NCAFM2023 Programme Booklet

Wednesday 1120 - 1140

EFFICIENT MODELING OF SELF-ASSEMBLING AND MANIPULATION OF ORGANIC MOLECULES ON IONIC SUBSTRATES

Paolo Nicolini, Mithun Manikandan, Prokop Hapala

Institute of Physics, Czech Academy of Sciences, Prague, Czech Republic Email: nicolini@fzu.cz, hapala@fzu.cz

The main challenge in developing the future molecular nanotechnology is our ability to assemble molecular components in a predictable way. While atomic force microscopy (AFM) and manipulation are priceless tools for prototyping molecular nanomachines, mass production will necessarily rely on deterministic self-assembling of simple building blocks. Simulations providing an atomistic insight are necessary for understanding AFM experiments, as well as to design new molecular assemblies. On the other hand, such simulations using general-purpose methods are often prohibitively expensive due to the exponentially-growing number of possible molecular configurations. We aim to address this challenge by developing an integrated simulation suite optimized for modeling small organic molecules on ionic substrates. The new code named FireCore (which is currently under development but it is already freely available on github[1]) integrates different levels of description, ranging from quantum mechanical treatment of the electronic degrees of freedom (within the density functional theory), to classical force fields. FireCore exploits GPU acceleration (which can potentially provide massive speedups with respect to state-of-the-art codes) and the grid-projected force field used in the ppafm code[2] to allow the screening of thousands of molecular assemblies on surface in a reasonable time. Configurations of molecules on substrate can be explored either automatically using global-optimization algorithms, or interactively (e.g. by dragging around the molecules with the mouse). Responsive simulation speed, a graphical user interface and the automatic assignment of force-field parameters make this program accessible to a broader audience without previous experience with atomistic simulations. Our ambition is to use FireCore for a complete computational design of photosensitive polymers which can self-assembly on ionic crystals in vacuum, similarly to what is done in DNA origami[3]. Such a polymer promises to merge bottom-up self-assembling and top-down photolitography to facilitate the development of next-generation molecular computers. Together with the framework, we will present our initial molecular designs and self-assembled structures simulated using this software.

Fig. (a) (Schematics of the simulation framework. (b) Example of interactive QM/MM simulation of a diacetylene polymer on NaCl substrate. 4 carbon atoms are treated quantum, while the rest (45) atoms are classical. Molecular orbitals can be plotted in real time as the mouse pulls one of the carbon atoms.

References [1] https://github.com/ProkopHapala/FireCore [2] P. Hapala et al., Phys. Rev. B, 2014, 90 , 085421. [3] P.W.K. Rothemund,Nature,2006, 440 , 297.

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