Indian Institute of Technology: It's India's premier institute, and offers a wide variety of courses. So why not try your luck in scientific research here?
University of Delhi: It has so many different departments including for sciences that you'll never be short on options.
Christ University, Bengaluru: This university has a few different courses and PhD options. And it's pretty good for sciences.
Central Institute of Mining and Fuel Research: It is one of the top institutes to do your PhD in India. It's competitive and highly prestigious
Tata Institute of Fundamental Research: As the name suggests, it's for research. You will get access to some of the best faculty around.