Synonyms
Definition
In computational chemistry coarse-grained (CG) models are defined as molecular models where some details (i.e., degrees of freedom) of the original chemical structure have been removed. The resulting models are a coarser description of the chemical systems compared with the original ones and can then be used to perform either molecular dynamics or Monte Carlo simulations [1]. The reduction of the models’ degrees of freedom enables the simulation of systems whose size is comparable with that of the experimental ones and the timescale spanned by these simulations can reach microseconds.
Overview
Computer modeling is a powerful technique to gain molecular level details of chemical systems under different physical conditions and enables to relate macroscopic observations with changes in the chemical and physical state of the system. However, all modeling techniques rely on computer hardware, and therefore their use is...
References
Allen, M.P., Tildesley, D.J.: Computer Simulation of Liquids. Oxford University Press, Oxford (2002)
Ponder, J.W., Case, D.A.: Force fields for protein simulations. Adv. Protein. Chem. 66, 27–85 (2003)
Karimi-Varzaneh, H., van der Vegt, N.F.A., Müller-Plathe, F., Carbone, P.: How good are coarse-grained polymer models? A comparison for atactic polystyrene. ChemPhysChem 13, 3428 (2012)
Voth, G.A.: Coarse-Graining of Condensed Phase and Biomolecular Systems, CRC edn. Taylor and Francis, Boca Raton (2008)
Carbone, P., Avendaño, C.: Coarse-grained methods for polymeric materials: Enthalpy and entropy driven models. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 4(1), 62–70 (2014)
Noid, W.G.: Perspective: Coarse-grained models for biomolecular systems. J. Chem. Phys. 7, 139 (2013)
Lyubartsev, A.P., Laaksonen, A.: Calculation of the effective interaction potentials from radial distribution functions – a reverse Monte-Carlo approach. Phys. Rev. E 52(4), 3730–3737 (1995)
Baschnagel, J., Binder, K., Doruker, P., Gusev, A.A., Hahn, O., Kremer, K., Mattice, W.L., Müller-Plathe, F., Murat, M., Paul, W., et al.: Bridging the gap between atomistic and coarse-grained models of polymers: Status and perspectives. Adv. Polym. Sci. 152, 41–156 (2000)
Marrink, S.J., Risselada, H.J., Yefimov, S., Tieleman, D.P., de Vries, A.H.: The MARTINI force field: Coarse grained model for biomolecular simulations. J. Phys. Chem. B 111(27), 7812–7824 (2007)
Shinoda, W., Devane, R., Klein, M.L.: Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants. Mol. Simul. 33(1–2), 27–36 (2007)
Avendaño, C., Lafitte, T., Galindo, A., Adjiman, C.S., Jackson, G., Müller, E.A.: SAFT-gamma force field for the simulation of molecular fluids. 1. A single-site coarse grained model of Carbon Dioxide. J. Phys. Chem. B 115(38), 11154–11169 (2011)
Ercolessi, F., Adams, J.B.: Interatomic potentials from 1st-principles calculations – the force-matching method. Europhys. Lett. 26(8), 583–588 (1994)
Noid, W.G., Chu, J.W., Ayton, G.S., Krishna, V., Izvekov, S., Voth, G.A., Das, A., Andersen, H.C.: The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models. J. Chem. Phys. 128(24), 244114 (2008)
Kullback, S., Leibler, R.A.: On information and sufficiency. Ann. Math. Stat. 22, 79 (1951)
Shell, M.S.: The relative entropy is fundamental to multiscale and inverse thermodynamic problems. J. Chem. Phys. 129, 144108 (2008)
Groot, R.D., Warren, P.B.: Dissipative particle dynamics: Bridging the gap between atomistic and mesoscopic simulation. J. Chem. Phys. 107, 4423–4435 (1997)
Espanol, P.: Dissipative particle dynamics. In: Handbook of Materials Modeling, pp. 2503–2512. Springer, Dordrecht (2005)
Altland, A., Simons, B.D.: Condensed Matter Field Theory, 2nd edn. Cambridge University Press, Leiden (2010)
Alexandridis, P., Lindman, B.: Amphiphilic Block Copolymers Self-Assembly and Applications. Elsevier, Amsterdam (2000). ISBN 978-0-444-82441-7
Ortiz, V., Nielsen, S.O., Discher, D.E., Klein, M.L., Lipowsky, R., Shillcock, J.: Dissipative particle dynamics simulations of polymersomes. J. Phys. Chem. B 109, 17708–17714 (2005)
Nawaz, S., Carbone, P.: Coarse-graining poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) (PEO-PPO-PEO) block copolymers using the MARTINI force field. J. Phys. Chem. B 118, 1648–1659 (2014)
Rogers, R.D., Seddon, K.R.: Ionic Liquids, Science 302, 792–793 (2003)
Wang, Y.T., Voth, G.A.: Unique spatial heterogeneity in ionic liquids. J. Am. Chem. Soc. 127, 12192–12193 (2005)
Karimi-Varzaneh, H., Muller-Plathe, F., Balasubramanian, S., Carbone, P.: Studying long-time dynamics of imidazolium-based ionic liquids with a systematically coarse-grained model. Phys. Chem. Chem. Phys. 12, 4714–4724 (2010)
Johnston, K., Harmandaris, V.: Hierarchical multiscale modeling of polymer–solid interfaces: atomistic to coarse-grained description and structural and conformational properties of polystyrene–gold systems. Macromolecules 46, 5741 (2013)
Abrams, F.C., Delle Site, L., Kremer, K.: Dual-resolution coarse-grained simulation of the bisphenol-A-polycarbonate/nickel interface. Phys. Rev. E 67, 21807 (2003)
Rzepiela, A.J., Louhivuori, M., Peter, C., Marrink, S.J.: Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites. Phys. Chem. Chem. Phys. 13, 10437–10448 (2011)
Di Pasquale, N., Marchisio, D., Carbone, P.: Mixing atoms and coarse-grained beads in modelling polymer melts. J. Chem. Phys. 137, 164111 (2012)
Praprotnik, M., Delle Site, L., Kremer, K.: Multiscale simulation of soft matter: from scale bridging to adaptive resolution. Annu. Rev. Phys. Chem. 59, 545–571 (2008)
Müller, M., de Pablo, J.J.: Computational approaches for the dynamics of structure formation in self-assembling polymeric materials. Annu. Rev. Mater. Res. 43, 1–34 (2013)
Daoulas, K.C., Müller, M., de Pablo, J.J., Nealey, P.F., Smith, G.D.: Morphology of multi-component polymer systems: single chain in mean field simulation studies. Soft Matter 2, 573–583 (2006)
Milano, G., Kawakatsu, T.: Hybrid particle-field molecular dynamics simulations for dense polymer systems. J. Chem. Phys. 130, 214106 (2009)
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Gowers, R., Carbone, P. (2015). Coarse-Grained and Hybrid Simulations of Nanostructures. In: Bhushan, B. (eds) Encyclopedia of Nanotechnology. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-6178-0_100940-1
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DOI: https://doi.org/10.1007/978-94-007-6178-0_100940-1
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Latest
Coarse-Grained and Hybrid Simulations of Nanostructures- Published:
- 26 December 2015
DOI: https://doi.org/10.1007/978-94-007-6178-0_100940-2
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Coarse-Grained and Hybrid Simulations of Nanostructures- Published:
- 14 May 2015
DOI: https://doi.org/10.1007/978-94-007-6178-0_100940-1