Coarse-grained particle-based

Particle-based simulation techniques include atomistic MD and coarse-grained molecular dynamics (CG-MD). Accelerated dynamics methods, such as hyperdynamics and replica exchange molecular dynamics (REMD), are very promising for circumventing the timescale problem characteristic of atomistic simulations. Structure and dynamics at the mesoscale level can be described within the framework of coarse-grained particle-based models using such methods as stochastic dynamics (SD), dissipative particle dynamics (DPD), smoothed-particle hydrodynamics (SPH), lattice molecular dynamics (LMD), lattice Boltzmann method (IBM), multiparticle collision dynamics (MPCD), and event-driven molecular dynamics (EDMD), also referred to as collision-driven molecular dynamics or discrete molecular dynamics (DMD). 

Coarse-Grained Particle-Based Simulations 1.16.4.3.1 Stochastic dynamics... 

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). 

Secondly, we might mention that there are two possible attitudes to a theory of valence based on the AO expansion method. The chemist uses the electron-pair model essentially as one of his axioms or, at least, as a good working hypothesis. This model is extremely familiar and useful any theory of such a model of valence should be capable of providing at least some foundation for and extension of his qualitative concepts. To the physicist, however, the simplest molecules are quite complex many-particle systems and he would perhaps find it surprising if we are able to obtain any useful results from our coarse-grained minimal basis model in view of the complexity of the interactions involved. We must try to balance these views in any evalution we make. 

Coarse-grained molecular d5mamics simulations in the presence of solvent provide insights into the effect of dispersion medium on microstructural properties of the catalyst layer. To explore the interaction of Nation and solvent in the catalyst ink mixture, simulations were performed in the presence of carbon/Pt particles, water, implicit polar solvent (with different dielectric constant e), and ionomer. Malek et al. developed the computational approach based on CGMD simulations in two steps. In the first step, groups of atoms of the distinct components were replaced by spherical beads with predefined subnanoscopic length scale. In the second step, parameters of renormalized interaction energies between the distinct beads were specified. 

Fig. 3 A comparison of different coarse grain lipid models. The Shelley model " of DMPC, and Marrink and Essex models of DPPC are compared to their atomistic equivalents (for ease of comparison, hydrogen atoms of the atomistic models are not shown). Solid lines represent harmonic bonds connecting CG particles, and the CG particle types for the Shelley and Marrink models are labelled (the labels are the same as those used in the main text). The point charges (represented by + and —) and point dipoles (represented by arrows) are shown for the Essex model (the charges and dipoles are located at the centre of their associated CG particle). The Shelley and Marrink models use LJ particles (represented by spheres), while the Essex model uses a combination of LJ particles (spheres) and Gay-Berne particles (ellipsoids). Finally, the blob model proposed by Chao et al is also shown for comparison. This model represents groups of atoms as rigid non-spherical blobs that use interaction potentials based on multipole expansions.

A large class of currently used CG models employs what some researchers call particle-based coarse-graining, in which a finite number of atoms of the molecular system are grouped into a single point mass (a CG particle, sometimes called a mesoparticle or a pseudo-particle). In the simulations of biomolecules, most commonly only a few heavy atoms (between 3 and 5) are replaced by a CG particle. 

Usually base and precious metal sulfide deposits also have important amounts of pyrite. The pyrite in hydrothermal ore deposits is most often coarse grained and relatively unreactive. Mining and milling the rock to fine particle sizes for the purpose of metal extraction, vastly increases pyrite surface area and exposes the pyrite in waste-tailings piles to oxidation and weathering. Serious AMD releases can result. 

Particle-based methods have been linked to continuum models in order to exploit the efficiency of hnite element schemes and yet account for boundary layers and other regions where continuum approaches may fail [135]. It is very likely that coarse grained methods will continue to be developed and used since many physical systems are too large or too complex to be treated by full MD. 

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