Download PDF by Hugo O. Villar (Eds.): Advances in Computational Biology

By Hugo O. Villar (Eds.)

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For F^ = 4 x 10"^^erg/A, the height of the barrier does not depend on system size to within calculational error, indicating that the transition for this parameter value is almost at a critical point. The temperature and size dependence of the specific heat are shown in Figure 6(a) for F^ = 5x10"^Srg/A corresponding to a first-order transition. As the system size increases, the peak height of C(T) increases while the width of the peaks decreases. The peak height scales as expected for a first-order transition, Eq.

The system size is then increased and the value of |i^ for the previous system size is used as trial value for the long simulation on the larger system. This rather lengthy iterative procedure assures a very accurate determination of the chemical potential at coexistence and hence leads to an accurate determination of the compositional phase diagram via the finite-size scaling analysis. The Ferrenberg-Swendsen reweighting technique becomes more troublesome the larger the size of the system studied because the distribution functions are narrower for larger systems.

It can therefore be characterized by a cross-sectional area, AQ, and the length of the hydrophobic core, (IQ. J^Q is the direct lipid-protein interaction constant, which depends on the properties of gramicidin hydrophobic surface. The parameter, F^Q, is related to the hydrophobic effect describing the hydrophobic area exposed to water by the longer species. E^ is the strength of the hydrogen bonding between the two monomers of a dimer. E. Model of Polypeptide Aggregation and Channel Formation In Section D we proposed a model for a specific case of ionic channel formation in a lipid bilayer environment: the monomer-dimer process for the formation of the gramicidin-A channel.

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