Stuart Lindsay works on analysis of individual molecules. His has explored how a single molecule can be measured and if they can be manipulated through computer modeling simulations. He has looked into these impacts on genetics and how chemical changes impact the degree to which a trait can be expressed from a gene. His work also spans into sustainable energy through the conduction of particular molecules functioning in molecular electronics. This also extends to single molecule sensor actuators.

Lindsay is the center director of the Biodesign Center for Single Molecule Biophysics, a regents professor for the School of Molecular Sciences and Department of Physics. He is a university professor in the School of Life Sciences Adjuncts and Affiliates, the ASU SFI Center, the Biosocial Complexity Initiative, and the Center for Biological Physics.

He was an elected Fellow at the National Academy of Inventors as well as the Institute of Physics in the UK.