Clusters atomistic nature

Owing to the importance of the free energy of formation of clusters as a function of cluster size, a number of methods have been developed to evaluate AG. A common approach utilizes continuum thermodynamics as in Eqs. (2.2) and (2.3). The use of continuum thermodynamics has been critiqued extensively in the literature, and we make no effort to review that criticism in this chapter. It is clear that the principal shortcoming of the continuum approach is the neglect of the inherent atomistic nature of clusters. Consequently continuum thermodynamics can be expected to be least appropriate for small clusters. We shall give some indication of the numerical accuracy of continuum thermodynamics for small clusters in Section V. 

The result of the interactions of some copolymer mimics of AMP with model bacterial membranes has been studied via atomistic molecular dynamics simulation (Figure 3.2). The model bacterial membrane expands homogeneously in a lateral manner in the membrane thickness profile compared with the polymer-free system. The individual polymers taken together are released into the bacterial membrane in a phased manner and the simulations propose that the most possible location of the partitioned polymers is near the l-palmitoyl-2-oleoyl-phosphatidylglycerol clusters. The partitioned polymers preferentially adopt facially amphiphilic conformations at the lipid-water interface, although lack intrinsic secondary structures, such as an a-helix or P-sheet, found in naturally occurring AMP [23]. 

Dissipative particle dynamics (DPD) is a meshless, coarse-grained, particle-based method used to simulate systems at mesoscopic length and timescales (Coveney and Espafiol 1997 Espafiol and Warren 1995). In simple terms, DPD can be interpreted as coarse-grained MD. Atoms, molecules, or monomers are grouped together into mesoscopic clusters, or beads, that are acted on by conservative, dissipative, and random forces. The interaction forces are pairwise additive in nature and act between bead centers. Connections between DPD and the macroscopic (hydrodynamic, Navier-Stokes) level of description (Espanol 1995 Groot and Warren 1997), as well as microscopic (atomistic MD) have been well established (Marsh and Coveney 1998). DPD has been used to model a wide variety of systems such as lipid bilayer membranes (Groot and Rabone 2001), vesicles (Yamamoto et al. 2002), polymersomes (Ortiz et al. 2005), binary immiscible fluids (Coveney and Novik 1996), colloidal suspensions (Boek et al. 1997), and nanotube polymer composites (Maiti etal.2005). 

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