Coarse-Grained MD

One aspect of MD simulations is that all molecules, including the solvent, are specified in full detail. As detailed above, much of the CPU time in such a simulation is used up by following all the solvent (water) molecules. An alternative to the MD simulations is Brownian dynamics (BD) simulation. In this method, the solvent molecules are removed from the simulations. The effects of the solvent molecules are then reintroduced into the problem in an approximate way. Firstly, of course, the interaction parameters are adjusted, because the interactions should now include the effect of the solvent molecules. Furthermore, it is necessary to include a fluctuating force acting on the beads (atoms). These fluctuations represent the stochastic forces that result from the collisions of solvent molecules with the atoms. We know of no results using this technique on lipid bilayers. 

Qualitatively, the bilayer structures that result from DPD simulations are reasonable [65], In the simulation box, it is possible to find a stable bilayer in which the head groups shield the apolar core from the water phase. This means that the model effectively features a start-and-stop mechanism for 

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These coarse-grained MD calculations helped consolidate the main features of microstructure formation in CLs of PEFCs. They showed that the final microstructure depends on carbon particle choices and ionomer-carbon... 

Similarly the experimental dynamic structure factor also seems to be in disagreement with the latest and most extensive coarse grained MD-simula-tions by Putz et al. [79]. Figure 3.26 compares the computed structure factors... 

Atomistic MD simulation/Coarse-grained MD simulation Continuum elastic modeling... 

Leon S, van der Vegt N, Delle Site L, Kremer K (2005) Bisphenol-A-polycarbonale entanglement analysis from coarse-grained MD simulations. Macromolecules 38 8078-8092... 

Atomistic and coarse-grained MD simulations of self-organization in catalyst layers suggest that the resulting structures are inherently unstable. Applicable solvents with different dielectric constants correspond to different stable conformations in terms of agglomerate sizes, sizes of ionomer domains, pore space... 

Dissipative particle dynamics (DPD) is a meshless, coarse-grained, particle-based method used to simulate systems at mesoscopic length and timescales (Coveney and Espafiol 1997 Espafiol and Warren 1995). In simple terms, DPD can be interpreted as coarse-grained MD. Atoms, molecules, or monomers are grouped together into mesoscopic clusters, or beads, that are acted on by conservative, dissipative, and random forces. The interaction forces are pairwise additive in nature and act between bead centers. Connections between DPD and the macroscopic (hydrodynamic, Navier-Stokes) level of description (Espanol 1995 Groot and Warren 1997), as well as microscopic (atomistic MD) have been well established (Marsh and Coveney 1998). DPD has been used to model a wide variety of systems such as lipid bilayer membranes (Groot and Rabone 2001), vesicles (Yamamoto et al. 2002), polymersomes (Ortiz et al. 2005), binary immiscible fluids (Coveney and Novik 1996), colloidal suspensions (Boek et al. 1997), and nanotube polymer composites (Maiti etal.2005). 

Simulations of physical properties of realistic Pt/support nanoparticle systems can provide interaction parameters that are used by molecular-level simulations of self-organization in CL inks. Coarse-grained MD studies presented in the section Mesoscale Model of Self-Organization in Catalyst Layer Inks provide vital insights on structure formation. Information on agglomerate formation, pore space morphology, ionomer structure and distribution, and wettability of pores serves as input for parameterizations of structure-dependent physical properties, discussed in the section Effective Catalyst Layer Properties From Percolation Theory. CGMD studies can be applied to study the impact of modifications in chemical properties of materials and ink composition on physical properties and stability of CLs. 

Coarse-grained MD simulations have been employed to study the kinetics of polymer flow into the slit - a process similar to the intercalation of polymer into clay gallery. It is showed that a moderate clay-polymer afftnity is needed to achieve the spontaneous intercalation of polymer and swelling of day [6j. A relatively higher... 

To overcome this shortcoming of atomistic simulations, and in order to retain sufficient chemical accuracy in the description of mesoscopic membrane properties, coarse-grain MD simulations have been extensively developed in the last two decades, and they have proven to he remarkably successful towards the investigation of multiple crucial membrane-mediated cellular phenomena. ... 

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