Coarse-grain network

The point where these different strands meet is as follows. In one dynamical network approach, of Manfred [73] macroscopic spacetime is considered to be a coarse-grained emergent phenomenon (called an order parameter manifold). It is assumed to be the result of some kind of geometric phase transition (very much in the spirit of the physics of self-organization). This framework was developed in quite some detail [75]. We argued in Ref. 76 that what we consider to be the elementary building blocks of continuous spacetime—the so-called physical points—are, on a finer scale, actually densely entangled subclusters of... 

Miiller-Plathe F (2002) Coarse-graining in polymer simulation From the atomistic to the mesoscopic scale and back. J Chem Phys Phys Chem 3 754—769 Muller R, Picot C, Zang YH, Froelich D (1990) Polymer chain conformation in the melt during steady elongational flow as measured by SANS. Temporary network model. Macromolecules 23(9) 2577—2582... 

Kurkcuoglu O, Jernigan RL, Doruker P (2004) Mixed levels of coarse-graining of large proteins using elastic network model succeeds in extracting the slowest motions. Polymer 45 649-657... 

The contributions of Vulpiani s group and of Kaneko deal with reactions at the macroscopic level. The contribution of Vulpiani s group discusses asymptotic analyses to macroscopic reactions involving flows, by presenting the mechanism of front formation in reactive systems. The contribution of Kaneko deals with the network of reactions within a cell, and it discusses the possibility of evolution and differentiation in terms of that network. In particular, he points out that molecules that exist only in small numbers can play the role of a switch in the network, and that these molecules control evolutionary processes of the network. This point demonstrates a limitation of the conventional statistical quantities such as density, which are obtained by coarse-graining microscopic quantities. In other words, new concepts will be required which go beyond the hierarchy in the levels of description such as micro and macro. 

Coarse-grained (phenomenological) level. Some other reduced model is adopted for the study of gene expression or signal transduction network. The modeling at this level is relevant when attempting to understand specific function of a cell. 

The last section is devoted to an application of ESPResSo to a typical soft matter problem. While the properties of uncharged pol uner networks have been well understood by now, this does not hold for charged networks. Even the coarse-grained simulation of such a polymer network requires a large number of beads as well as long time scales, so that such simulations got feasible only recently. We shortly present the used simulation techniques and some of the results. 

The PPTIS method coarse-grains the transition pathways to a one-dimensional Markovian state model . In principle, there is no need to limit oneself to only one dimension. It is possible to coarse-grain the folding pathways using a Markovian state network model, also called stochastic road map [91-93] or... 

Jeong, J.I., Jang, Y, Kim, M.K. A connection rule for alpha-carbon coarse-grained elastic network models using chemical bond information, J. Mol. Graph. Model. 2006,24,296. 

Kurkcuoglu, O., Jemigan, R. L., and Doruker, R, Collective dynamics of large proteins from mixed coarse-grained elastic network model, QSAR Combinatorial Sci., 24, 443 (2005). 

Lu, M. and Ma, J., A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography, Proc. Natl. Acad. Sci. U.S.A.,105, 15358 (2008). 

Periole, X., Cavalli, M., Marrink, S. J., and Ceruso, M. A. [2009]. Combining an elastic network with a coarse-grained molecular force field Structure, dynamics and intermolecular recognition, / Chem. Theory Comput 5, pp. 2531-2543. 

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