  Unlike computation or the numerical analysis of differential equations,
simulation does not have a well established conceptual and mathematical
foundation. Simulation is an arguable unique union of modeling and computation.
However, simulation also qualifies as a separate species of system
representation with its own motivations, characteristics, and implications.
This work outlines how simulation can be rooted in mathematics and shows which
properties some of the elements of such a mathematical framework has. The
properties of simulation are described and analyzed in terms of properties of
dynamical systems. It is shown how and why a simulation produces emergent
behavior and why the analysis of the dynamics of the system being simulated
always is an analysis of emergent phenomena. A notion of a universal simulator
and the definition of simulatability is proposed. This allows a description of
conditions under which simulations can distribute update functions over system
components, thereby determining simulatability. The connection between the
notion of simulatability and the notion of computability is defined and the
concepts are distinguished. The basis of practical detection methods for
determining effectively non-simulatable systems in practice is presented. The
conceptual framework is illustrated through examples from molecular
self-assembly end engineering.
