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The primary goal of this thesis is to explore the capabilities of MOOSE (Multiphysics Object Oriented Simulation Environment) and LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) and their potential to be coupled in order to simulate multiphase flow in a Hele-Shaw cell. After formulating the Darcy-Richards multi- phase flow equations for a finite element method application, I synthesized the nec- essary particle-particle interactions from existing literature and implemented them in LAMMPS. In addition, I created a parallelized C++ program to calculate the particle packing field through the heavy employ of OpenMP. With the conclusion of extensive testing suites for both LAMMPS and MOOSE, I developed a python program which was used to mesh LAMMPS and MOOSE by acting as a translation and book-keeping program. While the coupling scheme appears to function properly in test cases, it fails to capture the full impact of the particles on the fluid system and thus allows for penetration of the invading fluid into regions which ought to remain unsaturated.