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]
  Yaling Chen . Basic Theory and Competitive Exam Analysis of Dynamic Isotope Effect. University Chemistry, 2024, 39(8): 403-410. doi: 10.3866/PKU.DXHX202311093
3. [3]
  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
4. [4]
  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
5. [5]
  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
6. [6]
  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
7. [7]
  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
8. [8]
  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
9. [9]
  You Wu , Chang Cheng , Kezhen Qi , Bei Cheng , Jianjun Zhang , Jiaguo Yu , Liuyang Zhang . ZnO/D-A共轭聚合物S型异质结高效光催化产H₂O₂及其电荷转移动力学研究. Acta Physico-Chimica Sinica, 2024, 40(11): 2406027-. doi: 10.3866/PKU.WHXB202406027
10. [10]
  Yan Li , Xinze Wang , Xue Yao , Shouyun Yu . Kinetic Resolution Enabled by Photoexcited Chiral Copper Complex-Mediated Alkene E→Z Isomerization: A Comprehensive Chemistry Experiment for Undergraduate Students. University Chemistry, 2024, 39(5): 1-10. doi: 10.3866/PKU.DXHX202309053
11. [11]
  Shuang Meng , Haixin Long , Zhou Zhou , Meizhu Rong . Inorganic Chemistry Curriculum Design and Implementation of Based on “Stepped-Task Driven + Multi-Dimensional Output” Model: A Case Study on Intermolecular Forces. University Chemistry, 2024, 39(3): 122-131. doi: 10.3866/PKU.DXHX202309008
12. [12]
  Rui Li , Jiayu Zhang , Anyang Li . Two Levels of Understanding of Chemical Bonds: a Case of the Bonding Model of Hypervalent Molecules. University Chemistry, 2024, 39(2): 392-398. doi: 10.3866/PKU.DXHX202308051
13. [13]
  Wenliang Wang , Weina Wang , Sufan Wang , Tian Sheng , Tao Zhou , Nan Wei . “Schrödinger Equation – Approximate Models – Core Concepts – Simple Applications”: Constructing a Logical Framework and Knowledge Graph of Atom and Molecule Structures. University Chemistry, 2024, 39(8): 338-343. doi: 10.3866/PKU.DXHX202312084
14. [14]
  Cuiping Yang , Huiping Ding , Jinpeng Hou , Kai Li , Weiliang Tian . Reform and Exploration of “Comprehensive and Precise Process” Assessment in Chemical Engineering Principle Experimental Course. University Chemistry, 2024, 39(3): 178-190. doi: 10.3866/PKU.DXHX202309087
15. [15]
  Jianmin Hao , Ruifeng Wu , Ying Wang , Yijia Bai , Xuechuan Gao , Yuying Du . Reform and Practice of Physical Chemistry Course Based on Enhanced Process Assessment and Evaluation. University Chemistry, 2024, 39(8): 78-83. doi: 10.3866/PKU.DXHX202311103
16. [16]
  Fang Niu , Rong Li , Qiaolan Zhang . Analysis of Gas-Solid Adsorption Behavior in Resistive Gas Sensing Process. University Chemistry, 2024, 39(8): 142-148. doi: 10.3866/PKU.DXHX202311102
17. [17]
  Pingping Zhu , Yongjun Xie , Yuanping Yi , Yu Huang , Qiang Zhou , Shiyan Xiao , Haiyang Yang , Pingsheng He . Excavation and Extraction of Ideological and Political Elements for the Virtual Simulation Experiments at Molecular Level: Taking the Project “the Simulation and Computation of Conformation, Morphology and Dimensions of Polymer Chains” as an Example. University Chemistry, 2024, 39(2): 83-88. doi: 10.3866/PKU.DXHX202309063
18. [18]
  Manman Jin , Zhiguo Lv , Qingtao Niu . Teaching Reformation and Case Study for “Chemical Process Development and Design” Based on “Just-in-Time” Dynamic and Accurate Matching Industrial Needs. University Chemistry, 2024, 39(11): 108-116. doi: 10.12461/PKU.DXHX202403030
19. [19]
  Chang Liu , Tao Wu , Lijiao Deng , Xuzi Li , Xin Fu , Shuzhen Liao , Wenjie Ma , Guoqiang Zou , Hai Yang . Programmed DNA walkers for biosensors. Chinese Chemical Letters, 2024, 35(9): 109307-. doi: 10.1016/j.cclet.2023.109307
20. [20]
  Linhan Tian , Changsheng Lu . Discussion on Sextuple Bonding in Diatomic Motifs of Chromium Family Elements. University Chemistry, 2024, 39(8): 395-402. doi: 10.3866/PKU.DXHX202401056

Get Citation

PDF

XML

Metrics

PDF Downloads(660)
Abstract views(2151)
HTML views(28)

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