Methods for modeling cytoskeletal and DNA filaments

Steven S Andrews
2014 Physical Biology  
Close encounters with DNA C Maffeo, J Yoo, J Comer et al. -Modeling meiotic chromosome pairing: nuclear envelope attachment, telomere-led active random motion, and anomalous diffusion Wallace F Marshall and Jennifer C Fung -Recent citations Multi-scale tracking reveals scaledependent chromatin dynamics after DNA damage Judith Miné-Hattab et al -A coarse-grained computational model of the nuclear pore complex predicts Phe-Gly nucleoporin dynamics Joan Pulupa et al -Multisite Phosphorylation
more » ... ates the T Cell Receptor -Chain Potency but not the Switchlike Response Himadri Mukhopadhyay et al -This content was downloaded from IP address on 01/03 Abstract This review summarizes the models that researchers use to represent the conformations and dynamics of cytoskeletal and DNA filaments. It focuses on models that address individual filaments in continuous space. Conformation models include the freely jointed, Gaussian, angle-biased chain (ABC), and wormlike chain (WLC) models, of which the first three bend at discrete joints and the last bends continuously. Predictions from the WLC model generally agree well with experiment. Dynamics models include the Rouse, Zimm, stiff rod, dynamic WLC, and reptation models, of which the first four apply to isolated filaments and the last to entangled filaments. Experiments show that the dynamic WLC and reptation models are most accurate. They also show that biological filaments typically experience strong hydrodynamic coupling and/or constrained motion. Computer simulation methods that address filament dynamics typically compute filament segment velocities from local forces using the Langevin equation and then integrate these velocities with explicit or implicit methods; the former are more versatile and the latter are more efficient. Much remains to be discovered in biological filament modeling. In particular, filament dynamics in living cells are not well understood, and current computational methods are too slow and not sufficiently versatile. Although primarily a review, this paper also presents new statistical calculations for the ABC and WLC models. Additionally, it corrects several discrepancies in the literature about bending and torsional persistence length definitions, and their relations to flexural and torsional rigidities.
doi:10.1088/1478-3975/11/1/011001 pmid:24476634 fatcat:vku2tlbna5czhpwrx6ailu4tju