Coarse grained methods/representations

Simulation methods have been proved to be useful in the study of many different molecular systems, in particular in the case of flexible polymers chains [ 14]. According to the variety of structures and the theoretical difficulties inherent to branched structures, simulation work is a very powerful tool in the study of this type of polymer, and can be applied to the general problems outHned above. Sometimes, this utility is manifested even for behaviors which can be explained with simple theoretical treatments in the case of linear chains. Thus, the description of the theta state of a star chain cannot be performed through the use of the simple Gaussian model. The adequate simulation model and method depend strongly on the particular problem investigated. Some cases require a realistic representation of the atoms in the molecular models [10]. Other cases, however, only require simplified coarse-grained models, where some real mon-... 

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]. 

In the following, we present an approach to document modeling that allows to describe the three aspects postulated by Salminen et al. on a coarse-grained level within a single representation language. Firstly, we will discuss how individual document types and their dependencies can be described. Next, we will introduce a method to describe the dynamic behavior of documents. Finally, the modeling of syntactic as well as semantic content will be addressed. 

This chapter will review the generation of free-standing thin films and fibers with a coarse-grained simulation method on a high coordination lattice,performed in a manner that allows accurate reverse-mapping of individual replicas to a fully atomistic representation in continuous space.4 After describing some of the properties of these films and fibers, we will present some new information about the limits on the stability of the models of these nanofibers. 

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