Ing. Prokop Hapala, Ph.D.

I am mainly interested in computational design of molecular nanomachines, particularly molecular computers, and strategies for their nanofabrication. For this purpose, I also develop high-performance simulation methods to advance computational design in nanotechnology and surface chemistry. I am the principal investigator of a GACR Junior Star project CADTARSIS: “Computer-Aided Design of Templated Assembling, Replication, and Synthesis on Ionic Substrates.” This project focuses on designing new classes of photosensitive polymer templates capable of self-assembling on ionic crystal surfaces, akin to DNA origami. The ultimate goal is to integrate biomimetic bottom-up nanofabrication techniques with photolithography, enabling precise positioning of molecular components, such as switches and memory cells, and their interconnection into complex computational circuits – essentially molecular chips. The foundations of the proposed method are summarized in a paper Computational Design of Photosensitive Polymer Templates To Drive Molecular Nanofabrication, ACS Nano (2024).

Software development

I develop various high-speed computational methods and software for molecular and atomistic simulations, focusing on self-assembly at surfaces, surface chemistry, and the interpretation of high-resolution atomic force microscopy (AFM) and other scanning probe microscopy (SPM) techniques. These methods leverage both classical and quantum approaches to achieve an optimal balance between computational efficiency and accuracy.

• FireCore is an integrated simulation environment for surface chemistry and scanning probe microscopy. It enables rapid exploration of a vast configuraton spaces of molecules on crystalline surfaces by employing a specialized implementation of classical force-fields on GPUs, grid-projected forcefield (GridFF), and density functional theory (DFT) methods.
• PPAFM is currently the most used software for simulating high-resolution AFM images and other SPM techniques with sub-molecular resolution. It models the deflection of molecular probes (CO, Xe, Cl, and other small molecules) attached to the AFM tip apex using various grid-projected potentials. The software is described in Advancing scanning probe microscopy simulations: A decade of development in probe-particle models, Computer Physics Communications (2024)
• I am currently working on extension of PPAFM to simulate images from light-excited scanning tunneling microscopy (light-STM) of molecular clusters on ionic substrates, with potential applications in molecular computing and photonics. The software itself has not yet been published, but the methodology has been utilized in Real Space Visualization of Entangled Excitonic States in Charged Molecular Assemblies, ACS Nano (2021)