Recent observational techniques based upon confocal microscopy make it possible to observe cells at a scale that has never been probed before: the mesoscopic scale. In the eukaryotic cell nucleus, many objects demonstrating phenomena occurring at this scale, such as nuclear bodies, are current subjects of investigations. But from a modeling perspective, this scale has not been widely explored, and hence there is a lack of suitable models for such studies. By reviewing higher and lower scale modeling techniques, we analyze their relevance in the context of mesoscale phenomena. We emphasize important characteristics that should be included in a mesoscopic model: an explicit continuous three-dimensional space with discrete simplified molecules that still have the characteristics of steric volume exclusion and realistic distant interaction forces. Then we present 3DSPI, a model dedicated to studies of nuclear bodies based on a simple formalism inspired from molecular dynamics and coarse-grained models: particles interacting through a potential energy function and driven by an overdamped Langevin equation. Finally, we present the features expected to be included in the model, pointing out the difficulties that might arise.