Deformation Theory of Matrix Factorizations and F-Terms in the Boundary Changing Sector

We extend the deformation theory algorithm of matrix factorizations to systems with more than one D-brane. The obstructions to the deformations are F-term equations which can be integrated to an effective superpotential. We demonstrate the power of this formalism for several examples of minimal models with two or three D-branes. These are realistic toy examples for systems with multiple D-branes in Calabi-Yau threefolds since both classes of models have obstructed open moduli.