I have a hard time trying to think of the nature of the correspondence between these things and bits for a simulation besides positions of molecules, and I'm not sure in what context those bits are specified. A little help?

What you do is write a program that generates a set of particles and places them into the simulated cell, such that the resulting cell is viable and functionally equivalent to the original cell. Take the program and count its length in bits. If you haven't programmed before you may not have much intuition about this. In that case think of it this way: if you have to describe the shape/internal structure/distributions (ETA: and structures) of molecules, in natural language and/or mathematical notation, in sufficient detail that someone else could create a physics simulation of the cell based on your description, how many bits would that take, and what fraction of those would be taken up by the DNA sequences?