We propose a mesh-free and discrete (particle-based) multi-physics approach for modelling the hydrodynamics in flexible biological valves. In the first part of this study, the method is successfully validated against both traditional modelling techniques and experimental data. In the second part, it is further developed to account for the formation of solid aggregates in the flow and at the membrane surface. Simulations of various types of aggregates highlight the main benefits of discrete multi-physics and indicate the potential of this approach for coupling the hydrodynamics with phenomena such as clotting and calcification in biological valves.