Is there something like an undergraduate research programme (given by a good institution) in mathematics/theoretical physics which provides a research opportunity in which I can collaborate online and leads to a publication?
I think you should check The Open University's site.
Part-time research students pursue their projects at a distance, under individual guidance from expert supervisors.
So maybe it is a possibility if you actually would like to earn a degree from that university, but since this institute is famous for the excellent quality online and distance education I think you should write them a message and ask for information. I guess they would have good suggestions about your question.
PS. I've taken an online course from this University on the FutureLearn site, and the material's quality was very good.