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>There are many people trying to generate "good enough" simulations

Who? As a 3D software engineer moving into this space, this is extremely relevant to me. :-]

Pretty much anything in the "network biology" field will likely interest you, but here are a few sample articles (heavily biased toward people that I currently work with):

http://www.ncbi.nlm.nih.gov/pubmed/18344982

http://www.ncbi.nlm.nih.gov/pubmed/19337271

http://www.ncbi.nlm.nih.gov/pubmed/18462017

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