This is fairly simple to do using a scheduled JQL trigger:
Project automation - JIRA 2016-12-04 14-24-23.png
So this rule simply runs a JQL search once a day using the "Scheduled JQL search" trigger to find all issues matching the JQL:
duedate < now() and statusCategory != Done
You can then use further conditions and actions to perform tasks on those issues. This could also be run more often than once a day depending on your requirements!
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