The Mullins-Sekerka problem, also called two-sided Hele-Shaw flow, arises in modeling a binary material with two stable concentration phases. A coarsening process occurs, and large particles grow while smaller particles eventually dissolve. Single particles become spherical. This process is described by evolving harmonic functions within the two phases with the moving interface driven by the jump in the normal derivatives of the harmonic functions at the interface. The harmonic functions are continuous across the interface, taking on values equal to the mean curvature of the interface. This dissertation reformulates the three-dimensional problem as one on the two-dimensional interface by using boundary integrals. A semi-implicit scheme to solve the free boundary problem numerically is implemented. Numerical analysis tasks include discretizing surfaces, overcoming node bunching, and dealing with topology change in a toroidal particle. A particle (node)-cluster technique is developed with the aim of alleviating excessive run time caused by filling the dense matrix used in solving a system of linear equations.