Coarse-graining methods

The method aims to pass the distribution of structural parameters from the atomistic structure to the coarse-grained. The procedure involves performing an atomistic MD simulation and calculating the 

Since Boltzmann transport equation (BTE), which is derived to LBKE, is particle assumption-based theory, an SRS model can be implemented to BTE as follows  

Using the Hamiltonian, we can obtain attractive or repulsive forces that play a role of external forces in Equation (22). A spin analogy/ lattice gas model will be developed that can describe the oversimplified molecular structure, while still capturing the essence of the molecule/ surface interaction. The relaxation time in SRS-LBM will contain shear rate and other nanoscopic information. 

This section deals with multi-scale models for the PEFC and consists of three subsections, 4.1,4.2, and 4.3, that relate to molecular-level models, bridging models between scales and device/process level models, respectively. The objectives of these subsections are to survey the development and application of these models. 

The PEM generally consists of polytetrafluoroethylene chains with hydrophilic perfluorosulfonate side groups. Water molecules within the system agglomerate in the vicinity of hydrophilic groups (i.e., sulfonic acid groups) and form hydrophilic clusters. A network of these clusters forms passages for proton conduction within PEM, which is 

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Dissipative Particle Dynamics (DPD) is a coarse graining method that groups several atoms into simulation sites whose dynamics is governed by conservative and frictional forces designed to reproduce thermodynamics and hydrodynamics [132,133]. Since the effective interactions are constmcted to reproduce macroscopic properties soft repulsive forces can be used, thereby avoiding the small MD step sizes needed to integrate the system when full interactions are taken into account. In addition, random... 

Particle-based methods have been linked to continuum models in order to exploit the efficiency of hnite element schemes and yet account for boundary layers and other regions where continuum approaches may fail [135]. It is very likely that coarse grained methods will continue to be developed and used since many physical systems are too large or too complex to be treated by full MD. 

Saunders, M. G., and G. A. Voth, Coarse-graining methods for computational biology, in Annual Review of Biophysics, vol 42, K. A. Dill, ed. 2013, Annual Reviews Palo Alto. pp. 73-93. 

Saunders, M.G., Voth, G.A. Coarse-graining methods for computational biology. Annu. Rev. Biophys. 42, 73-93 (2013)... 

Fig. 1.11 (a) A typical coarse-graining method replaces groups of atoms by ellipsoidal rigid bodies, (b) The Gay-Beme potential models the anisotropic interaction between nonspherical coarse-grained molecules potentials are described by the orientation of the molecules with respect to a fixed frame and the separation between their centers of mass... 

Keywords Molecular Simulation Quanmm Atomistic Coarse-Grained Methods... 

Fritz D (2009) Coarse-graining methods and polymer dynamics. PhD Thesis, University of Mainz... 

Multiscale Coarse-Graining Method (Force Matching Method)... 

Noid WG, Chu JW, Ayton GS, Krishna V, Izvekov S, Voth GA, Das A, Andersen HC (2008) The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarsegrained models. J Chem Phys 128(24) 244114... 

Das A, Andersen HC (2009) The multiscale coarse-graining method. HI. A test of pairwise additivity of the coarse-grained potential and of new basis functions for the variational calculation. J Chem Phys 131(3) 034102... 

Izvekov S, Chung PW, Rice BM (2010) The multiscale coarse-graining method assessing its accuracy and introducing density depraidcait coarse-grain potentials. J Chem Phys 133 064109... 

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