Nov 3 – 4, 2022
Europe/Prague timezone

Integrated simulation package for on-surface chemistry and SPM

Not scheduled
atrium (IT4Innovations)



Studentská 6231/1B 708 00 Ostrava-Poruba
Poster Poster session Conference Dinner and Poster Session


Prokop Hapala (FZU - Institute of Physics of the Czech Academy of Sciences)


On-surface chemistry complemented with scanning probe microscopy (SPM) opens a completely new area of single-molecular organic synthesis and nano-fabrication. But this unparalleled level of atomic control and insight can be achieved only by close collaboration between SPM experiments with simulations. Currently these simulations are often unnecessarily costly and laborious due to lack of optimized software. Therefore, we are developing a new integrated package dedicated to autonomous search for absorption geometries of molecules on substrate and simulation of respective AFM images ( We aim to (1) streamline and speed-up these simulations to enable high throughput screening of chemical reactions and molecular architectures on surface and (2) to simplify the simulations to such a degree which allows it to be used by non-experts and experimentalists. Significant speed-up necessary for this goal is achieved by combination of density functional theory with classical force-fields in QM/MM manner, and by extensive use of GPU acceleration.

Primary authors

Prokop Hapala (FZU - Institute of Physics of the Czech Academy of Sciences) Paolo Nicolini (Czech Technical University in Prague)

Presentation materials

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