Theoretical methods serve as excellent tools in analyzing and interpreting the processes involved in the self-assembly of (bio)molecules on surfaces, ranging from modeling the deprotonated and neutral molecules in the gas phase, over their deposition and migration on the surface, to the pattern formation on the substrate.
Standard and specially developed global optimization techniques and barrier exploration methods, implemented in our own modular G42+ package, allow us to determine possible stable conformations of individual molecules on a variety of surfaces, and to suggest possible patterns in their self-assembly. Molecular dynamics simulations model the kinetics of the deposition and self-assembly. Quantum chemical calculations using e.g. Quantum Espresso, VASP, or CASTEP, are employed to validate the conformations and patterns on ab initio level, to probe the dynamics and the intra- and intermolecular interactions, and to compute STM images for comparison with the experiment.