Coarse-grain potentials

Although each of these models have their own merits, it is currently not clear how much predictive power these coarse-grained potentials have. Nevertheless, coarse-graining is a valid way of studying protein folding, and in the near future might have the much sought after power to predict novel folds. 

In a work by Chen et al. [186], Brownian dynamics was used to simulate the formatimi of micelles constituted of PS-PEO in water, with the particular aim of investigating the processes involved in flash nanoprecipitation . The effective (coarse-grained) potential was carefully mapped to experimentally determined... 

Moore, T.C., lacovella, C.R., McCabe, C. Derivation of coarse-grained potentials via multistate iterative Boltzmann inversion. J. Chem. Phys. 140, 224104 (2014)... 

Qian, H.J., et al. Temperature-transferable coarse-grained potentials for ethylbenzene, polystyrene, and their mixtures. Macromoleeules 41, 9919—9929 (2008)... 

If we now coajTse-grain the medium and denote by V the average value of the potential over some region of volnme fi, then the coarse-grained potential will have the distribution... 

The following section describes the application of QM-parameterized atomistic and coarse-grain potentials to tissue engineering. 

Wei J, Li C, van der Vegt NFA, Peter C (2011) Transferability of coarse grained potentials implicit solvent models for hydrated ions. J Chem Theory Comput, Doi 10.1021/ct2001396... 

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... 

Mullinax JW, Noid WG (2009) Extended ensemble approach for deriving transferable coarse-grained potentials. J ChemPhys 131 104110... 

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... 

Chiu CC et al (2010) Coarse-grained potential models for phenyl-based molecules II. Application to fullerenes. J Phys Chem B 114(19) 6394-6400... 

Krishna, V, Noid, W.G., and Voth, G.A. (2009) The multiscale coarse-graining method. IV. Transferring coarse-grained potentials between temperatures. J. Chem. Phys., 131 (2), 024103. 

Moreover, properties such as lipid lateral diffusion, lipid flip/flop, membrane elasticity and surface tension can be heavily biased in MD simulations by too small boundaries. The study in ref. 68 reported a model made of over 60 different lipid types, in a stoichiometric ratio compatible to that experimentally determined using lipidomics approaches, for a total of 20 000 lipid molecules, and simulated for 40 microseconds using coarse-grained potentials. 

Fig. 7 The AA/MG idea from ref. 144 a portion of interest of the protein is described at the all-atom level and coupled to the rest of the system described by a Coarse Grained potential. 

The coarse-grained potential (2.54) is the most general variant of an effective potential that would even allow for a correct quantitative description of the thermodynamic system behavior. However, typically, coarse-grained models are still drastically simplified such that models like the HP and the AB models for proteins (see Section 1.5) only represent approximate and sometimes crude versions of coarse-grained models. This further reduction of complexity is justified as long as the main features of system-relevant thermodynamic processes are reproduced, at least qualitatively,... 

Effective Meso-Scale Coarse Graining Potentials from Atomistic Simulations. 

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