Ask HN: State of the Art in Simulated Cells?

If I took a different thesis topic, I had two options to choose between, I'd have worked on DNA simulation at the university rather than a documentation system at a company. That was...many...years ago but I can't quite let go of the thought.

I've taken a virology course on Coursera which was fascinating, they're tiny molecular machines and last weekend I began to doodle on a kind of hierarchical simulation architecture to try and simulate a cell or even a C. Elegans, but I have only a basic grasp of computational biology and not even that in computational chemistry. I've read somewhere that we can simulate a elegans worm but it's at like 0.5fps.

Does anyone have books or articles to recommend to get me started a bit more properly?