This paper focuses on the challenges of modeling cyber-physical systems (CPSs) that arise from the intrinsic heterogeneity, concurrency, and sensitivity to timing of such systems. It uses a portion of an aircraft vehicle management system (VMS), specifically the fuel management subsystem, to illustrate the challenges, and then discusses technologies that at least partially address the challenges. Specific technologies described include hybrid system modeling and simulation, concurrent and heterogeneous models of computation, the use of domain-specific ontologies to enhance modularity, and the joint modeling of functionality and implementation architectures.