You seem to have realised at least some of the following, but I shall state it for the record.
Matlab is an interpreted language. I think modern versions have a JIT compiler and some kind of bytecode, but the importance of accuracy means they don't tend to get too tricky.
Some things that may allow you to utilize more of your computer's resources:
Use builtin, library and vectorised operations wherever you can, these tend to be written in C/java/fortran and are highly optimized:
A.*B
is far faster than doing it with a for loop.
Unroll tight loops (any with <10 instructions) if you can -- manually make it do several operations before looping, even eliminate the loop entirely if it's a set small number of instructions. The JIT may take care of this, but it helped on the last version of matlab I was using. You may be able to refactor or vectorize your equations somewhat so that more calculations can be done before you need to use them, sometimes even adding steps/temporary variables can help if it makes it more parallelizable (and memory bandwidth isn't the issue at hand).
Pre-allocate memory where you can.It can be hard to tell with a language like matlab when you are allocating memory, but if you know ahead of time how big a vector/matrix is going to be, pre-set it to a zero array of that size before using it. Whatever you do, avoid incrementally increasing its size in a loop. (again, the jit can sometimes fix this for you, but don't rely on it).
Factorise out and pre-calculate invariants. Explicitly set performance intensive loops to certain lengths if you know what they will be rather than calculating as you go or using a while loop. If there is a number you are calculating repeatedly that is the same or periodic in some way, see if you can pre-calculate it.
The most important part is probably the first (built in functions and vectorization) which will tend to overwhelm the effect of the others. Also your algorithmic efficiency will in turn overwhelm effects from this. There is almost always a way of making an algorithm (asymptotically) faster, or making a tradeoff between time and space which is in your favour. The only question is whether the amount of effort required on your part is worth it.