Steps on surfaces have long been explored for their own sake, and exploited as growth mediators. However, another type of linear surface defect - the domain boundary - has been largely neglected. Here we introduce domain boundaries of the 5x5 dimer-adatom-stacking fault reconstruction, explore their properties and demonstrate that they too can be used to mediate growth in a useful manner. When a thin layer of Ge is grown on Si(111) lattice strain induces the overlayer to reconstruct as Ge5x5. Using solid phase epitaxy, many domains of 5x5 can be grown. The domain interiors have excellent order, and with careful annealing, the boundaries that separate them are straight and uniform. Well-ordered boundaries propagate along the two high symmetry directions <1 -1> or <1 1> and are called A-type or B-type respectively. Boundaries of the second type are unique to Ge5x5. Registration with the substrate restricts the misfit between domains to discrete possibilities which are labeled according to a modified version of the system used for domain boundaries of Si(111)7x7. The distribution of observed boundary types is strongly peaked and reflects the relative energies of boundaries of different character. The expanded labeling scheme can be used to sketch the kinetic processes which lead to the distribution peaks. The dominant boundary by far is the one known as B[-2 2], which accounts for almost half of all observed boundaries. The atomic structure for this type of boundary has been established as a truncated 7x7 unit cell. Thus, these boundaries are linear arrays of quasi-7x7 embedded in a sea of 5x5. On the Si(111)7x7 surface the Group 13 elements, when deposited at sub-ML coverages and low temperatures, form magic clusters. The perfect uniformity and precise registration that earns them the moniker ‘magic’ make these clusters unusual among self-organized atomic scale objects. The clusters that form on 5x5 lack the uniformity of their counterparts on 7x7. However, with many domains, deposited In or Ga segregate to the quasi-7x7 B[-2 2] boundaries and there form magic clusters. The boundary thus acts as a template for growing straight lines of precisely spaced, atomically identical, nanoscale clusters. / Thesis (Ph.D, Physics, Engineering Physics and Astronomy) -- Queen's University, 2009-07-29 08:50:16.874