Eric writes:

"I like chemistry as a medium, because the state space itself supports a lot of 
complexity, and the temporal variability of reactions, plus the fact that 
catalytic relations exist, offer large separations of timescales that can be 
used to fill functional classes like memories."  

One could imagine coupling a physical simulation to a search procedure for 
functional behaviors like memories and doorways.   The detection combinatorics 
would be challenging, assuming the physical simulation were possible at 
sufficient fidelity, but perhaps could be constrained by virtue of spatial 
locality.   

I don't know much about coarse-graining organic chemistry simulators.  For 
comparison, with molecular dynamics a billion atoms is possible (on a budget of 
a few megawatts), but not for more than tens of nanoseconds.   I've found game 
physics engines like Bullet Physics are nice for coarse-grained models because 
they are fast (optimized to graphics processors) and easy to interleave control 
or detection logic.  However, they couldn't (without more work) decompose the 
space across memory domains of a cluster. 

Marcus


 
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