Kinetics, nucleation stable nuclei

Generally, nucleation is a kinetic process where a small number of atoms form a stable cluster of atoms arranged closely to the structure of the new phase or phases, named nucleus, within the old phase. This nucleus subsequently operates as the primary construction block for a growing grain (see Figure 3.1). 

Fig. 5 Models of prion replication, (a) The template assistance model predicts that a PrPSo monomer is more stable than PrPc, but is kinetically inaccessible. In the rare event that a PrPSo monomer is created spontaneously (or provided exogenously), it can template the misfolding of another PrPc molecule by direct interaction. The dashed line shows that the newly created PrPSc monomer can act as another seed to formation of PrPSc. (b) The nucleation polymerization model predicts that barrier to prion protein conversion is the formation of a nucleus in which the protein adopts a PrPSo-like structure. The formation of such a low order aggregate is not favored however, once it has formed, polymerization from a pool of PrPc molecules can take place efficiently. Fragmentation of the polymer increases the number of ends for the recruitment of PrPc monomers...

The above considerations raise a very important question What do we measure in a progressive nucleation experiment Is dN t)/dt a nucleation rate, a rate of appearance of active sites or it is a combination of the tree rate constants As we have seen, depending on the values ofK , Ka and Ka ihs. experimentally accessible physical quantities ht and to may have completely different physical significance although what we only can and do measure in a direct nucleation experiment is the number of nuclei vs. time, N(t) vs. t, relationship. Note that for sufficiently high values of Kf, or Kf (cases 2.4.2.2.2, equation (2.141) or 2.42.2.3, equation (2.144), respectively) the induction time to may become too short to be experimentally detected. Therefore even in the case of experimental N t) relationships without induction periods [2.72, 2.176] one would not be able to assert that the constant rate / of appearance of stable clusters on the electrode surface would relate to the actual process of nucleus formation. Clearly, we are in exactly the same situation when data on the nucleation kinetics are obtained indirectly, by measuring the current of progressive nucleation [2.169]. 

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