well one thing I can think of off the top of my head is to goto the task manager, matlab process, and set priority as high or realtime, and assign an affinity to the process. although I do not recommend it. Windows is multitasking, and will assign as much cpu as required to the process (the process uses just as much cpu as it needs). and windows is not real time, so the statistics shown in windows task manager may not be "current".
If simulation speed is what's bothering you, you can code your algorithm in c (or cpp) as opposed to a matlab script, dump the result into a file, and read those files into matlab for plotting and stuff. alternatively you can interface your c code to matlab (google "mex").
hope this helps.