Coarse-graining approach

The coarse-graining approach is commonly used for thermodynamic properties whereas the systematic or random sampling methods are appropriate for static structural properties such as the radial distribution function. 

Fig. 3.11. Illustration of fine- and coarse-grained approaches. There are m substages and their associated transition rates (small letters) corresponding to one stage...

As for any modeling of continuum structures, the properties of the phases must be known for this kind of approach to work. Here, estimates obtained by atomistic methods of other techniques, described in the earlier chapters of this review, may be employed, or empirically known values may be used. It is hoped that the co-development of these continuum techniques and atomistic and coarse-grained approaches will lead to a seamless integration of the different techniques. 

Coarse-grained approaches, multiparticle collision dynamics, 90-92 Coarse velocity, linear thermodynamics, regression theorem, 18-20 Coherence spectroscopy, two-pathway excitation ... 

Gorban, A. N., Kazantzis, N., Kevrekidis, I. G., Ottinger, H. C. and Theodoropoulos, K., "Model Reduction and Coarse-Graining Approaches for Multiscale Phenomena". Springer, New York (2006). 

C. Theodoropoulos and E. Luna-Ortiz, 2006, A Reduced Input/Output Dynamic Optimisation Method for Macroscopic and Microscopic Systems , in Model Reduction and Coarse-Graining Approaches for Multiscale Phenomena, A. Gorman, N. Kazantzis, LG. Kevrekidis, H.C. Ottinger and C. theodoropoulos (eds) pp. 535-560. 

A more ab initio coarse-graining approach is that by Scheraga and coworkers [50], who model the protein as a chain of beads representing the alpha carbon atoms, with an additional bead for the side chain. By integrating out the degrees of freedom in an all-atom model of the protein, these authors... 

The coarse-grained approach utilizes a simplified system representation with fewer degrees of freedom, resulting in faster simulations but with reduced spatial and/or temporal resolution [97-99]. Different coarse-graining (CG) schemes have been devised to preserve the most relevant properties of the molecular system. Such methods can be applied to describe time scales that are far beyond the scope of allatom M D or KMC simulations, and thus extend the scope of molecular simulation to the nanoscale. Some examples of successful application of CG methods are the simulation of the different phases of the lipid-water system, interactions of peptides and proteins with biological membranes, and the electrodeposition of copper to form nanowires, nanofilms and nanoclusters in kinetic-limited regimes [182]. 

Ayton, G. S., and Voth, G. A. [2009). A hybrid coarse-graining approach for lipid bilayers at large length and time scales, / Phys. Chem. B, 113, pp. 4413-4424. 

Our effort focuses on a first-principles-based strategy in order to provide not only the accuracy from finer grain calculations, but improved scalability and a seamless coupling. We exemplify this next with a coarse-grain approach for representing the dynamics of DNA. 

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