A Brownian dynamics algorithm for colloids in curved manifolds

被引:34
作者
Castro-Villarreal, Pavel [1 ]
Villada-Balbuena, Alejandro [2 ]
Miguel Mendez-Alcaraz, Jose [2 ]
Castaneda-Priego, Ramon [3 ]
Estrada-Jimenez, Sendic [1 ]
机构
[1] Univ Autonoma Chiapas, Ctr Estudios Fis & Matemat Basicas & Aplicadas, Tuxtla Gutierrez 29050, Chiapas, Mexico
[2] CINVESTAV, Dept Fis, Mexico City 07360, DF, Mexico
[3] Univ Guanajuato, Dept Ingn Fis, Div Ciencias & Ingn, Guanajuato 37150, Mexico
关键词
SELF-DIFFUSION; SIMULATIONS; PROTEIN; MOTION;
D O I
10.1063/1.4881060
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
The many-particle Langevin equation, written in local coordinates, is used to derive a Brownian dynamics simulation algorithm to study the dynamics of colloids moving on curved manifolds. The predictions of the resulting algorithm for the particular case of free particles diffusing along a circle and on a sphere are tested against analytical results, as well as with simulation data obtained by means of the standard Brownian dynamics algorithm developed by Ermak and McCammon [J. Chem. Phys. 69, 1352 (1978)] using explicitly a confining external field. The latter method allows constraining the particles to move in regions very tightly, emulating the diffusion on the manifold. Additionally, the proposed algorithm is applied to strong correlated systems, namely, paramagnetic colloids along a circle and soft colloids on a sphere, to illustrate its applicability to systems made up of interacting particles. (C) 2014 AIP Publishing LLC.
引用
收藏
页数:10
相关论文
共 52 条
[1]   DIFFUSION OF MOLECULES ON BIOLOGICAL-MEMBRANES OF NONPLANAR FORM - A THEORETICAL-STUDY [J].
AIZENBUD, BM ;
GERSHON, ND .
BIOPHYSICAL JOURNAL, 1982, 38 (03) :287-293
[2]  
Alberts B., 2002, The shape and structure of proteins, Vfourth, DOI 10.1093/aob/mcg023
[3]   SELF-DIFFUSION IN BICONTINUOUS CUBIC PHASES, L3 PHASES, AND MICROEMULSIONS [J].
ANDERSON, DM ;
WENNERSTROM, H .
JOURNAL OF PHYSICAL CHEMISTRY, 1990, 94 (24) :8683-8694
[4]  
[Anonymous], 2000, CLASSICAL MECH
[5]  
[Anonymous], 2004, The geometry of physics
[6]   Spatial curvature effects on molecular transport by diffusion [J].
Balakrishnan, J .
PHYSICAL REVIEW E, 2000, 61 (04) :4648-4651
[7]   Algorithms for Brownian dynamics computer simulations: Multivariable case [J].
Branka, AC ;
Heyes, DM .
PHYSICAL REVIEW E, 1999, 60 (02) :2381-2387
[8]   Asymmetry in colloidal diffusion near a rigid wall [J].
Carbajal-Tinoco, Mauricio D. ;
Lopez-Fernandez, Ricardo ;
Arauz-Lara, Jose Luis .
PHYSICAL REVIEW LETTERS, 2007, 99 (13)
[9]   Algorithm for generating a Brownian motion on a sphere [J].
Carlsson, Tobias ;
Ekholm, Tobias ;
Elvingson, Christer .
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL, 2010, 43 (50)
[10]   Diffusion in a quasi-one-dimensional system on a periodic substrate [J].
Carvalho, J. C. N. ;
Nelissen, K. ;
Ferreira, W. P. ;
Farias, G. A. ;
Peeters, F. M. .
PHYSICAL REVIEW E, 2012, 85 (02)