Prokop Hapala focuses on the computational design of molecular machines, particularly molecular computers, their fabrication methods, and the development of rapid simulation methods to facilitate computational design in nanotechnology and surface chemistry. He is the principal investigator of the GAČR Junior Star project titled CADTARSIS: "Computer-Aided Design of Templated Assembling, Replication, and Synthesis on Ionic Substrates", which focuses on developing new photosensitive polymer templates capable of self-assembling on ionic crystal surfaces similarly to DNA origami. The ultimate goal of this project is to link biomimetic nano-manufacturing methods with photolithography, enabling the precise placement of molecular components, such as switches and memory cells, and connecting them into complex computational circuits (molecular chips). The foundations of the proposed method are summarized in the article Computational design of photosensitive polymer templates to drive molecular nanofabrication, ACS Nano (2024).