“I can use the computer to design a PCR experiment from start to finish, and then simulate that experiment and see simulated results.”
Why model a PCR experiment? It takes less time to run one and then you get real data.
When I started my real job many years ago some chem engineer from another department who gave a journal club on modeling a biological synthesis reaction. He came up to me later in the day and asked what I thought. I told him modeling was stupid and useless an explained why. Turned out his work focused on modeling such reactions. Awkward.
There are a couple of reasons. One is that, in the modeling, the software can look for DNA sequence homologies somewhere else in the genome, that I would not have been looking for while designing the primers (since the primers are specific to the sequence I want to amplify). Homologies can cause the formation of unwanted PCR products, complicating the experimental results. Another is so that I can see the sizes of the products--a quality control check of my design, basically. PCR can be an extremely tricky reaction to run, so I like to spend time vetting as much of the experimental design as possible before I spend time and money ordering primers, running optimization experiments, etc.
When I was a new and inexperienced graduate student, I couldn't get a PCR reaction to work for the life of me. By the time I graduated, I almost never had a PCR reaction fail.