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System Dynamics is nothing more than a palatable front-end to a set of Differential-Algebraic Equations (DAEs): i.e. a set of differential equations, with a set of subsidiary algebraic equations for defining intermediate and rate quantities. Each compartment is a state variable, and each flow contributes to the rate-of-change expression for the associated state variable(s). Therefore, implementing a published differential-equation model in Simile is straightforward: you simply add one compartment for every state variable, give each compartment a single inflow, and enter the differential equation as the flow expression, having first added the required influence arrows.
Since Simile can use simple Euler integration for numerically solving its set of differential equations, handling sets of difference equations is no different: the only difference is when you come to run the model, when you set the time step to 1 rather than some small value.