Group of Surface Molecular Design - ProkopHapala/FireCore GitHub Wiki
Group of Surface Molecular Design
I lead the Group of Surface Molecular Design at the Institute of Physics, Czech Academy of Sciences. Our research focuses on the theoretical description of organic molecules on inorganic solid surfaces, aiming to develop scalable bottom-up nanofabrication methods for molecular electronics and nanotechnology. We are particularly interested in high-resolution scanning probe microscopy (HR-SPM), surface-templated chemical synthesis, and self-assembly processes.
Research Highlights
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High-Resolution Imaging Mechanisms: During my Ph.D., I elucidated the mechanism behind sub-molecular resolution using CO and Xe terminated atomic force microscopy (AFM) tips. This work led to the development of the Probe Particle AFM (PPAFM) simulation software, now a standard tool in the field.
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Machine Learning in AFM Interpretation: In my postdoctoral research at Aalto University, I employed a GPU-accelerated version of PPAFM to train the world's first machine learning model for automatic interpretation of AFM images of non-planar molecules.
Awards and Recognitions
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Neuron Award 2021: Received the prestigious Neuron Prize for promising young scientists in chemistry.
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Junior Star Grant 2021 CADTARSIS: Our project, "Computer-Aided Design of Templated Assembling, Replication, and Synthesis on Ionic Substrates," focuses on developing novel programmable polymers that self-assemble on ionic crystal surfaces, similar to DNA origami. These polymers aim to facilitate the assembly of molecular components, such as switches and memory cells, into computational circuits and other nanomachines. For more details, visit the project page. As well as to our recent publication
Software Development
- FireCore is an integrated simulation environment dedicated to on-surface chemistry and scanning-probe microscopy. The software streamlines high-throughput screening of molecular configurations and processes on crystalline surfaces, integrating GPU-accelerated classical force fields and density-functional methods.
- PPAFM simulates high-resolution AFM and other scanning probe microscopy (SPM) techniques with sub-molecular resolution. It models the deflection of a probe particle attached to the tip, representing a flexible tip apex, and has become a standard tool in the field. It has also modules for simulation of other scanning probe microscopy methods like STM, IETS. Recently I'm also working on extension of PPAFM to simulate light-scanning tunneling microscopy (light-STM) images of molecular clusters on ionic substrates, with potential applications in molecular computing and photonics. The recent publications are: