Molecular dynamics simulations, coarse-grained

Fig. 5.5. Illustration of the coarse-graining procedure for a united atom chain. The chain is a segment of PE at 509 K from molecular dynamics simulations with the united atom model [Eqs. (5.7)—(5.11)]. One coarse-grained bond represents the end-to-end distance of n = 5 consecutive united atom bonds. From [32]...

At the mesoscopic scale, interactions between molecular components in membranes and catalyst layers control the self-organization into nanophase-segregated media, structural correlations, and adhesion properties of phase domains. Such complex processes can be studied by various theoretical tools and simulation techniques (e.g., by coarse-grained molecular dynamics simulations). Complex morphologies of the emerging media can be related to effective physicochemical properties that characterize transport and reaction at the macroscopic scale, using concepts from the theory of random heterogeneous media and percolation theory. 

Treptow, W., Marrink, S.J., Tarek, M. Gating motions in voltage-gated potassium channels revealed by coarse-grained molecular dynamics simulations. J. Phys. Chem. B 2008, 112, 3277-82. 

Besides microscopic technologies, the molecular dynamics simulation using coarse grain models to speed up the simulations improved the understanding of the effects of tentacle surface modifications (Cavalloti, 2008). The tentacular structure of lEX materials is characterized by a macroscopic reorganization caused by... 

In this review, we show our own results of thermal molecular motion of PS at the free surface by mainly scanning force microscopy and at the substrate interface by space-resolved fluorescence spectroscopy. To do so, we also adopt coarse-grained molecular dynamics simulation to strengthen experimental results. Finally, we... 

On the basis of our results using scanning force microscopy such as S VM and LFM, we claim that the mobility at the surface of PS films is not the same as that in the bulk. However, in such measurements, a probe tip made of silicon or silicon nitride makes contact with the surface to be measured. This may induce some artifacts in the results. If an effect of tip contact on the surface dynamics cannot be negligible, our conclusion must be reconsidered. Thus, T is here discussed on the basis of coarse-grained molecular dynamics simulation using a bead-spring model of Grest... 

Fig. 20 Depth dependence of Tg for PS obtained by coarse-grained molecular dynamics simulation. The 0 depth is at the substrate interface, and the value is in a real space. The upper abscissa is expressed by the chain dimension using radius of gyration (/fg) for an unpertiffbed polymer chain. The e value correspraids to Lennard-Jones energy between segments and substrate wall...

Anderson, K. L., Sinsawat, A., Vaia, R. A., and Farmer, B. L., Control of silicate nanocomposite morphology in binary fluids coarse-grained molecular dynamics simulations, J. Polym. Sci. B, 43, 1014-1024(2005). 

Figure 15.3 Generalized flow diagram of physics-based models, (a] Sequence information for PDB ID 4JRC is built into a (b] linear, coarsegrained molecular structure, (c] The coarse-grained structure undergoes molecular dynamics simulations with a parameterized force field, (d] The optimal structure is chosen and then (e] converted to an all-atom structure, which is minimized to form (f] the final three-dimensional structure. Disclaimer this diagram is generalized and not comprehensive to all physics-based models.

In most cases, the DNA CG models presented here are used in Langevin-based molecular dynamics (MD) simulations that propagate the positions and velocities of the CG sites in time and space. As described in the examples, when the appropriate sampling strategies are used, these simulations provide detailed information about the conformation space, in particular, appropriately describing the thermodynamics associated with the different conformations. Moving beyond equilibrium structural distributions, much less attention has been paid to the dynamical behavior of molecular systems in coarse-grained simulations, which should be addressed in future studies. 

May ER, Kopelevich DI, Narang A (2008) Coarse-grained molecular dynamics simulations of phase transitimis in mixed lipid systems containing LPA, DOPA, and DOPE lipids. Biophys J 94 878... 

Bhargava, B.L., DeVane, R., Klein, M.L., Balasubramanian, S. Nanoscale organization in room temperature ionic liquids a coarse grained molecular dynamics simulation study. Soft Matter 3, 1395-1400 (2007)... 

Padding, J., Briels, W. Time and length scales of polymer melts studied by coarse-grained molecular dynamics simulations. J. Chem. Phys. 117, 925-943 (2002)... 

Karimi-Varzaneh, H., Qian, H., Chen, X., Carbone, P., MuUer-Plathe, F. Ibisco a molecular dynamics simulation package fm coarse-grained simulation. J. Comp. Chem. 32, 1475-1487 (2011)... 

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