Grotjohn's research interests include the modeling, design, diagnostics, and applications of plasma-assisted materials processes and processing machines. A strong focus of his work is the use of models, including electromagnetic, plasma dynamic, and plasma chemistry models, for the design and control of microwave plasma reactors used for materials processing. Specific processes studied have included diamond chemical vapor deposition (CVD), amorphous carbon deposition, semiconductor etching, and microwave-generated plasma discharges operated as ion and radical sources. In coordination with the modeling studies are his plasma diagnostic studies. His recent work looks in particular at mini- and micro-scale plasma discharges and their application.