Molecular dynamics simulations of the interaction between OH radicals in plasma with poly-<i>β</i>-1–6-N-acetylglucosamine

Shuhui YANG (杨姝惠); Tong ZHAO (赵彤); Jingxian CUI (崔静娴); Zhiyun HAN (韩智云); Liang ZOU (邹亮); Xiaolong WANG (王晓龙); Yuantao ZHANG (张远涛)

doi:10.1088/2058-6272/abb454

Plasma Science and Technology > 2020 > 22(12): 125401. > DOI: 10.1088/2058-6272/abb454

Shuhui YANG (杨姝惠), Tong ZHAO (赵彤), Jingxian CUI (崔静娴), Zhiyun HAN (韩智云), Liang ZOU (邹亮), Xiaolong WANG (王晓龙), Yuantao ZHANG (张远涛). Molecular dynamics simulations of the interaction between OH radicals in plasma with poly-β-1–6-N-acetylglucosamine[J]. Plasma Science and Technology, 2020, 22(12): 125401. DOI: 10.1088/2058-6272/abb454

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Molecular dynamics simulations of the interaction between OH radicals in plasma with poly-β-1–6-N-acetylglucosamine

¹ School of Electrical Engineering, Shandong University, Ji'nan 250061, People's Republic of China
² State Grid Shandong Electric Power Construction Company, Ji'nan 250061, People's Republic of China

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Received Date: June 18, 2020
Revised Date: August 21, 2020
Accepted Date: August 31, 2020

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Abstract

Abstract

Cold atmospheric plasma shows a satisfactory ability to inactivate bacterial biofilms that are difficult to remove using conventional methods in some cases. However, the researches on the inactivation mechanism are not quite sufficient. Poly-β-1–6-N-acetylglucosamine (PNAG), which is one of the important components in some biofilms, was used as the research subject, and the related mechanism of action triggered by different concentrations of the OH in plasma was studied using reactive molecular dynamics simulations. The results showed that OH radicals could not only trigger the hydrogen abstraction reaction leading to cleavage of the PNAG molecular structure, but undergo an OH addition reaction with PNAG molecules. New reaction pathways appeared in the simulations as the OH concentration increased, but the reaction efficiency first increased and then decreased. The simulation study in this paper could, to some extent, help elucidate the microscopic mechanism of the interaction between OH radicals in plasma and bacterial biofilms at the atomic level.
- cold atmospheric plasma,
- molecular dynamics,
- reactive oxygen species,
- bacterial biofilm

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References

[1]	Akhavan B et al 2018 Appl. Mater. Today 12 72
[2]	Su X et al 2018 Appl. Environ. Microbiol. 84 e02836-17
[3]	Liao X Y et al 2019 Crit. Rev. Food Sci. Nutr. 59 2562
[4]	Lee M H et al 2009 New J. Phys. 11 115022
[5]	Fridman G et al 2008 Plasma Processes Polym. 5 503
[6]	Keidar M et al 2011 Br. J. Cancer 105 1295
[7]	Graves D B 2012 J. Phys. D Appl. Phys. 45 263001
[8]	Stewart P S and Costerton J W 2001 Lancet 358 135
[9]	Mah T F et al 2003 Nature 426 306
[10]	Otto M 2008 Curr. Top. Microbiol. Immunol. 322 207
[11]	Moormeier D E and Bayles K W 2017 Mol. Microbiol.104 365
[12]	Singh S et al 2017 Open Microbiol. J. 11 53
[13]	Los A et al 2020 Appl. Environ. Microbiol. 86 e02619–02619
[14]	Patange A et al 2019 Int. J. Food Microbiol. 293 137
[15]	Matthes R et al 2013 Plasma Processes Polym. 10 161
[16]	Alkawareek M Y et al 2012 PLoS One 7 e44289
[17]	Govaert M et al 2019 Innovat. Food Sci. Emerg. Technol.52 376
[18]	Li Y L et al 2019 Plasma Chem. Plasma Process. 39 35
[19]	Modic M et al 2017 Int. J. Antimicrob. Agents 49 375
[20]	Handorf O et al 2018 Appl. Environ. Microbiol. 84 e01163-18
[21]	Gabriel A A et al 2016 Innovat. Food Sci. Emerg. Technol.36 311
[22]	Machala Z, Chládeková L and Pelach M 2010 J. Phys. D Appl.Phys. 43 222001
[23]	Zhang Q et al 2012 J. Appl. Phys. 111 123305
[24]	Liao X et al 2018 J. Food Sci. 83 401
[25]	Chandana L et al 2018 Sci. Total Environ. 640–641 493
[26]	Khan M S I, Lee E J and Kim Y J 2016 Sci. Rep. 6 37072
[27]	Abolfath R M, Van Duin A C T and Brabec T 2011 J. Phys.Chem. A 115 11045
[28]	Cui J X et al 2018 J. Phys. D Appl. Phys. 51 355401
[29]	Zhao T et al 2017 Phys. Plasma 24 103518
[30]	Van Duin A C T et al 2001 J. Phys. Chem. A 105 9396
[31]	Yusupov M et al 2012 New J. Phys. 14 093043
[32]	Yusupov M et al 2013 J. Phys. Chem. C 117 5993
[33]	Yusupov M et al 2015 Plasma Processes Polym. 12 162
[34]	Neyts E C et al 2014 J. Phys. D Appl. Phys. 47 293001
[35]	Bogaerts A et al 2014 Plasma Processes Polym. 11 1156
[36]	Liu D X et al 2010 Plasma Sources Sci. Technol. 19 025018
[37]	Bruggeman P and Schram D C 2010 Plasma Sources Sci.Technol. 19 045025
[38]	Kikuchi Y et al 2011 Jpn. J. Appl. Phys. 50 01AH03
[39]	Yusupov M et al 2014 J. Phys. D Appl. Phys. 47 025205
[40]	Hefny M M et al 2016 J. Phys. D Appl. Phys. 49 404002
[41]	Tian W and Kushner M J 2014 J. Phys. D Appl. Phys. 47 165201
[42]	Chenoweth K, Van Duin A C T and Goddard W A 2008 J. Phys. Chem. A 112 1040
[43]	Weismiller M R et al 2010 J. Phys. Chem. A 114 5485
[44]	Senftle T P et al 2016 npj Comput. Mater. 2 15011
[45]	Monti S et al 2013 Phys. Chem. Chem. Phys. 15 15062
[46]	Neyts E C, Van Duin A C T and Bogaerts A 2012 J. Am.Chem. Soc. 134 1256
[47]	Rahaman O et al 2011 J. Phys. Chem. B 115 249
[48]	Little D J et al 2018 PLoS Pathog. 14 e1006998
[49]	Flemming H C and Wingender J 2010 Nat. Rev. Microbiol.8 623
[50]	Bales P M et al 2013 PLoS One 8 e67950
[51]	Gening M L et al 2010 Eur. J. Org. Chem. 2010 2415
[52]	Izano E A et al 2007 Microb Pathog 43 1
[53]	Fang Z et al 2016 Eur. Phys. J. D 70 79
[54]	Zhang X H et al 2018 Plasma Processes Polym. 15 1700241
[55]	Srivastava N and Wang C J 2011 J. Appl. Phys. 110 053304

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Molecular dynamics simulations of the interaction between OH radicals in plasma with poly-β-1–6-N-acetylglucosamine