Grained Molecular Dynamics Simulations

In recent years, CGMD simulations have found a wide range of applications in soft materials and biomolecular systems. In these systems, the CGMD approach has proven highly insightful and reliable (Voth, 2008). 

In the rigorous formulation of statistical mechanics, the coarse-grained system must represent a reasonable approach in view of the following formula  

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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. 

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). 

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)... 

Ziebarth J, Wang Y (2010) Coarse-grained molecular dynamics simulations of DNA condensation by block copolymer and formation of core-corona structures. J Phys Chem B 114 6225-6232... 

Arkhipov, A., Freddolino, P.L., Imada, K., Namba, K. Schulten, K. Coarse-grained molecular dynamics simulations of a rotating bacterial flagellum. Biophys. 91 (2006b), pp. 4589—4597. 

Therefore, quantum molecular dynamics simulations will generate the most detailed modeling of interatomic interactions as electrons are the basis of aU such interactions. Quantum simulations allow for certain phenomena like electron transport within a system to be modeled, which cannot be modeled in force-field or coarse grain molecular dynamics simulations because they do not explicitly model electrons. Also, in order to model chemical reactions, quantum simulations are the most accurate approach (Note there have been force-field and coarse-grain molecular dynamics simulations that have modeled the formation and breaking of bonds, but some a priori knowledge must then be included in the model to allow for the reaction to take place). The major limitations of quantum simulations is that the simulations are very computationally intensive, which results in the capability to model only small system sizes ( 10 particles) and time s). Thus the systems that can be modeled are limited to... 

Shi, Q., Izvekov, S. and Voth, G.A. (2005) Atomistic, mixed and coarse-grained molecular dynamics simulation of a membrane-bound ion channel. Journal of Physical Chemistry E, 110, 15045-8. 

Sinsawat, A. et al. (2003) Influence of polymer matrix composition and architecture on polymer nanocomposite formation Coarse-grained molecular dynamics simulation. J. Polym. Sci. Part B Polym. Phys.. 41, irj2-i27(>. 

Depa, P.K. and Maranas, J.K. (2005) Speed up of dynamic observables in coarse-grained molecular-dynamics simulations of unentangled polymers. 

Padding, ),T, and Briels, W.J. (2003) Coarse-grained molecular dynamics simulations of polymer melts in transient and steady shear flow. J. Chem. Phys., 118 (22), 10276-10286. 

Simulation of polymerization from a concave substrate could prove to be a challenging task because of the complexity of the system. However, Liu et al. used coarse-grained molecular dynamic simulation to investigate the effect of curvature on polymer growth and dispersity [90]. Unfortunately, the polymerization was considered to be a perfectly living polymerization (i.e., in the absence of termination and other side reactions), thus it does not help in elucidating the role of termination in SI-ATRP. 

Wang, Y., Jiang, W, Yan, T. Voth, G. A. (2007). Understanding ionic liquids through atomistic and coarse-grained molecular dynamics simulations, Acc. Chem. Res. 40(11) 1193-1199. 

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