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Sorry for the late reply. My primary software package is Abaqus Explicit, both structural and FSI (coupled Eularian Lagrangian, no messing around!). I think a couple of groups do model their frames (specialized had a frame where the decal was actually the stress contours, again this was done in abaqus!), BUT i dont think its effective (probably making more enemies than job opportunities at this point...). Carbon fiber is a real pain to model (I should know, my girlfriend did her PhD on modelling carbon fiber, makes interesting dinner table talk...), especially thin walled stuff with complex geometries, like bike frames. You could say the material is orthotropic and simplify your model, but that is a massive limitation. Furthermore, i seriously doubt bicycle companies use FEA for robust design optimisation (my area), which could be used to make some light frames!
Having said that, CFD is commonly used to good effect. One of my old lecturers was actually contracted by the british olympic TT team to work out what the most aerodynamic bolt shape is for the wheels.
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Isotropic
I don't think that's strictly true. There's a lot of FEA being done by most of the big manufacturers, particularly with composite frames.
The link to the original work on this is worth a read - https://janheine.wordpress.com/2014/12/31/the-biomechanics-of-planing/
Which code(s) are you using?