Coarse grained molecular dynamics

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. 

An alternative mesoscale approach for high-level molecular modeling of hydrated ionomer membranes is coarse-grained molecular dynamics (CGMD) simulations. One should notice an important difference between CGMD and DPD techniques. CGMD is essentially a multiscale technique (parameters are directly extracted from classical atomistic MD) and it... 

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. 

R.E. Rudd, J.Q. Broughton Coarse-grained molecular dynamics and the atomic limit of finite elements. Phys. Rev. B 58, R5893-R5896 (1998)... 

Rudd, R.E. and Broughton, J.Q. (1998) Coarse-grained Molecular Dynamics and the Atomic Limit of Finite Elements. Phys. Rev. B, 58, R5893-R5896. 

A new coarse grained molecular dynamics model was developed to study the role of thermal, mechanical and chemical reactions in the onset of the ablation process of PMMA [58]. In this model, the laser energy is absorbed in different ways, i.e. pure heating and Norrish type I and II reactions. Mechanical stresses and pressure are dominant for very short pulses in the stress confinement regime and can initiate... 

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...

Srinivas G, Discher DE, Klein M (2004) Self-assembly and properties of diblock copolymers by coarse-grain molecular dynamics. Nat Mater 3 6338-6344... 

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). 

Shinoda, W., et al.. Probing the structure of PEGylated-lipid assemblies by coarse-grained molecular dynamics. Soft Matter, 2013. 9(48) pp. 

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)... 

Dissipative particle dynamics refers to a particle-based numerical method in which the dynamics of particles that interact through conservative, dissipative, and random forces are computed. The method is coarse-grained molecular dynamics and has the ability to capture flow at mesoscopic scales, i.e., those scales that lie between microscopic and macroscopic ones. 

Delcorte, A., Garrison, B.J. (2007) Sputtering polymers with buckminsterfullerene projectiles a coarse-grain molecular dynamics study. J. Phys. Chem. C, 111, 15312-15324. 

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... 

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). 

Calculating the structural properties of the component from its chemical composition (e.g., for the case of polymer electrolyte membrane fuel cell (PEMFC) electrodes, by using coarse-grain molecular dynamics (CGMD)) (Fig. 10)... 

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