Explicit Solvent Models Atomistic Simulations

Operating fuel cell involves solvent environment, and it is important to study water formation reaction under solvent conditions to understand the solvation effects on overall reaction kinetics. Adding water molecules explicitly or entire water bilayer to unit cells of simulating catalyst is considered as explicit solvent model. This method, however, does not resemble fully saturated system, and water molecules are introduced during the simulation that directly participates in the ORR [148]. Poisson-Boltzmann implicit solvent model is a method to resemble solvent as a continuum rather than individual molecules in explicit models [160,162]. This method is computationally inexhaustive and accurate enough to reproduce reliable results for the atomistic energy calculations. 

If a solvent is to be considered as explicitly present in a simulation, obviously there must be some atomistic manner in which it is represented in the energy expression - this being the fundamental distinction from a continuum solvation model. However, since the solvent molecules greatly outnumber the solute molecule(s), there are advantages of efficiency that accrue from adopting as simple a representation as possible, and that is reflected in many of the solvent models in common use. 

Fully atomistic simulations are the most realistic of the three simulation methods. They include a fully detailed description of the amino acids comprising the protein, and they are thus much more true to life than the other models. In addition, solvent molecules may be added explicitly or implicitly to the simulation. Because of this extreme detail, a simulation of a small protein may require the treatment of thousands of atoms. Fully atomic simulations are thus extremely computationally expensive, and only short time scales can be explored. As computational power continues to increase, so do the time scales accessible with this method. Nevertheless, fully atomic simulations still cannot capture kinetic information they are, however, useful in understanding important local interactions that drive protein folding. 

An early version of a CG model with explicit solvent was developed by Smit et al., to study the dynamical interface between water and oil [26]. A similar strategy was also used by Goetz and Lipowsky [30] to simulate the self-assembly of a model surfactant into micelles and bilayers. Later, Klein and coworkers employed thermodynamic properties derived from atomistic simulations to develop a CG model for surfactants that includes the chemical structure [24, 31]. In this form, the procedure used to obtain the simplified potential functions of the CG model bears some level of similarity to the force-matching method used to fit simple potential functions for pairs of atoms against a fully electronic description [32]. Voth and coworkers later essentially followed this latter approach to also define an algorithm based on the force-matching procedure specific for CG-MD [33-35]. 

Much more sophisticated models are needed to explicitly deal with the role of the solvent and presumably the only sensible way to make headway here is by means of detailed, that is, atomistic computer simulations. Unfortunately, detailed computer simulations of the self-assembly of large polymeric objects are often not very practical because they require excessive computer processing times, in particular if the solvent molecules are... 

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