Is it possible to execute c# program in background

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I am writing a simulation in C# (VS 2002) preliminary estimates show that the program will run for 3-4 weeks. When the prototype runs it takes over 99% of the CPU. I would like if possible for the simulation to use limited CPU resources when the PC is in use and take over all the available resources when I am not using the PC. What are my options?
Thanks
Alex

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