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.
1. [1]
  Shule Liu . Application of SPC/E Water Model in Molecular Dynamics Teaching Experiments. University Chemistry, 2024, 39(4): 338-342. doi: 10.3866/PKU.DXHX202310029
2. [2]
  Jiageng Li , Putrama . 数值积分耦合非线性最小二乘法一步确定反应动力学参数. University Chemistry, 2025, 40(6): 364-370. doi: 10.12461/PKU.DXHX202407098
3. [3]
  Zhiwen HUANG , Qi LIU , Jianping LANG . W/Cu/S cluster-based supramolecular macrocycles and their third-order nonlinear optical responses. Chinese Journal of Inorganic Chemistry, 2025, 41(1): 79-87. doi: 10.11862/CJIC.20240184
4. [4]
  Yujie WANG , Laobang WANG , Zheng ZHANG , Qi LIU , Jianping LANG . Construction of W/Cu/S cluster-based supramolecular compounds via alkynyl/sulfur cycloaddition and their third-order nonlinear optical properties. Chinese Journal of Inorganic Chemistry, 2025, 41(10): 2069-2077. doi: 10.11862/CJIC.20250129
5. [5]
  Shanghua Li , Malin Li , Xiwen Chi , Xin Yin , Zhaodi Luo , Jihong Yu . High-Stable Aqueous Zinc Metal Anodes Enabled by an Oriented ZnQ Zeolite Protective Layer with Facile Ion Migration Kinetics. Acta Physico-Chimica Sinica, 2025, 41(1): 100003-0. doi: 10.3866/PKU.WHXB202309003
6. [6]
  Yaling Chen . Basic Theory and Competitive Exam Analysis of Dynamic Isotope Effect. University Chemistry, 2024, 39(8): 403-410. doi: 10.3866/PKU.DXHX202311093
7. [7]
  Jiayu Gu , Siqi Wang , Jun Ling . Kinetics of Living Copolymerization: A Brief Discussion. University Chemistry, 2025, 40(4): 100-107. doi: 10.12461/PKU.DXHX202406012
8. [8]
  Xiaohang JIN , Qi LIU , Jianping LANG . Room‑temperature solid‑state synthesis, structure, and third‑order nonlinear optical properties of phosphine‑ligand‑protected silver thiolate clusters. Chinese Journal of Inorganic Chemistry, 2025, 41(8): 1505-1512. doi: 10.11862/CJIC.20250125
9. [9]
  Jinfu Ma , Hui Lu , Jiandong Wu , Zhongli Zou . Teaching Design of Electrochemical Principles Course Based on “Cognitive Laws”: Kinetics of Electron Transfer Steps. University Chemistry, 2024, 39(3): 174-177. doi: 10.3866/PKU.DXHX202309052
10. [10]
  Yeyun Zhang , Ling Fan , Yanmei Wang , Zhenfeng Shang . Development and Application of Kinetic Reaction Flasks in Physical Chemistry Experimental Teaching. University Chemistry, 2024, 39(4): 100-106. doi: 10.3866/PKU.DXHX202308044
11. [11]
  Wenwen Zhang , Peichao Zhang , Conghao Gai , Xiaoyun Chai , Yan Zou , Qingjie Zhao . Unveiling Kinetics at Natural Abundance: ¹³C NMR Isotope Effect Experiments. University Chemistry, 2025, 40(10): 203-207. doi: 10.12461/PKU.DXHX202411076
12. [12]
  Xuzhen Wang , Xinkui Wang , Dongxu Tian , Wei Liu . Enhancing the Comprehensive Quality and Innovation Abilities of Graduate Students through a “Student-Centered, Dual Integration and Dual Drive” Teaching Model: A Case Study in the Course of Chemical Reaction Kinetics. University Chemistry, 2024, 39(6): 160-165. doi: 10.3866/PKU.DXHX202401074
13. [13]
  Dexin Tan , Limin Liang , Baoyi Lv , Huiwen Guan , Haicheng Chen , Yanli Wang . Exploring Reverse Teaching Practices in Physical Chemistry Experiment Courses: A Case Study on Chemical Reaction Kinetics. University Chemistry, 2024, 39(11): 79-86. doi: 10.12461/PKU.DXHX202403048
14. [14]
  Jiajie Cai , Chang Cheng , Bowen Liu , Jianjun Zhang , Chuanjia Jiang , Bei Cheng . CdS/DBTSO-BDTO S-scheme photocatalyst for H₂ production and its charge transfer dynamics. Acta Physico-Chimica Sinica, 2025, 41(8): 100084-0. doi: 10.1016/j.actphy.2025.100084
15. [15]
  Jichao XU , Ming HU , Xichang CHEN , Chunhui WANG , Leichen WANG , Lingyi ZHOU , Xing HE , Xiamin CHENG , Su JING . Construction and hydrogen peroxide-activated chemodynamic activity of ferrocene?benzoselenadiazole conjugate. Chinese Journal of Inorganic Chemistry, 2025, 41(8): 1495-1504. doi: 10.11862/CJIC.20250144
16. [16]
  Linlin Wu , Yonghua Zhou , Zhongbei Li , Liu Deng , Younian Liu , Limiao Chen , Jianhan Huang . Digital Education Promoting Applied Chemistry Comprehensive Experiments: A Case Study of Catalytic Oxidation of Hydrogen Chloride and Reaction Kinetics. University Chemistry, 2025, 40(9): 273-278. doi: 10.12461/PKU.DXHX202411018
17. [17]
  Xinyu Xu , Jiale Lu , Bo Su , Jiayi Chen , Xiong Chen , Sibo Wang . Steering charge dynamics and surface reactivity for photocatalytic selective methane oxidation to ethane over Au/Ti-CeO₂. Acta Physico-Chimica Sinica, 2025, 41(11): 100153-0. doi: 10.1016/j.actphy.2025.100153
18. [18]
  Yiying Yang , Dongju Zhang . Elucidating the Concepts of Thermodynamic Control and Kinetic Control in Chemical Reactions through Theoretical Chemistry Calculations: A Computational Chemistry Experiment on the Diels-Alder Reaction. University Chemistry, 2024, 39(3): 327-335. doi: 10.3866/PKU.DXHX202309074
19. [19]
  Yue Wu , Jun Li , Bo Zhang , Yan Yang , Haibo Li , Xian-Xi Zhang . Research on Kinetic and Thermodynamic Transformations of Organic-Inorganic Hybrid Materials for Fluorescent Anti-Counterfeiting Application information: Introducing a Comprehensive Chemistry Experiment. University Chemistry, 2024, 39(6): 390-399. doi: 10.3866/PKU.DXHX202403028
20. [20]
  Yuxin CHEN , Yanni LING , Yuqing YAO , Keyi WANG , Linna LI , Xin ZHANG , Qin WANG , Hongdao LI , Wenmin WANG . Construction, structures, and interaction with DNA of two Sm^Ⅲ₄ complexes. Chinese Journal of Inorganic Chemistry, 2025, 41(6): 1141-1150. doi: 10.11862/CJIC.20240258

Get Citation

PDF

XML

Metrics

PDF Downloads(660)
Abstract views(2350)
HTML views(45)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142