This work presents a new approach for analyzing barrel stave pore
structures using implicit solvation modeling. This approach offers significant
advantages compared to all-atom explicit simulations [42,60].
One advantage is the fast convergence. Within a few ns one can see
whether a certain structure is stable or not. A second advantage is the
ability to obtain estimates of the thermodynamic stabilities of the various
structures. A third advantage is that it tests our understanding of
the physical forces that play a role in peptide-induced pore formation.
Of course, the approach is not without limitations. The implicit solvation
model is highly approximate and the cylindrical shape of the pore is imposed
at the outset. There is substantial experimental and theoretical
evidence supporting this idea [60,61] but it is an assumption. The results