Coarse grain simulations

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. 

Molinero, V. and Goddard, W.A. HI M3B a coarse grain simulations of malto-oligosaccharides and their water mixtures, /. Phys. Chem. B, 108,1414, 2004. 

We present here coarse grain simulation results of two simple binary water-carbohydrate mixtures that shed light on the mechanism of water diffusion in the supercooled and glassy state, the coupling of water mobility in the glass to the sub-Tg dynamics of the matrix, and the effect of the internal modes of the saccharide on the decoupling of water motion from carbohydrate translation. 

Mesoscale simulation methods [34] bridge between the short length and time scales typically probed by atomistic and coarse-grained simulations at a higher computational cost and the larger scales typically probed by continuum simulations of bulk material behavior. Figure 7.4 is a schematic illustration of length and time scales, adapted from Shelley and Shelley [35]. 

It is not easy to formulate simple rules that could be applied consistently to predict reliably these subtle balances between competing factors. Atomistic and/or coarse-grained simulations may be able to help improve our understanding of the interplay between the competing factors. 

This chapter will review the generation of free-standing thin films and fibers with a coarse-grained simulation method on a high coordination lattice,performed in a manner that allows accurate reverse-mapping of individual replicas to a fully atomistic representation in continuous space.4 After describing some of the properties of these films and fibers, we will present some new information about the limits on the stability of the models of these nanofibers. 

Elezgaray, and Laguerre, M. (2006]. A systematic method to derive force fields for coarse-grained simulations of phospholipids, Computer Physics Communications 175,4, pp. 264-268, doi http //dx.doi.org/10. 1016/j.cpc.2006.01.009, URL http //www.sciencedirect.com/science/ article/pii/S0010465506001585. 

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. 

Cragnolini, T, Derreumaux, R, and Pasquali, S. (2013). Coarse-grained simulations of RNA and DNA duplexes. The journal of Physical Chemistry B117, 27, pp. 8047-8060. 

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)... 

Breitsprecher, K., P. KoSovan, and C. Holm. 2014. Coarse-grained simulations of an ionic liquid-based capacitor I. Density, ion size, and valency effects. Journal of Physics Condensed Matter 26 284108. 

In Equation 7.2, pt +i represents the probability of the system changing from current configuration i to a new configuration i + 1, AE the change in potential energy associated with the attempted move, the Boltzmann constant, and T the temperature of the system. MC simulations are often performed in NVT and pVT ensembles, and widely applied to polymers as well as polymers in contact with filler particles. Brownian dynamics (BD) and dissipative particle dynamics (DPD) are further particle-based coarse-grained simulation methods similar to MD simulation. BD employs a continuum solvent model rather than explicit solvent molecules in MD and the total force is ... 

The thermodynamic effects of finite size and the kinetic barriers, AG, for the formation of vapor phase have been fully developed [41-46]. Macroscopic thermodynamics predicts that when we have two non-polar surfaces immersed in a liquid and bring them closer together, at a critical distance, Dc, liquid will be replaced by vapor (2). Due to a considerable free energy barrier for confinement-induced evaporation, however, the liquid phase is often metastable below Dc [36, 41, 43, 45, 47]. Coarse-grained simulations confirmed [45] macroscopic scaling predictions [48, 49] ... 

Abstract We review recent work on scale-bridging modeling approaches applied to aqueous electrolytes and polyelectrolytes, connecting the local quantum chemical details to classical statistical and thermodynamics properties. We discuss solvation and pairing of ions in water, ways to include solvent degrees of freedom in effective ion-ion interactions, and coarse-grained simulations of polyelectrolytes including dielectric boundary effects. 

Murtola T, Karttunen M, Vattulainen U (2009) Chem Phys 131 055101 Villa A, Peter C, van der Vegt NFA (2010) Transferability of nonbonded interaction potentials for coarse grained simulations benzene in water. J Chem Theory Comput 6 2434-2444... 

Hess B, Leon S, van der Vegt NFA, Kremer K (2006) Long time polymer trajectories from coarse grained simulations bisphenol-A-polycarbonate. Soft Matter 2 409 14... 

Keywords Atomistic simulation Coarse-graining simulation Computational chemistry Multiscale modeling... 

---