Molecular simulations, viii

More advanced methods for extending the length of molecular dynamics simulations are discussed in Section VIII. 

Computational studies starting with collagen triple-helix structures now available in the Protein Data Bank are becoming increasingly important for collagen. As described above, molecular dynamics simulations can suggest models that are amenable to experimental verification. Computational analyses and molecular dynamics studies have also been carried out on Gly substitutions in the triple helix (see Section VIII below). 

The static - double-layer effect has been accounted for by assuming an equilibrium ionic distribution up to the positions located close to the interface in phases w and o, respectively, presumably at the corresponding outer Helmholtz plane (-> Frumkin correction) [iii], see also -> Verwey-Niessen model. Significance of the Frumkin correction was discussed critically to show that it applies only at equilibrium, that is, in the absence of faradaic current [vi]. Instead, the dynamic Levich correction should be used if the system is not at equilibrium [vi, vii]. Theoretical description of the ion transfer has remained a matter of continuing discussion. It has not been clear whether ion transfer across ITIES is better described as an activated (Butler-Volmer) process [viii], as a mass transport (Nernst-Planck) phenomenon [ix, x], or as a combination of both [xi]. Evidence has been also provided that the Frumkin correction overestimates the effect of electric double layer [xii]. Molecular dynamics (MD) computer simulations highlighted the dynamic role of the water protrusions (fingers) and friction effects [xiii, xiv], which has been further studied theoretically [xv,xvi]. 

The previous analysis may be extended to spatially periodic suspensions whose basic unit cell contains not one, but many particles. Such models would parallel those employed in liquid-state theories, which are widely used in computer simulations of molecular behavior (Hansen and McDonald, 1976). This subsection briefly addresses this extension, showing how the trajectories of each of the particles (modulo the unit cell) can be calculated and time-average particle stresses derived subsequently therefrom. This provides a natural entree into recent dynamic simulations of suspensions, which are reviewed later in Section VIII. 

All of the simulation approaches, other than harmonic dynamics, include the basic elements that we have outlined. They differ in the equations of motion that are solved (Newton s equations, Langevin equations, etc.), the specific treatment of the solvent, and/or the procedures used to take account of the time scale associated with a particular process of interest (molecular dynamics, activated dynamics, etc.). For example, the first application of molecular dynamics to proteins considered the molecule in vacuum.15 These calculations, while ignoring solvent effects, provided key insights into the important role of flexibility in biological function. Many of the results described in Chapts. VI-VIII were obtained from such vacuum simulations. Because of the importance of the solvent to the structure and other properties of biomolecules, much effort is now concentrated on systems in which the macromolecule is surrounded by solvent or other many-body environments, such as a crystal. 

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