Computational Design of Functional Molecular Systems on Crystalline Substrates


On-surface chemistry assisted by scanning probe microscopy (SPM) provides an unparalleled tool for prototyping molecular nano-machines and for studying their operation [1]. Due to its novelty, the field still lacks theoretical support that would be comparable to situation e.g. in biochemistry. In the PhD project, we will try to overcome these limitations by computational design of a new molecular architecture (loosely inspired by DNA origami [2]) that is able to self-assemble into pre-programmed structures on atomically flat crystalline substrate and to provide templates for assembling other functional molecules (molecular switches, transistors, memories, motors, or photo-emitters). The long-term goal is to kick-start a way ultimately leading to molecular computers and other complex nano-machines.

The design will be conducted using a newly developed simulation software combining quantum mechanical methods with classical force fields optimized for anhydrous environment at crystalline surfaces [3]. The student is expected to participate in the development of this software, therefore a previous programming experience (or at least an interest to learn programming) is desirable. The software and simulations performed by the student are expected to aid also other state-of-the-art experiments conducted in collaboration with world leading low-temperature UHV AFM/STM laboratories [4].

  1. Towards single molecule switches
    Zhang, J. L., et al., Chemical Society Reviews 44(10), 2998–3022 (2015).
  2. Challenges and opportunities for structural DNA nanotechnology
    Pinheiro, A. V., et al., Nature Nanotechnology 6(12), 763–772 (2011).
  3. FIREBALL/AMBER: An efficient local-orbital DFT QM/MM method for biomolecular systems
    Mendieta-Moreno, J. I., et al., Journal of Chemical Theory and Computation 10(5), 2185–2193 (2014).
  4. The effect of hydration number on the interfacial transport of sodium ions
    Peng, J., et al., Nature 557(7707), 701–705 (2018).