Retrospective Notebook: This entry was not written on this day, but derived later from working notes I made that day.
My first ever biobrick simulator molecules created today! A single device, comprising a constitutive promoter, RBS, GFP coding sequence, a Terminator, and an RNAP. Later I would switch from coding sequences to 'translational units', as they are becoming the new standard in the registry, and the biobrick simulator has yet to incorporate mRNA.
RNAP's DNA binding function, and protein production, would not be implemented for a while yet.
I had believed I would be able to manage most of the interactions in world by the 'collision' event. It fires when two objects collide, and provides information about them. Unfortunately, it doesn't provide the right information for an object made up of multiple linked objects/prims (aka primitives), so I would end up building a workaround.
I had at this point realized the need to minimize the freefloating objects tendency to escape. The method I used was to continuously set the object's speed and rotation to zero, on a short timer inside the object, but this would turn out to be very glitchy, and would be improved as well.
Spent some time grappling with just what functionality a 'promoter' has, and determined that the opposite of a repressable promoter wouldn't actually be an activatable promoter and vice versa... it would be a 'repressable terminator', or 'activatable terminator'. (Since the function of a promoter is to permit RNA polymerase to bind, the opposite of that is to cause RNAP to unbind.)
An 'activatable terminator' very roughly correlates to the idea of an 'operator site', a repressor binding site removed from its promoter. I didn't believe there was any such thing as a 'repressable terminator' (a terminator that is functional by default, but can be disabled by the action of some protein?), until I stumbled across anti-terminators while doing unrelated research much later. The curious are encouraged to look up the proteins N Lambda and Q Lambda.
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