GAGSim3D is a Windows program that produces a highly controllable and repeatable 3D computer model of a 3D collagen/GAG matrix. Collagen fibrils are generated in a quasi-hexagonal packing scheme, using a “jitter” parameter to introduce deviations from perfect crystalline organization. A seed (random number) creates a unique collagen pattern and therefore a unique GAG distribution. Any given model can be repeated by using the same seed.
GAG length in the 3D geometric model is specified by an input distribution (mean ± standard deviation). D-period bands are labeled every 67 nm along the length of the collagen fibrils and their location is not dependent on bands of neighboring fibrils. GAGs are generated by first choosing a collagen fibril and D-period band, then projecting a GAG from the band at an angle such that the GAG linked to another D-period band on a neighboring fibril. This construction is consistent with the often hypothesized aggregation of GAG chains from adjacent fibrils to create interfibrillar crosslinks GAGs are not allowed to pass through the space occupied by other GAGs or collagen fibrils.
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