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Active Brownian particles simulated in molecular dynamics |
| Liya Wang(王丽雅)1,4, Xinpeng Xu(徐新鹏)2, Zhigang Li(李志刚)3, Tiezheng Qian(钱铁铮)4 |
1 Faulty of Civil Engineering and Mechanics, Jiangsu University, Zhenjiang 212013, China;
2 Faculty of Physics, Guangdong-Technion-Israel Institute of Technology, Shantou 515063, China;
3 Department of Mechanical and Aerospace Engineering, Hong Kong University of Science and Technology, Hong Kong, China;
4 Department of Mathematics, Hong Kong University of Science and Technology, Hong Kong, China |
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Abstract In the numerical studies of active particles, models consisting of a solid body and a fluid body have been well established and widely used. In this work, such an active Brownian particle (ABP) is realized in molecular dynamics (MD) simulations. Immersed in a fluid, each ABP consists of a head particle and a spherical phantom region of fluid where the flagellum of a microswimmer takes effect. Quantitative control over the orientational persistence time is achieved via an external stochastic dynamics. This control makes it possible to validate ABP's diffusion property in a wide range of particle activity. In molecular description, the axial velocity of ABP exhibits a Gaussian distribution. Its mean value defines the active velocity which increases with the active force linearly, but shows no dependence on the rotational diffusion coefficient. For the active diffusion coefficient measured in free space, it shows semi-quantitative agreement with the analytical result predicted by a minimal ABP model. Furthermore, the active diffusion coefficient is also calculated by performing a quantitative analysis on the ABP's distribution along x axis in a confinement potential. Comparing the active diffusion coefficients in the above two cases (in free space and in confinement), the validity of the ABP modeling implemented in MD simulations is confirmed. Possible reasons for the small deviation between the two diffusion coefficients are also discussed.
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Received: 25 May 2020
Revised: 22 June 2020
Accepted manuscript online: 15 July 2020
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PACS:
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05.40.-a
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(Fluctuation phenomena, random processes, noise, and Brownian motion)
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05.40.Jc
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(Brownian motion)
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83.10.Rs
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(Computer simulation of molecular and particle dynamics)
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| Fund: Project supported by Hong Kong RGC CRF, China (Grant No. C1018-17G), GRF, China (Grant No. 16228216), and Jiangsu University Foundation (Grant No. 20JDG20). |
Corresponding Authors:
Tiezheng Qian
E-mail: maqian@ust.hk
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Cite this article:
Liya Wang(王丽雅), Xinpeng Xu(徐新鹏), Zhigang Li(李志刚), Tiezheng Qian(钱铁铮) Active Brownian particles simulated in molecular dynamics 2020 Chin. Phys. B 29 090501
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| [1] |
Ramaswamy S 2010 Annu. Rev. Condens. Matter Phys. 1 323
|
| [2] |
Bechinger C, Di Leonardo R, Löwen H, Reichhardt C, Volpe G and Volpe G 2016 Rev. Mod. Phys. 88 045006
|
| [3] |
Zöttl A and Stark H 2016 J. Phys.: Condens. Matter 28 253001
|
| [4] |
Romanczuk P, Bär M, Ebeling W, Lindner B and Schimansky-Geier L 2012 Eur. Phys. J. Spec. Top. 202 1
|
| [5] |
Berg H C and Anderson R A 1973 Nature 245 380
|
| [6] |
Cisneros L H, Kessler J O, Ganguly S and Goldstein R E 2011 Phys. Rev. E 83 061907
|
| [7] |
Cates M E 2012 Rep. Prog. Phys. 75 042601
|
| [8] |
Harshey R M 2003 Annu. Rev. Microbiol. 57 249
|
| [9] |
Selmeczi D, Li L, Pedersen L I, Nrrelykke S, Hagedorn P H, Mosler S, Larsen N B, Cox E C and Flyvbjerg H 2008 Eur. Phys. J. Spec. Top. 157 1
|
| [10] |
Boedeker H U, Beta C, Frank T D and Bodenschatz E 2010 Europhys. Lett. 90 28005
|
| [11] |
Friedrich B M and Jülicher F 2007 Proc. Natl. Acad. Sci. USA 104 13256
|
| [12] |
Buttinoni I, Bialké J, Kümmel F, Löwen H, Bechinger C and Speck T 2013 Phys. Rev. Lett. 110 238301
|
| [13] |
Palacci J, Cottin-Bizonne C, Ybert C and Bocquet L 2010 Phys. Rev. Lett. 105 088304
|
| [14] |
Volpe G, Gigan S and Volpe G 2014 Am. J. Phys. 82 659
|
| [15] |
Marchetti M C, Joanny J F, Ramaswamy S, Liverpool T B, Prost J, Rao M and Simha R A 2013 Rev. Mod. Phys. 85 1143
|
| [16] |
Purcell E M 1977 Am. J. Phys. 45 3
|
| [17] |
Chen X, Yang X, Yang M and Zhang H 2015 EPL 111 54002
|
| [18] |
Lauga E 2016 Annu. Rev. Fluid Mech. 48 105
|
| [19] |
Furukawa A, Marenduzzo D and Cates M E 2014 Phys. Rev. E 90 022303
|
| [20] |
Lauga E and Powers T R 2009 Rep. Prog. Phys. 72 096601
|
| [21] |
Hernandez-Ortiz J P, Stoltz C G and Graham M D 2005 Phys. Rev. Lett. 95 204501
|
| [22] |
Elgeti J, Winkler R and Gompper G 2015 Rep. Prog. Phys. 78 056601
|
| [23] |
Baskaran A and Marchetti M C 2009 Proc. Natl. Acad. Sci. USA 106 15567
|
| [24] |
de Graaf J, Menke H, Mathijssen A J, Fabritius M, Holm C and Shendruk T N 2016 J. Chem. Phys. 144 134106
|
| [25] |
Howse J R, Jones R A, Ryan A J, Gough T, Vafabakhsh R and Golestanian R 2007 Phys. Rev. Lett. 99 048102
|
| [26] |
Ai B Q and Li F G 2017 Soft Matter 13 2536
|
| [27] |
Suma A, Gonnella G, Marenduzzo D and Orlandini E 2014 Europhys. Lett. 108 56004
|
| [28] |
Peruani F, Deutsch A and Bär M 2006 Phys. Rev. E 74 030904
|
| [29] |
Kudrolli A, Lumay G, Volfson D and Tsimring L S 2008 Phys. Rev. Lett. 100 058001
|
| [30] |
Gao T and Li Z 2017 Phys. Rev. Lett. 119 108002
|
| [31] |
Cates M and Tailleur J 2013 EPL 101 20010
|
| [32] |
Menzel A M 2015 Phy. Rep. 554 1
|
| [33] |
Stenhammar J, Tiribocchi A, Allen R J, Marenduzzo D and Cates M E 2013 Phys. Rev. Lett. 111 145702
|
| [34] |
Pototsky A and Stark H 2012 EPL 98 50004
|
| [35] |
Maggi C, Marconi U M B, Gnan N and Di Leonardo R 2015 Sci. Rep. 5 10742
|
| [36] |
Das S, Gompper G and Winkler R G 2018 New J. Phys. 20 015001
|
| [37] |
Volpe G and Volpe G 2013 Am. J. Phys. 81 224
|
| [38] |
Szamel G 2014 Phys. Rev. E 90 012111
|
| [39] |
Tailleur J and Cates M 2009 EPL 86 60002
|
| [40] |
Ye S, Liu P, Wei Z, Ye F, Yang M and Chen K 2020 Chin. Phys. B 29 058201
|
| [41] |
Tian W D, Gu Y, Guo Y K and Chen K 2017 Chin. Phys. B 26 100502
|
| [42] |
Howard M P, Gautam A, Panagiotopoulos A Z and Nikoubashman A 2016 Phys. Rev. Fluids 1 044203
|
| [43] |
Weeks J D, Chandler D and Andersen H C 1971 J. Chem. Phys. 54 5237
|
| [44] |
Plimpton S 1995 J. Comput. Phys. 117 1
|
| [45] |
Vicsek T, Czirók A, Ben-Jacob E, Cohen I and Shochet O 1995 Phys. Rev. Lett. 75 1226
|
| [46] |
Martens K, Angelani L, Di Leonardo R and Bocquet L 2012 Eur. Phys. J. E. 35 84
|
| [47] |
Ruiz-Franco J, Rovigatti L and Zaccarelli E 2018 Eur. Phys. J. E. 41 80
|
| [48] |
Espanol P and Warren P B 2017 J. Chem. Phys. 146 150901
|
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