The C(S) sites in the preceding section are commonly considered as "open sites" in many nucleation reactions. These are essentially empty sites on the particle surface at which other surface species can reside. For example, consider the following reaction:

2A4 => 32C(B) + xOpen(S) + 20H(S)

A4 is the pyrene molecule, containing 10 hydrogen (H) atoms and 16 carbon (C) atoms. The above reaction says that all 20 H atoms reside as surface species on the nucleated particle, which contains 32 C atoms. The number of open/empty sites, denoted by x in the above reaction, must satisfy the surface site balance (Equation 19–37 ). This number is usually a floating-point number so its consistent calculation (to the precision of computer arithmetic) is essential for site conservation. When such a site is flagged as a "native" site, then Ansys Chemkin automatically calculates the value of x. You can specify the native site by using the /NATIVE/ tag in the surface-chemistry input. If no NATIVE tag is included, then the first surface species listed for the dispersed-phase material will be assumed to be the native site.

The native surface species is used not only in a nucleation reaction but also when the net surface area of the particle increases. For example, consider the following surface reaction:

Open(S) + C2H2 => H(S) + 2C(B) + H

In this reaction, acetylene finds an open site on the particle surface and deposits 2 carbon atoms on the particle. One H atom is also added to the surface while one open site is consumed. The addition of bulk species, however, also creates new surface area and therefore new open sites. While the reaction has the correct element balance and sets one open site covered by one surface H atom, the reaction does not specify the number of new open sites formed due to new surface area. This number is internally computed by Ansys Chemkin. Note that the number of new open sites generated is dependent on the class of the particle on which this reaction happens. For example, suppose the above reaction happens on a particle of class . After the reaction is completed, the new particle is of class . Since the particles are considered to be spherical, the surface areas of these two particles are and , respectively. Correspondingly, the total number of surface species before and after reaction are and , where is the surface site density. Since the reaction correctly accounts for the open site occupied by , the total number of new open sites formed is .

Particle surface area is destroyed when particles coagulate and when surface reactions etch particles. When particle area is destroyed, it means that fewer surface sites remain after the reaction. However, it may not necessarily mean that only native sites are destroyed. Therefore, during the net production rate calculation, Ansys Chemkin first computes the net rate of surface area generation by all surface reactions and coagulation. If this rate is positive then the rate of generation of native species is computed, as described in the previous paragraph. When the net area generation rate is negative, the rate of generation (which also will be negative) of all surface species (including the native) is considered to be proportional to the activity of each species. In other words, when new area is formed, new native species are formed and when area is destroyed all surface species are destroyed in correct proportion. Note that the destroyed surface species can be considered to be trapped or buried in the bulk and thus lost from the system.