How do you simulate a supercapacitor in PLECS? or in MATLAB for that matter
Any capacitor has series inductance and resistance, these can be found in most capacitor datasheets. If your modeling it mathematically or graphically make sure you model the parasitics. 

There is also a paper (Modeling, Evaluation and Simulation of a
Supercapacitor Module for Energy Storage
Application) that goes into detail on other effects that are different effects can be modeled for supercapacitors (the modeled capacitance can be dependent on the charge discharge rate)







simulate this circuit &ndash; Schematic created using CircuitLab