外场中任意形状刚性粒子的布朗动力学模拟
Brownian dynamics simulation of rigid particles of arbitrary shape in external fields.
作者信息
Fernandes Miguel X, de la Torre José García
机构信息
Departamento de Química-Física, Facultad de Química, Universidad de Murcia, Campus de Espinardo, 30071 Murcia, Spain.
出版信息
Biophys J. 2002 Dec;83(6):3039-48. doi: 10.1016/S0006-3495(02)75309-5.
Abstract
We have developed a Brownian dynamics simulation algorithm to generate Brownian trajectories of an isolated, rigid particle of arbitrary shape in the presence of electric fields or any other external agents. Starting from the generalized diffusion tensor, which can be calculated with the existing HYDRO software, the new program BROWNRIG (including a case-specific subprogram for the external agent) carries out a simulation that is analyzed later to extract the observable dynamic properties. We provide a variety of examples of utilization of this method, which serve as tests of its performance, and also illustrate its applicability. Examples include free diffusion, transport in an electric field, and diffusion in a restricting environment.
摘要
我们开发了一种布朗动力学模拟算法，用于在存在电场或任何其他外部因素的情况下，生成任意形状的孤立刚性粒子的布朗轨迹。从可以使用现有HYDRO软件计算的广义扩散张量开始，新程序BROWNRIG（包括针对外部因素的特定案例子程序）进行模拟，随后对模拟结果进行分析以提取可观测的动态特性。我们提供了该方法的各种应用示例，这些示例既作为其性能的测试，也说明了其适用性。示例包括自由扩散、电场中的传输以及受限环境中的扩散。
相似文献
1
Brownian dynamics simulation of rigid particles of arbitrary shape in external fields.
Biophys J. 2002 Dec;83(6):3039-48. doi: 10.1016/S0006-3495(02)75309-5.
2
Dynamic electrophoresis of charged colloids in an oscillating electric field.
Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Jun;89(6):062317. doi: 10.1103/PhysRevE.89.062317. Epub 2014 Jun 26.
3
Tunable diffusion of magnetic particles in a quasi-one-dimensional channel.
Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Jan;87(1):012307. doi: 10.1103/PhysRevE.87.012307. Epub 2013 Jan 14.
4
Multiscale dissipative particle dynamics.
Philos Trans A Math Phys Eng Sci. 2002 Mar 15;360(1792):317-31. doi: 10.1098/rsta.2001.0956.
5
Dynamic electro-optic properties of macromolecules and nanoparticles in solution: a review of computational and simulation methodologies.
Colloids Surf B Biointerfaces. 2007 Apr 15;56(1-2):4-15. doi: 10.1016/j.colsurfb.2006.10.007. Epub 2006 Oct 12.
6
Electromagnetic field of a charge moving in a cold magnetized plasma.
Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Jan;87(1):013109. doi: 10.1103/PhysRevE.87.013109. Epub 2013 Jan 30.
7
Brownian dynamics simulations with hard-body interactions: spherical particles.
J Chem Phys. 2012 Oct 28;137(16):164108. doi: 10.1063/1.4761827.
8
Chemical reaction dynamics within anisotropic solvents in time-dependent fields.
J Chem Phys. 2005 Jan 1;122(1):14509. doi: 10.1063/1.1829252.
9
Lattice Boltzmann equation for relativistic quantum mechanics.
Philos Trans A Math Phys Eng Sci. 2002 Mar 15;360(1792):429-36. doi: 10.1098/rsta.2001.0937.
10
Self-propelled Brownian spinning top: dynamics of a biaxial swimmer at low Reynolds numbers.
Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Feb;85(2 Pt 1):021406. doi: 10.1103/PhysRevE.85.021406. Epub 2012 Feb 21.
引用本文的文献
1
Modelling red blood cell optical trapping by machine learning improved geometrical optics calculations.
Biomed Opt Express. 2023 Jun 27;14(7):3748-3762. doi: 10.1364/BOE.488931. eCollection 2023 Jul 1.
2
Constant-pH Brownian Dynamics Simulations of a Protein near a Charged Surface.
ACS Omega. 2020 Nov 12;5(46):30282-30298. doi: 10.1021/acsomega.0c04817. eCollection 2020 Nov 24.
3
Effects of Hydrodynamic Interactions on the Near-Surface Diffusion of Spheroidal Molecules.
ACS Omega. 2019 Oct 3;4(16):17016-17030. doi: 10.1021/acsomega.9b02618. eCollection 2019 Oct 15.
4
Forced Unfolding Mechanism of Bacteriorhodopsin as Revealed by Coarse-Grained Molecular Dynamics.
Biophys J. 2016 Nov 15;111(10):2086-2098. doi: 10.1016/j.bpj.2016.09.051.
5
Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm.
Elife. 2016 Nov 1;5:e19274. doi: 10.7554/eLife.19274.
6
Brownian dynamics of subunit addition-loss kinetics and thermodynamics in linear polymer self-assembly.
Biophys J. 2013 Dec 3;105(11):2528-40. doi: 10.1016/j.bpj.2013.10.009.
7
Diffusion in crowded biological environments: applications of Brownian dynamics.
BMC Biophys. 2011 Mar 2;4:3. doi: 10.1186/2046-1682-4-3.
8
Brownian dynamics study of the association between the 70S ribosome and elongation factor G.
Biopolymers. 2011 Sep;95(9):616-27. doi: 10.1002/bip.21619. Epub 2011 Mar 10.
9
Browndye: A Software Package for Brownian Dynamics.
Comput Phys Commun. 2010 Nov 1;181(11):1896-1905. doi: 10.1016/j.cpc.2010.07.022.
10
Effects of macromolecular crowding on intracellular diffusion from a single particle perspective.
Biophys Rev. 2010 Feb;2(1):39-53. doi: 10.1007/s12551-010-0029-0. Epub 2010 Feb 6.
本文引用的文献
1
Building hydrodynamic bead-shell models for rigid bioparticles of arbitrary shape.
Biophys Chem. 2001 Dec 25;94(3):265-74. doi: 10.1016/s0301-4622(01)00244-7.
2
Boundary element modeling of biomolecular transport.
Biophys Chem. 2001 Nov 28;93(2-3):197-213. doi: 10.1016/s0301-4622(01)00221-6.
3
Hydration from hydrodynamics. General considerations and applications of bead modelling to globular proteins.
Biophys Chem. 2001 Nov 28;93(2-3):159-70. doi: 10.1016/s0301-4622(01)00218-6.
4
An analytical solution to the problem of the orientation of rigid particles by planar obstacles. Application to membrane systems and to the calculation of dipolar couplings in protein NMR spectroscopy.
J Am Chem Soc. 2001 Dec 5;123(48):12037-47. doi: 10.1021/ja011361x.
5
HYDROMIC: prediction of hydrodynamic properties of rigid macromolecular structures obtained from electron microscopy images.
Eur Biophys J. 2001 Oct;30(6):457-62. doi: 10.1007/s002490100176.
6
HYDRONMR: prediction of NMR relaxation of globular proteins from atomic-level structures and hydrodynamic calculations.
J Magn Reson. 2000 Nov;147(1):138-46. doi: 10.1006/jmre.2000.2170.
7
Calculation of hydrodynamic properties of globular proteins from their atomic-level structure.
Biophys J. 2000 Feb;78(2):719-30. doi: 10.1016/S0006-3495(00)76630-6.
8
Hydrodynamic properties of rigid particles: comparison of different modeling and computational procedures.
Biophys J. 1999 Jun;76(6):3044-57. doi: 10.1016/S0006-3495(99)77457-6.
9
Calculation of NMR relaxation, covolume, and scattering-related properties of bead models using the SOLPRO computer program.
Eur Biophys J. 1999;28(2):119-32. doi: 10.1007/s002490050191.
10
SOLPRO: theory and computer program for the prediction of SOLution PROperties of rigid macromolecules and bioparticles.
Eur Biophys J. 1997;25(5-6):361-72. doi: 10.1007/s002490050049.
Zotero 插件