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Brownian Dynamics of Segmented Biopolymers: A Formal Theory and Numerical Simulations
Author(s) -
Nalum Naess Stine,
Elgsaeter Arnljot
Publication year - 2002
Publication title -
macromolecular theory and simulations
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.37
H-Index - 56
eISSN - 1521-3919
pISSN - 1022-1344
DOI - 10.1002/1521-3919(20021101)11:8<913::aid-mats913>3.0.co;2-r
Subject(s) - holonomic constraints , brownian dynamics , statistical physics , brownian motion , holonomic , classical mechanics , constraint (computer aided design) , metric (unit) , physics , mathematics , geometry , operations management , quantum mechanics , economics
The motivation and basic concepts of Brownian dynamics of segmented biopolymers using spatial coordinates rather than the standard bead–rod–spring polymer model are well accounted for in the literature. Here we report on recent advances in the theoretical description of polymer chains consisting of rigid subunits with arbitrary shape. The new results include a more generalized analysis of the metric force and the differences between biopolymers linked by springs or holonomic constraints, respectively. We also discuss numerical algorithms at different levels of coordinate contraction. Finally, in order to test the validity of the formal theory and numerical algorithms a detailed example is presented. For two‐needle chains with holonomic constraint and in thermodynamic equilibrium we find perfect agreement between theory and results from the numerical simulations.