Mixing and segregation of ring polymers: Spatial confinement and molecular crowding effects

New Journal of Physics

Volumn 16, Issue , 2014, Pages

  Shin, Jaeoh ^a   Cherstvy, Andrey G ^a   Metzler, Ralf ^a,b  

^a UNIVERSITY OF POTSDAM   (Germany)

^b TAMPERE UNIVERSITY OF TECHNOLOGY   (Finland)

Author keywords

confinement; crowding; polymers

Indexed keywords

CELLS; COMPUTER SIMULATION; MIXING; MOLECULES; PLASMA CONFINEMENT;

CELL DIVISION PROCESS; CELLULAR COMPARTMENTS; CROWDING; MACROMOLECULAR CROWDING; MIXING AND SEGREGATIONS; NON-MONOTONIC DEPENDENCE; STATISTICAL BEHAVIOR; SYSTEMATIC VARIATION;

POLYMERS;

EID: 84901704144     PISSN: 13672630     EISSN: None     Source Type: Journal    
DOI: 10.1088/1367-2630/16/5/053047     Document Type: Article

References (88)

1. Jun S and Wright A 2010 Nature Rev. Microbiol. 8 600
2. Hancock R 2012 PLoS ONE 7 e36045
3. Dekker J, Marti-Renom A and Mirny L A 2013 Nature Rev. Genet. 14 390
4. Lee T B K et al 2013 Science 342 731
5. Bates D and Kleckner N 2005 Cell 121 899 (Pubitemid 40806421)
6. Cremer T and Cremer C 2001 Nature Rev. Genet. 2 292 (Pubitemid 33674777)
7. Dorier J and Stasiak A 2009 Nucl. Acids Res. 37 6316
8. Rosa A and Everaers R 2008 PLoS Comput. Biol. 4 e1000153
9. Rosa A, Becker N B and Everaers R 2010 Biophys. J. 98 2410
10. Bronstein I, Israel Y, Kepten E, Mai S, Shav-Tal Y, Barkai E and Garini Y 2009 Phys. Rev. Lett. 103 018102
11. Kroy K and Glaeser J 2007 New J. Phys. 9 416 (Pubitemid 350241885)
12. Marenduzzo D et al 2009 Proc. Natl. Acad. Sci. USA 106 22269
13. Saper G et al 2013 Nucl. Acids Res. 41 1569
14. Leforestier A, Siber A, Livolant F and Podgornik R 2011 Biophys J. 100 2209
15. Hanke A, Metzler R, Dommersnes P G, Kantor Y and Kardar M 2003 Europ. Phys. J. E 12 347
16. Zhang C et al 2009 Proc. Natl. Acad. Sci. USA 106 16651
17. Zimmerman S B and Murphy L D 1996 FEBS Lett. 390 245 (Pubitemid 26248952)
18. McGuffee A R and Elcock A H 2010 PLoS Comp. Biol. 6 e1000694
19. Zimmerman S B and Minton A P 1993 Annu. Rev. Biophys. Biomol. Struct. 22 27
20. Yanagisawa M, Sakaue T and Yoshikawa K 2014 Intl. Rev. Cell & Molec. Biol. 307 175
21. Denton A R 2014 Intl. Rev. Cell & Molec. Biol. 307 27
22. Weiss M 2014 Intl. Rev. Cell & Molec. Biol. 307 383
23. Goychuk I 2012 Adv. Chem. Phys. 150 187
24. Jeon J-H, Martinez-Seara Monne H, Javanainen M and Metzler R 2012 Phys. Rev. Lett. 109 188103
25. Jeon J-H, Leijnse N, Oddershede L and Metzler R 2013 New J. Phys. 15 045011
26. Guigas G, Kalla C and Weiss M 2007 Biophys. J. 93 316 (Pubitemid 47041676)
27. Barkai E, Garini Y and Metzler R 2012 Phys. Today 65 29
28. Höfling F and Franosch T 2013 Rep. Prog. Phys. 76 046602
29. Golding I and Cox E C 2006 Phys. Rev. Lett. 96 098102 (Pubitemid 43385256)
30. Weber S C, Spakowitz A J and Theriot J A 2010 Phys. Rev. Lett. 104 238102
31. Szymanski J and Weiss M 2009 Phys. Rev. Lett. 103 038102
32. Jeon J-H, Tejedor V, Burov S, Barkai E, Selhuber-Unkel C, Berg-Sørensen K, Oddershede L and Metzler R 2012 Phys. Rev. Lett. 106 048103
33. Tabei S M A, Burov S, Kim H Y, Kuznetsov A, Huynh T, Jureller J, Philipson L H, Dinner A R and Scherer N F 2013 Proc. Natl. Acad. Sci. USA 110 4911
34. Zhou H X 2004 J. Mol. Recognit. 17 368
35. Echeverria C and Kapral R 2012 Phys. Chem. Chem. Phys. 14 6755
36. Brackley C A, Cates M E and Marenduzzo D 2013 Phys. Rev. Lett. 111 108101
37. Stiehl O, Weidner-Hertrampf K and Weiss M 2013 New J. Phys. 15 113010
38. Kühn T et al 2011 PLoS One 6 e22962
39. Jun S 2010 Polymer physics for understanding bacterial chromosomes Bacterial Chromatin ed R T Dame and C J Dorman (Berlin: Springer) 97-116 chapter 6
40. Jun S and Mulder B 2006 Proc. Natl. Acad. Sci. USA 103 12388 (Pubitemid 44267269)
41. Metzler R, Kantor Y and Kardar M 2002 Phys. Rev. E 66 022102 (Pubitemid 40618684)
42. Rubinstein M 1986 Phys. Rev. Lett. 57 3023
43. Micheletti C and Orlandini E 2012 Macromol. 45 2113
44. Tubiana L et al 2011 Phys. Rev. Lett. 107 188302
45. Micheletti C, Marenduzzo D and Orlandini E 2011 Phys. Rep. 504 1
46. Jung Y et al 2012 Soft Matter 8 2095
47. Benedetti F, Dorier J, Burnier Y and Stasiak A 2014 Nucl. Acids Res. 42 2848
48. Narros A et al 2013 Macromol. 46 3654
49. Reigh S Y and Yoon D Y 2013 ACS Macro Lett. 2 296
50. Kim J et al 2013 Soft Matter 9 6142
51. Mateos-Langerak J et al 2009 Proc. Natl. Acad. Sci. USA 106 3812
52. Bohn M and Heermann D W 2010 J. Chem. Phys. 132 044904
53. Bohn M et al 2010 Macromol. 43 2564
54. Fritsche M and Heermann D W 2012 Soft Matter 7 6906
55. Racko D and Cifra P 2013 J. Chem. Phys. 138 184904
56. Dorier J and Stasiak A 2013 Nucl. Acids Res. 41 6808
57. Halverson J D et al 2014 Rep. Prog. Phys. 77 022601
58. Reisner W, Pedersen J N and Austin R H 2012 Rep. Prog. Phys. 75 106601
59. Micheletti D et al 2014 ACS Macro Lett. 3 255
60. Orlandini E et al 2010 Phys. Rev. E 82 050804(R)
61. Parisi G and Sourlas N 1981 Phys. Rev. Lett. 46 871
62. Kim J S et al 2011 Phys. Rev. Lett. 106 168102
63. Kim J S and Szleifer I 2010 J. Phys. Chem. C 114 20864
64. Schmit J D, Kamber E and Kondev J 2009 Phys. Rev. Lett. 102 218302
65. Marcovitz A and Levy Y 2013 Biophys. J. 104 2042
66. Gopinathan A and Kim Y W 2007 Phys. Rev. Lett. 99 228106 (Pubitemid 350198417)
67. Chen Y and Luo K 2013 J. Chem. Phys. 138 204903
68. Lappala A, Zaccone A and Terentjev E M 2013 Scientific Reports 3 3103
69. Shin J, Cherstvy A G and Metzler R 2014 in preparation
70. Shin J, Cherstvy A G and Metzler R 2014 Phys. Rev. X 4 021002
71. Rybenkov V V, Vologodskii A V and Cozzarelli N R 1997 Nucl. Acids Res. 25 1412 (Pubitemid 27303670)
72. McGuffee A R and Elcock A H 2013 PLoS Comp. Biol. 6 e1000694
73. Mika J T 2010 et al Mol. Microbiol. 77 200
74. Savelyev A, Materese C K and Papoian G A 2011 J. Am. Chem. Soc. 133 19290
75. Cherstvy A G 2011 J. Biol. Phys. 37 227
76. Cherstvy A G 2011 J. Phys. Chem. B 115 4286
77. Ando T and Skolnick J 2010 Proc. Natl. Acad. Sci. USA 107 18457
78. Wensink H H et al 2012 Proc. Natl. Acad. Sci. USA 109 14308
79. Hegde G A et al 2011 J. Chem. Phys. 135 184901
80. Jung Y et al 2009 Phys. Rev. E 79 061912
81. Cherstvy A G and Teif V B 2013 J. Biol. Phys. 39 363
82. Winkler R G 2006 Phys. Rev. Lett. 97 128301 (Pubitemid 44414320)
83. Huang C C et al 2012 J. Phys.: Cond. Matt. 24 284131
84. Chuang J, Kantor Y and Kardar M 2001 Phys. Rev. E 65 011802
85. Luo K, Ala-Nissila T, Ying S-C and Metzler R 2009 Europhys. Lett. 88 68006
86. Flyvbjerg H and Petersen H G 1989 J. Chem. Phys. 91 461
87. di Ventura B et al 2013 Mol. Systems Biol. 9 686
88. Coquel A S et al 2013 PLoS Comput. Biol. 9 e1003038