Journal
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
Volume 10, Issue 11, Pages 5054-5089Publisher
MDPI
DOI: 10.3390/ijms10115054
Keywords
polymer; simulation; Monte Carlo; primitive path; knot; entanglement; random packing; hard-sphere; melt; system size effect; polydispersity
Funding
- MRSEC Program of the National Science Foundation [DMR05-20415]
- SNF [IZ73Z0-128169]
- European Community [NMP3-CT-2005-016375 and NMP3-CT-2006-033339]
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We review the methodology, algorithmic implementation and performance characteristics of a hierarchical modeling scheme for the generation, equilibration and topological analysis of polymer systems at various levels of molecular description: from atomistic polyethylene samples to random packings of freely-jointed chains of tangent hard spheres of uniform size. Our analysis focuses on hitherto less discussed algorithmic details of the implementation of both, the Monte Carlo (MC) procedure for the system generation and equilibration, and a postprocessing step, where we identify the underlying topological structure of the simulated systems in the form of primitive paths. In order to demonstrate our arguments, we study how molecular length and packing density (volume fraction) affect the performance of the MC scheme built around chain-connectivity altering moves. In parallel, we quantify the effect of finite system size, of polydispersity, and of the definition of the number of entanglements (and related entanglement molecular weight) on the results about the primitive path network. Along these lines we approve main concepts which had been previously proposed in the literature.
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