Spatial particle-based methods differ from the methods described above by their explicit representation of space.
One example of a particle-based simulator that allows for a representation of cellular compartments is SRSim. SRSim is integrated in the LAMMPS molecular dynamics simulator and allows the user to specify the model in BNGL. SRSim allows users to specify the geometry of the particles in the simulation, as well as interaction sites. It is therefore especially good at simulating the assembly and structure of complex biomolecular complexes, as evidenced by a recent model of the inner kinetochore.
MCell allows individual molecules to be traced in arbitrarily complex geometric environments which are defined by the user. This allows for simulations of biomolecules in realistic reconstructions of living cells, including cells with complex geometries like those of neurons. The reaction compartment is a reconstruction of a dendritic spine.
MCell uses an ad-hoc formalism within MCell itself to specify a multi-state model: In MCell, it is possible to assign "slots" to any molecular species.  Each slot stands for a particular modification, and any number of slots can be assigned to a molecule.  Each slot can be occupied by a particular state. The states are not necessarily binary. For instance, a slot describing binding of a particular ligand to a protein of interest could take the states "unbound", "partially bound",  and "fully bound".
The slot-and-state syntax in MCell can also be used to model multimeric proteins or macromolecular complexes. When used in this way, a slot is a placeholder for a subunit or a molecular component of a complex, and the state of the slot will indicate whether a specific protein component is absent or present in the complex. A way to think about this is that MCell macromolecules can have several dimensions: A "state dimension" and one or more "spatial dimensions". The "state dimension" is used to describe the multiple possible states making up a multi-state protein, while the spatial dimension(s) describe topological relationships between neighboring subunits or members of a macromolecular complex. One drawback of this method for representing protein complexes, compared to Meredys, is that MCell does not allow for the diffusion of complexes, and hence, of multi-state molecules. This can in some cases be circumvented by adjusting the diffusion constants of ligands that interact with the complex, by using checkpointing functions or by combining simulations at different levels.