Unbiased rotational moves for rigid-body dynamics

被引:31
作者
Beard, DA
Schlick, T
机构
[1] NYU, Courant Inst Math Sci, Dept Chem, New York, NY 10012 USA
[2] Univ Washington, Dept Bioengn, Seattle, WA 98195 USA
[3] NYU, Howard Hughes Med Inst, New York, NY 10012 USA
关键词
D O I
10.1016/S0006-3495(03)74717-1
中图分类号
Q6 [生物物理学];
学科分类号
071011 ;
摘要
We introduce an unbiased protocol for performing rotational moves in rigid-body dynamics simulations. This approach - based on the analytic solution for the rotational equations of motion for an orthogonal coordinate system at constant angular velocity - removes deficiencies that have been largely ignored in Brownian dynamics simulations, namely errors for finite rotations that result from applying the noncommuting rotational matrices in an arbitrary order. Our algorithm should thus replace standard approaches to rotate local coordinate frames in Langevin and Brownian dynamics simulations.
引用
收藏
页码:2973 / 2976
页数:4
相关论文
共 11 条
[1]   A BROWNIAN DYNAMICS ALGORITHM FOR ARBITRARY RIGID BODIES - APPLICATION TO POLARIZED DYNAMIC LIGHT-SCATTERING [J].
ALLISON, SA .
MACROMOLECULES, 1991, 24 (02) :530-536
[2]   Computational modeling predicts the structure and dynamics of chromatin fiber [J].
Beard, DA ;
Schlick, T .
STRUCTURE, 2001, 9 (02) :105-114
[3]   Brownian dynamics simulations of supercoiled DNA with bent sequences [J].
Chirico, G ;
Langowski, J .
BIOPHYSICAL JOURNAL, 1996, 71 (02) :955-971
[4]   HYDRODYNAMIC PROPERTIES OF COMPLEX, RIGID, BIOLOGICAL MACROMOLECULES - THEORY AND APPLICATIONS [J].
DELATORRE, JG ;
BLOOMFIELD, VA .
QUARTERLY REVIEWS OF BIOPHYSICS, 1981, 14 (01) :81-139
[5]   BROWNIAN DYNAMICS WITH HYDRODYNAMIC INTERACTIONS [J].
ERMAK, DL ;
MCCAMMON, JA .
JOURNAL OF CHEMICAL PHYSICS, 1978, 69 (04) :1352-1360
[6]   Brownian dynamics simulation of rigid particles of arbitrary shape in external fields [J].
Fernandes, MX ;
de la Torre, JG .
BIOPHYSICAL JOURNAL, 2002, 83 (06) :3039-3048
[7]  
Goldstein H., 2002, CLASSICAL MECH, P134
[8]   Macroscopic modeling and simulations of supercoiled DNA with bound proteins [J].
Huang, J ;
Schlick, T .
JOURNAL OF CHEMICAL PHYSICS, 2002, 117 (18) :8573-8586
[9]   Combined wormlike-chain and bead model for dynamic simulations of long linear DNA [J].
Jian, HM ;
Vologodskii, AV ;
Schlick, T .
JOURNAL OF COMPUTATIONAL PHYSICS, 1997, 136 (01) :168-179
[10]   A Brownian dynamics program for the simulation of linear and circular DNA and other wormlike chain polyelectrolytes [J].
Klenin, K ;
Merlitz, H ;
Langowski, J .
BIOPHYSICAL JOURNAL, 1998, 74 (02) :780-788