Jumping from atom to atom? I have no idea, good question. I think the answer is not in a computer.
Currently computer based predictions work as is:
We know what certain conditions can cause, and therefore observe them, and the program will tell us, according to our knowledge, the probabilities of events with the present conditions.
The margin of error is big, as we don't know everything about these events, such as weather. Our knowledge grows, yes but we still have much to learn. We also can make mistakes in our observations.
EDIT:
We probably don't need to observe EVERY atom in the Universe to simulate it. We just need to know the parameters and conditions that define its behavior.
OBSERVATION!
Nothing to see here, move along.