Induced charge computation method

With these computational methods, we can predict the binding sites of the proteins and the structures of the proteins which are not observed in experiments. By calculating Rg or AGbind. strength of fiber can be compared. Moreover, measuring the contribution of hydrophobic and electrostatic interactions becomes a kind of index to design where and how to induce mutations of hydrophobic or charged amino acids to proteins. 

The requirement needed to incorporate the solvent effects into a state-specific (multireference) method is fulfilled by using the effective Hamiltonian defined in Equation (1.159). The only specificity to take into account is that in order to calculate Va we have to know the density matrix of the electronic state of interest (see the contribution by Cammi for more details). Such nonlinear character of Va is generally solved through an iterative procedure [35] at each iteration the solvent-induced component of the effective Hamiltonian is computed by exploiting Equation (1.157) with the apparent charges determined from the standard ASC equation with the first order density matrix of the preceding step. At each iteration n the free energy of each state K is obtained as... 

Ion channel studies motivated Allen et al. [47] who have developed an elegant variational formalism to compute polarization charges induced on dielectric interfaces. They solved the variational problem with a steepest descent method and applied their formulation in molecular dynamics (MD) simulations of water permeation through nanopores in a polarizable membrane [48-50], Note that the functional chosen by Allen et al. [47] is not the only formalism that can be used. Polarization free energy functionals [51-53] are more appropriate for dynamical problems, such as macromolecule conformational changes and solvation [54-57],... 

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