# Ion Beam Nanopatterning of Biomaterial Surfaces
## 2 Nanoscale Pattern Formation on Solid Surfaces during Ion Beam Irradiation
### Surface Chemistry  
The chemical composition of the irradiated surface is of course an important factor as well, which influences the distribution of the deposited energy, the surface binding energy, and the strength of the different surface smoothing mechanisms. Therefore, it is important to consider the fact that ion irradiation itself may alter the surface chemistry. This is particularly obvious when reactive ions such as O\({}_{2}\)+ or N\({}_{2}\)+ are used, which may react with the atoms of the target surface and, thus, form thin oxide and nitride films, respectively. Due to the developing surface topography, these films may display pronounced local variations in thickness and stoichiometry and, thereby, have dramatic effects on the evolution of the nanopatterns, while the fabricated surface may exhibit a highly heterogeneous stoichiometry [95,96].  
Figure 2: Ripple periodicity \(\lambda\) as a function of ion energy E with corresponding AFM images. The nanopatterns were generated by irradiation of Si surfaces with Xe+ ions at room temperature and 65\({}^{\circ}\) incidence with respect to the surface normal. The applied fluence was 2 \(\times\) 10\({}^{17}\) cm\({}^{-2}\). The red line is a linear fit to the data. The AFM images have a size of 4 \(\times\) 4 \(\upmu\)m\({}^{2}\).  
However, even when inert ions such as noble gas ions are employed, changes in surface chemistry may occur. In polymer materials, for instance, ion impact may lead to both polymer chain scission and crosslinking [51], both of which may affect their mechanical properties. With regard to inorganic surfaces, changes in surface chemistry due to inert ion irradiation occur only in compound materials. Since the sputtering yield depends on the species of the target atoms, different sputtering yields for individual atomic species may be observed in multicomponent materials [84]. In this case, one or more of the atomic species will be sputtered preferentially and, thereby, depleted in the near-surface region. Over time, this depletion will balance the larger (partial) sputtering yield of this species and, finally, result in a stationary state in which the altered surface composition remains constant but is moved into the bulk due to sputter erosion. This preferential depletion/enrichment of atomic species may not only result in an altered chemical composition of the nanopatterned surface but also affect pattern formation itself. For instance, it was shown that the formation of hexagonally ordered nanodots on compound semiconductors (see Figure 1d) critically depends on the preferential enrichment of one atomic species over the other [97].  
Finally, the application of broad (defocused) ion beams may result in the deposition of foreign material on the target surface. This may happen in certain irradiation geometries, in which part of the ion beam hits the walls of the vacuum chamber or other equipment in such a way that sputtered material from these surfaces ends up on the target surface. In particular, metallic contaminations of this sort have been found to induce highly complex pattern behaviors and astonishing surface topographies especially on semiconductor surfaces [75]. While the controlled deposition of such contaminants is sometimes considered a promising approach for broadening the range of available patterns, precise control is typically rather difficult to achieve.  
From a biomaterials point of view, the different effects discussed in this and the previous subsection stress the importance of a thorough surface-analytical characterization of the nanopatterned substrates prior to contact with biological systems. Small variations in surface energy or stoichiometry may have severe effects on the behavior of adsorbing proteins and the response of adhering cells. This is particularly important because the effects that nanoscale surface topography exerts on biological systems are often rather moderate [89; 98] and may easily be masked by such chemical effects.