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An Analytic Toolbox for Simulated Filament Networks

Published online by Cambridge University Press:  11 September 2014

Ronald J. Pandolfi,
Lauren Edwards and
Linda S. Hirst
Ronald J. Pandolfi
Affiliation:
Dept. of Physics, School of Natural Sciences, University of California, Merced, California 95343, USA
Lauren Edwards
Affiliation:
Dept. of Physics, School of Natural Sciences, University of California, Merced, California 95343, USA
Linda S. Hirst
Affiliation:
Dept. of Physics, School of Natural Sciences, University of California, Merced, California 95343, USA
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Abstract

Semi-flexible polymer networks generate a diverse family of structures. The network generating behaviors of specific semi-flexible biological filaments are well known (i.e. F-actin, microtubules, DNA etc.), however recent developments in tunable synthetic filaments extend the range of accessible structures. A similarly tunable model was developed using the molecular dynamics platform NAMD to provide a guide for generating synthetic filament networks. Structural characteristics of simulated networks may be quantitatively examined using connectivity analysis, radial pair distribution functions and scaling analysis. These methods provide a basis to calculate morphological properties, including mesh size, packing order, network connectivity, avg. cluster size, filaments per bundle, and space-filling dimensionality. An analytic toolset for describing the structure of filament networks is thus provided by detailing these methods.

Keywords

polymersimulationbiomimetic (assembly)

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