Global free energy

Let A = yc, , 1 < / < Nc, be conformations generated for C using a computational method. Because the global free energy minimum conformation is expected to statistically dominate the thermodynamic ensemble, the predicted binding activity for C is determined by (C)=min F y. ) = F(yf ). 

As before, our simulation data are subject to statistical (sampling) uncertainties, which are particularly pronounced near the extremes of particle numbers and energies visited during a run. When data from multiple runs are combined, as shown in Fig. 10.3, the question arises of how to determine the optimal amount by which to shift the raw data in order to obtain a global free energy function. As reviewed in... 

Nucleation is defined as the point where the protonucleus is sufficiently large that its surface area to volume ratio exceeds a critical point, and further growth results in a reduction in global free energy surface effects are now small compared to the inside of the crystal. This is the point where enthalpy dominates over entropy. Subsequent crystal growth and further nucleation events will occur until thermodynamic equilibria is reached, as defined by Eq. 3. The rate of nucleation is defined as the rate at which clusters grow through this critical point. 

The critical nucleus corresponds to p = 1 = m, and the global free-energy minimum corresponds to infinitely large dimensions of the cylinder in both length and radius. 

Proteins unfold reversibly when denatured by chemical means or mild heating Single-funnel hypothesis The native state is the global free energy minimum Multi-funnel hypothesis The denatured state retains native secondary structure and protein remains within/close to native funnel. 

Fig. 16.4 The alignment of free energy curves from all the windows to get the global free energy of a reaction by WHAM...

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