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UML Modeling of Finite State Machines and Molecular Machines

Biological systems at the molecular level are composed of hierarchically structured objects that continuously interact and influence each other by directly altering each others' composition. The software in many technology systems is hierarchically constructed using objects that pass messages to each other which then trigger transitions in finite state machines. On the surface these appear to be quite different interaction mechanisms. This paper takes a detailed look at these two mechanisms, and, using concepts from UML with models executed using the Xholon framework, argues that these are just points on a continuum. A progression of UML models are developed, as a starting point for a future more comprehensive exploration of this space that encompasses both finite state machines and biological machinery at the molecular level.