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Chin. Phys. B, 2020, Vol. 29(1): 018701    DOI: 10.1088/1674-1056/ab5941
INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY Prev   Next  

Phase transition of DNA compaction in confined space: Effects of macromolecular crowding are dominant

Erkun Chen(陈尔坤)1, Yangtao Fan(范洋涛)2, Guangju Zhao(赵光菊)1, Zongliang Mao(毛宗良)1, Haiping Zhou(周海平)3, Yanhui Liu(刘艳辉)1
1 College of Physics, Guizhou University, Guiyang 550025, China;
2 Collaborative Innovation Center for Optoelectronic Semiconductors and Efficient Devices, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China;
3 Department of Computer Science and Engineering, Shaoxing University, Shaoxing 312000, China
Abstract  With a view of detecting the effects of macromolecular crowding on the phase transition of DNA compaction confined in spherical space, Monte Carlo simulations of DNA compaction in free space, in confined spherical space without crowders and in confined spherical space with crowders were performed separately. The simulation results indicate that macromolecular crowding effects on DNA compaction are dominant over the roles of multivalent counterions. In addition, effects of temperature on the phase transition of DNA compaction have been identified in confined spherical space with different radii. In confined spherical space without crowders, the temperature corresponding to phase transition depends on the radius of the confined spherical space linearly. In contrast, with the addition of crowders to the confined spherical space, effects of temperature on the phase transition of DNA compaction become insignificant, whereas the phase transition at different temperatures strongly depends on the size of crowder, and the critical volume fraction of crowders pertains to the diameter of crowder linearly.
Keywords:  macromolecular crowding      Monte Carlo simulation      DNA compaction      phase transition  
Received:  06 September 2019      Revised:  26 October 2019      Published:  05 January 2020
PACS:  87.15.ak (Monte Carlo simulations)  
  87.16.A- (Theory, modeling, and simulations)  
  87.15.Cc (Folding: thermodynamics, statistical mechanics, models, and pathways)  
  87.14.G- (Nucleic acids)  
Fund: Project supported by the National Natural Science Foundation of China (Grant Nos. 11464004 and 11864006), the State Scholarship Fund, China (Grant No. 20173015) and Guizhou Scientific and Technological Program, China (Grant No. 20185781).
Corresponding Authors:  Haiping Zhou, Yanhui Liu     E-mail:  hpzhou2885@163.com;ionazati@itp.ac.cn

Cite this article: 

Erkun Chen(陈尔坤), Yangtao Fan(范洋涛), Guangju Zhao(赵光菊), Zongliang Mao(毛宗良), Haiping Zhou(周海平), Yanhui Liu(刘艳辉) Phase transition of DNA compaction in confined space: Effects of macromolecular crowding are dominant 2020 Chin. Phys. B 29 018701

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