Here's one interpretation of your question, which you may or may not have intended, but for which I have an answer.
Computers are obviously real physical devices and therefore can be modeled by the laws of physics. But we don't use the laws of physics that would be needed to describe a real computer as a model of computation because it's too complex. To make a model of computation, we define something like a Turing machine that is simple enough to be mathematically tractable. However, now we've untethered the model from the physical world, because we don't say how the Turing machine is built or what forces drive it to run.
So can we devise some simple models that capture "computation", but whose fundamental rules are physical in nature? My answer to this would be to check out the Feynman Lectures on Computation: http://www.amazon.com/Feynman-Lectures-Computation-Richard-P/dp/0738202967
He talks about a lot of different simple physical systems that carry out a computation. For example, there is the billiard ball model of Fredkin and Toffoli (http://en.wikipedia.org/wiki/Billiard-ball_computer), where the point was to explicitly account for energy requirements and to design a computer that can run for arbitrarily many steps for arbitrarily little energy. In particular, the chapter on reversible computing has a lot of these kinds of examples.
We think about this issue a lot in my lab. For example, we've done some work on what it means for chemical reaction networks to do computation: http://www.dna.caltech.edu/DNAresearch_publications.html#DeterministicCRNs and http://www.dna.caltech.edu/DNAresearch_publications.html#ComputationalCRNs
We also think about how seeded crystal formation can carry out computation: http://www.dna.caltech.edu/DNAresearch_publications.html#Simulations as well as actually trying to make it happen experimentally: http://www.dna.caltech.edu/DNAresearch_publications.html#OrigamiSeed, and some other work based on computing using a physical phenomenon called DNA strand displacement: http://www.dna.caltech.edu/DNAresearch_publications.html#DNALogicCircuits