There are several examples in the APMonitor webpage regarding parameter estimation. Please check the link below. It also provides the data and model that you can use for practice.
TCLab C - Parameter Estimation
You can also get the idea how to implement the higher order differential equations in GEKKO in the link below. You basically want to introduce additional variable which links the first derivative variable to the 2nd derivative variable. That way, you can collapse the higer order DE down into the multiple 1st order DEs.
Solve 2nd Order Differential Equation
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