Bond between sphere particles in a multi-sphere particle

The current multi-sphere model assumes a rigid body (non-deformable) for each multi-sphere particle. Is it possible to extend this multi-sphere model as to include bond between sphere particles within multi-sphere body, so that the multi-sphere particle can deform upon impact?

Plus, I've observed some strange behaviors of multi-sphere particle motions when periodic boundaries are used. For example, when I insert multi-sphere particles (with gravity) into a hopper, and assign periodic boundaries in the direction normal to the cross-section, lots of particles strangely appear on the very top of the vertical boundary after a while (see the attached figure). So I just want to confirm if there is similar user experience that utilized both multi-sphere model and periodic boundaries?