Coarse-grained representation

In the coarse grained representation the equivalent statement to Eq. (3.71) in the steady state reads ... 

PML can also represent polymers at different levels of certainty where the structure is known, it can be encoded and where this information is not available, a polymer can be codified in terms of other concepts, such as the monomers it was prepared from. Furthermore, PML provides essentially a coarse-grained representation larger structural fragments can be mapped back to fully atomistic fragments, if desired. PML, therefore, allows data to be associated with a polymer representation at the atom, molecular fragment, molecule and molecule ensemble level, and. 

Defined by Eq. 1.5, c(r) becomes a coarse-grained representation of the discrete particle positions. 

Figure 6.2 1-Propanol a 3D atomistic representation b simplified coarse-grained representation.

The anisotropy of the local environment is assessed using an order parameter S, defined using the angle, 0z, between the z axis and a bond in the coarse-grained representation of the system. 

In the context of simulation, computational expense typically prevents the use of model systems that are exact replicas of those used in experiments. As a result, the model systems used in calculations of mechanochemical processes generally employ truncated or coarse-grained representations of the external groups used to apply F, or even exclude these groups entirely. The limited treatment of the external groups, or even their complete elimination from the calculations, requires the use of approximate schemes for subjecting molecules to F in calculations. 

Thompson, J.J., Tabatabaei Ghomi, H., Lill, M.A. Application of information theory to a three-body coarse-grained representation of proteins in the PDB insights into the structural and evolutionary roles of residues in protein structure. Proteins, 82, 3450-3465 (2014)... 

Mesoscopic regimes involving scales of the porous system exceeding 1 ns and 1 p,m entail the fast modes of motion to be eliminated in favor of a coarse-grain representation (see Figure 26.1). At this... 

FIGURE 26.9 The schematics of atomistic bottom-up coarse-graining paradigm by Ref. [45]. The Voronoi cell contains particles, which are closest to the cell center. The centers of all the Voronoi cells correspond to the centers of coarse-grained representation of the system — dissipative particles — which can be approximated by spheres. 

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