We present a model of multithreaded computation with an emphasis on estimating parallelism overheads of programs written for modern many-core architectures. We establish a Graham-Brent theorem so as to estimate execution time of programs running on a given number of streaming multiprocessors. We evaluate the benefits of our model with fundamental algorithms from scientific computing. For two case studies, our model is used to minimize parallelism overheads by determining an appropriate value range for a given program parameter. For the others, our model is used to compare different algorithms solving the same problem. In each case, the studied algorithms were implemented and the results of their experimental comparison are coherent with the theoretical analysis based on our model.