For my PhD thesis, I have conceptualised an experimental setup which is similar to an already existing patented design. Can I do research work on that setup (conceptualised by me) by simply citing that patent ? Are there other things to keep in mind ?
You should probably consult an IP lawyer. Your institution probably has someone who can help with this. Depending on what you are doing you may be using the patent idea or not (ie violating). You might be able to get a license from the patent holder. Lots of possibilities here.
In one scenario, the patent owner may be interested in your work.
But there is too little stated in your question and too much implied to be able to give nay definite answer.
I think not all patents have the same rules. Sometimes only commercial use is forbidden, research use may be ok. Some patent holders are reasonable and will give you explicit permission to use it if you ask nicely. Others refuse. It doesn't hurt to ask, though.
If your design is only similar, but not exactly the same, it may not even be covered by the patent. You should look carefully at exactly what the patent is for. Or better yet, ask a patent lawyer to look at it (your institution probably has one).
In practice, patent enforcement usually happens when the patent holder finds out, and then sues you for causing them to lose income they "deserve" by virtue of holding the patent. Since you will probably obtain little income from the patent, the case will not be very strong even if they do decide to sue. But more importantly, the journal where you expect to publish may have stricter rules on patents than your local regulators, so I would check their policies as well.