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An antiphase domain (APD) is a region of a crystal where the atoms are configured in the opposite order to those in the perfect lattice system and therefore is an Crystallographic defect. In other words, an APD is a region formed from antisite defects of a parent lattice. In general, APDs form antiphase boundaries (APBs) with the parent lattice. This concept is illustrated in the diagram below 
Figure 1. Highlighted area showing an antiphase domain in GaAs on Si.
(figures courtesy of JJJAP, VOL. 26, No.6, JUNE, 1987, pp. L944-L946)
The shaded region, B, is an example of an APD. In the figure, GaAs is grown on a misoriented surface of Si (details are not discussed here). The misorientation causes the growth of the APD in region B. The presence of the APD results in Ga sites 1, 1’, 2, 2’, 3, 3’ being bonded to another antisite Ga to form an APB.
In mixed oxidation state materials like magnetite, antiphase domains and antiphase domain boundaries can occur as a result of charge-ordering even though there are no changes in atom locations. For example, the reconstructed magnetite (100) surface contains alternating FeII pairs and FeIII pairs in the first subsurface layer. An antiphase domain boundary can form if two subsurface FeII pairs meet when two terraces grow together.
- Although the journal paper cited below emphasizes self-annihilation of APBs, the picture was taken as an illustration of an APD
- Parkinson, G. S.; Manz, T. A.; Novotny, Z.; Sprunger, P. T.; Kurtz, R. L.; Schmid, M.; Sholl, D. S.; Diebold, U. (2012). "Antiphase domain boundaries at the Fe3O4(001) surface". Phys. Rev. B 85 (19): 195450:1–7. Bibcode:2012PhRvB..85s5450P. doi:10.1103/PhysRevB.85.195450.
- Check Jpn. J. Appl. Phys. 26 (1987) pp. L944-L946 for more information regarding the antiphase domain