Al-Khalili's research interests lie mainly in the field of theoretical nuclear physics. This has mostly been in the development of few-body quantum scattering methods to study nuclear reaction mechanisms and nuclear structure, particularly as applied to the study of exotic nuclei produced by radioactive beam facilities around the world. He has pioneered the application of few-body Glauber methods in nuclear scattering and reactions at intermediate and high energies. His interests have spanned a wide range of reaction energies from the study of the light nuclei using electromagnetic probes such as electron scattering and photo-induced pion production reactions, to reactions of astrophysical interest. Over the past few years, he has become interested studying quantum mechanisms in biology and has published several papers on quantum tunneling in DNA.
Al-Khalili collaborates with colleagues, and jointly supervises postdocs and research students, within the nuclear theory group at Surrey on a range of topics of current interest. Active collaboration with theorists and experimentalists in Europe, the US and Canada, in particular where relating to research on exotic nuclear beams at the major labs. He is the theory coordinator for the R3B collaboration at GSI. Collaborates with PDRA DR Qiang Zhao at Surrey and Professor Frank Close (Oxford) on problems in hadron physics. Collaborates with both theorists and experimentalists at TRIUMF Lab, Vancouver, and Jyvaskyla Lab in Finland on decay studies of exotic nuclei, particularly relating to nuclear astrophysics Collaborates with both physicists and Microbiologists on topics relating to quantum effects in biological systems.