286.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 17283-17286
-
-
Banavar, J.R.1
Hoang, T.X.2
Maddocks, J.H.3
Maritan, A.4
Poletto, C.5
Stasiak, A.6
Trovato, A.7
-
48
-
-
45849132753
-
Confinement-induced morphologies of cylinder-forming asymmetric diblock copolymers
-
Yu, B., Q. Jin, D. Ding, B. Li, and A.-C. Shi. 2008. Confinement-induced morphologies of cylinder-forming asymmetric diblock copolymers. Macromolecules. 41:4042-4054.
-
(2008)
Macromolecules
, vol.41
, pp. 4042-4054
-
-
Yu, B.1
Jin, Q.2
Ding, D.3
Li, B.4
Shi, A.-C.5
|