The effect of composition on diffusion of macromolecules in a crowded environment

Physical Biology

Volumn 12, Issue 4, 2015, Pages

  Kondrat, Svyatoslav ^a,b   Zimmermann, Olav ^a,b   Wiechert, Wolfgang ^a,b   Lieres, Eric Von ^a,b  

^a FORSCHUNGSZENTRUM JÜLICH   (Germany)

^b JARA High Performance Computing   (Germany)

Author keywords

anomalous subdiffusion; Brownian dynamics; crowding; cytoplasm; macromolecular diffusion

Indexed keywords

MACROMOLECULE;

BIOLOGICAL MODEL; CHEMISTRY; CYTOPLASM; DIFFUSION; MACROMOLECULE;

CYTOPLASM; DIFFUSION; MACROMOLECULAR SUBSTANCES; MODELS, BIOLOGICAL;

EID: 84937546400     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/12/4/046003     Document Type: Article

References (51)

1. Fulton A B 1982 Cell 30 345
2. Mastro A M, Babich M A, Taylor W D and Keith A D 1984 Proc. Natl Acad. Sci. USA 81 3414
3. Minton A P 1997 Curr. Opin. Biotechnol. 8 65
4. Minton A P 2000 Curr. Opin. Struct. Biol. 10 34
5. Ellis R J 2001a Trends Biochem. Sci. 26 597
6. Ellis R J 2001b Curr. Opin. Struct. Biol. 11 114
7. Minton A P 2006 Curr. Biol. 16 R269
8. Kim J S and Yethiraj A 2009 Biophys. J. 96 1333
9. Weiss M, Elsner M, Kartberg,and F and Nilsson T 2004 Biophys. J. 87 3518
10. Dix J A and Verkman A 2008 Annu. Rev. Biophys. 37 247
11. Geyer T 2011 BMC Biophys. 4 7
12. Dlugosz M and Trylska J 2011 BMC Biophys. 4 3
13. Mereghetti P, Kokh D, McCammon J A and Wade R C 2011 BMC Biophys. 4 2
14. Schöneberg J and Noé F 2013 PLOS One 8 e74261
15. Foffi G, Pastore A, Piazza F and Temussi P A 2013 Phys. Biol. 10 040301
16. Qin S, Mittal J and Zhou H-X 2013 Phys. Biol. 10 045001
17. Sanfelice D, Politou A, Martin S R, Rios P D L, Temussi P and Pastore A 2013 Phys. Biol. 10 045002
18. Abriata L A, Spiga E and Peraro M D 2013 Phys. Biol. 10 045006
19. Fanelli D, McKane A J, Pompili G, Tiribilli B, Vassalli M and Biancalani T 2013 Phys. Biol. 10 045008
20. Minton A P 1981 Biopolymers 20 2093
21. Ridgway D, Broderick G, Lopez-Campistrous A, Ruaini M, Winter P, Hamilton M, Boulanger P, Kovalenko A and Ellison M J 2008 Biophys. J. 94 3748
22. McGuffee S R and Elcock A H 2010 PLoS Comput. Biol. 6 e1000694
23. Ando T and Skolnick J 2010 Proc. Natl Acad. Sci. USA 107 18457
24. Minton A P 2001 J. Biol. Chem. 276 10577
25. Verkman A S 2002 Trends Biochem. Sci. 27 27
26. Banks D S and Fradin C 2005 Biophys. J. 89 2960
27. Regner B M, Vučinić D, Domnisoru C, Bartol T M, Hetzer M W, Tartakovsky D M and Sejnowski T J 2013 Biophys. J. 104 1652
28. Elowitz M B, Surette M G, Wolf P-E, Stock J B and Leibler S 1999 J. Bacteriol. 181 197 (PMID: 9864330)
29. Konopka M C, Shkel I A, Cayley S, Record M T and Weisshaar J C 2006 J. Bacteriol. 188 6115
30. Henderson D, Duh D-M, Chu X and Wasan D 1997 J. Colloid. Interface. Sci. 185 265
31. Israelachvili J N 1991 Intermolecular and Surface Forces (New York: Academic)
32. Levin Y 2002 Rep. Prog. Phys. 65 1577
33. Rotne J and Prager S 1969 J. Chem. Phys. 50 4831
34. Yamakawa H 1970 J. Chem. Phys. 53 436
35. Smith E R, Snook I K and van Megen W 1987 Physica A 143 441
36. Huang D M, Faller R, Do K and Moulè A J 2010 J. Chem. Theory Comput. 6 526
37. Dlugosz M, Zielinski P and Trylska J 2011 J. Comput. Chem. 32 2734
38. http://browniandynamics.org/index.html
39. Ermak D L and McCammon J A 1978 J. Chem. Phys. 69 1352
40. Iniesta A and de la Torre J G 1990 J. Chem. Phys. 92 2015
41. Frenkel D and Smith B 1996 Understanding Molecular Simulations (New York: Academic)
42. Gubbins K E, Liu Y-C, Moore J D and Palmer J C 2011 Phys. Chem. Chem. Phys. 13 58
43. Hertz P 1909 Math. Ann. 67 387
44. Chandrasekhar S 1943 Rev. Mod. Phys. 15 1
45. Andrews S and Bray D 2004 Phys. Biol. 1 137
46. Andrews S S, Addy N J, Brent R and Arkin A 2010 PLoS Comput. Biol. 6 e1000705
47. Metzler R, Barkai E and Klafter J 1999 Phys. Rev. Lett. 82 3563
48. Ilyin V, Procaccia I and Zagorodny A 2010 Phys. Rev. E 81 030105
49. Fritsch C C and Langowski J 2012 J. Chem. Phys. 137 064114
50. Höfling F and Franosch T 2013 Rep. Prog. Phys. 76 046602
51. Hellmann M, Klafter J, Heermann D W and Weiss M 2011 J. Phys: Condens. Matter 23 234113