Figure 3

Dependence of Geometry: Starting from a molecular species with two binding sites (a), the polymerizations following the simple complexation rule (b) may lead to very different molecule complexes. When assuming a linear conformation of both binding sites (c), linear, rod-like structures will assemble. Using a 90 degree angle between both components (d) would mostly lead to closed quadratic structures. Other geometries including inclinations out of the plane (e) can create helices of different radii and helicities, etc. Please note, that the geometry model that is necessary to distinguish closed quadratic structures and helices from a worm-like chain in (d) and (e) requires the use of dihedral angles (See Section Discussion for details). While dihedral angles are not yet implemented in our software SRSim, similar effects can be achieved by using slightly more complex elementary molecules, as it was done in out spheric self-assembly simulation.