Citation: ZHANG Yong, XIAO Zhong-Dang. Brownian Dynamics Simulation of Three Nonlinear Interactions on the Folding Process of Single Completely Stretched DNA Chain[J]. Acta Physico-Chimica Sinica, ;2011, 27(11): 2705-2710. doi: 10.3866/PKU.WHXB20111111 shu

Brownian Dynamics Simulation of Three Nonlinear Interactions on the Folding Process of Single Completely Stretched DNA Chain

ZHANG Yong ^1,2 ,
XIAO Zhong-Dang ^1,

1.
1. State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 211189, P. R. China;
2. Department of Physics, Southeast University, Nanjing 211189, P. R. China

Received Date: 23 May 2011
Available Online: 2 September 2011
Fund Project: 国家自然科学基金(20875014, 30901285)资助项目 (20875014, 30901285)

The folding dynamics of a completely stretched dexoxyribonucleic acid (DNA) molecule chain is an important feature of single DNA mechanics. By constructing a fully parameterized bead-spring chain model and applying a highly efficient second order semi-implicit predictor-corrector al rithm, we studied the influence of three nonlinear interactions including the excluded volume interaction, the finite extensible nonlinear elastic interaction, and the fluctuating hydrodynamic interaction on the folding process. Simulation results show that the excluded volume interaction decreases the relative radius of gyration of the DNA chain obviously but has no influence on the relaxation time. Instead, the hydrodynamic interaction clearly decreases the relaxation time but it does not change the relative radius of gyration. In addition, the finite extensible elastic interaction was found to decrease the relative radius of gyration of the short chain clearly and increase the relaxation time of the long chain obviously. Furthermore, we obtained a smooth change for the relative radius of gyration with time. The scaling exponent of the relaxation time with the length of chain has two different values under all three nonlinear interactions. These results complete our understanding about single DNA molecule chain mechanics in solution.
- Single DNA molecule chain,
- Bead-spring model,
- Nonlinear interaction,
- Brownian dynamics simulation,
- Folding process
1. [1]
  (1) Rivetti, C.; Guthold, M.; Bustamante, C. J. Mol. Biol. 1996, 264, 919.
2. [2]
  (2) Valle, F.; Favre, M. E.; De Los Rios, P.; Rosa, A.; Dietler, G. Phys. Rev. Lett. 2005, 95, 158105.
3. [3]
  (3) Maier, B.; Rädler, J. O. Phys. Rev. Lett. 1999, 82, 1911.
4. [4]
  (4) Maier, B.; Rädler, J. O. Macromolecules 2000, 33, 7185.
5. [5]
  (5) Hsieh, C.; Li, L.; Larson, R. G. J. Non-Newton. Fluid 2003, 113, 147.
6. [6]
  (6) Somasi, M.; Khomami, B.;Woo, N. J.; Hur, J. S.; Shaqfeh, E. S. G. J. Non-Newton. Fluid 2002, 108, 227.
7. [7]
  (7) Jendrejack, R. M.; de Pablo, J. J.; Graham, M. D. J. Chem. Phys. 2002, 116, 7752.
8. [8]
  (8) Schroeder, C. M.; Shaqfeh, E. S. G.; Chu, S. Macromolecules 2004, 37, 9242.
9. [9]
  (9) Ibáñez-García, G. O.; Hanna, S. Soft Matter 2009, 5, 4464.
10. [10]
  (10) Prabhakar, R.; Prakash, J. R. J. Non-Newton. Fluid 2004, 116, 163.
11. [11]
  (11) Jendrejack, R. M.; Graham, M. D.; Pablo, J. J. D. J. Chem. Phys. 2000, 113, 2894.
12. [12]
  (12) Rotne, J.; Prager, S. J. Chem. Phys. 1969, 50, 4831.
13. [13]
  (13) Hoda, N.; Kumar, S. Phys. Rev. E 2009, 79, 208011.
14. [14]
  (14) Li, L.; Larson, R. G.; Sridhar, T. J. Rheol. 2000, 44, 291.
15. [15]
  (15) Öttinger, H. C. Stochastic Processes in Polymeric Fluids; Springer Press: Berlin, 1996.
16. [16]
  (16) Smith, D. E.; Perkins, T. T.; Chu, S. Macromolecules 1996, 29, 1372.
17. [17]
  (17) Smith, D. E.; Chu, S. Science 1998, 281, 1335.
18. [18]
  (18) Smith, D. E.; Babcock, H. P.; Chu, S. Science 1999, 283, 1724.
19. [19]
  (19) Reese, H. R.; Zimm, R. H. J. Chem. Phys. 1990, 92, 2650.
20. [20]
  (20) Rakwoo, C.; Yethiraj, A. J. Chem. Phys. 2001, 114, 7688.
21. [21]
  (21) Pham, T. T.; Bajaj, M.; Prakash, J. R. Soft Matter 2008, 4, 1196.
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