Literature DB >> 12436902

Coarse-graining in polymer simulation: from the atomistic to the mesoscopic scale and back.

Florian Müller-Plathe1.   

Abstract

Polymers can be theoretically and computationally described by models pertaining to different length scales and corresponding time scales. These models have traditionally been used independently of each other. Recently, considerable progress has been made in systematically linking models of different scales. This Review focuses on the generation of lattice and off-lattice coarse-grained polymer models, whose "monomers" correspond to roughly a chemical repeat unit, from chemically detailed atomistic simulations of the same polymers. Computational methods are described as well as applications to polymers in the melt and in solution. The success of multiscale simulations in solving real-world polymer problems that could not be solved in any other way suggests that they will have an important role to play in the future.

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Year:  2002        PMID: 12436902     DOI: 10.1002/1439-7641(20020916)3:9<754::aid-cphc754>3.0.co;2-u

Source DB:  PubMed          Journal:  Chemphyschem        ISSN: 1439-4235            Impact factor:   3.102


  36 in total

1.  Characterizing protein energy landscape by self-learning multiscale simulations: application to a designed β-hairpin.

Authors:  Wenfei Li; Shoji Takada
Journal:  Biophys J       Date:  2010-11-03       Impact factor: 4.033

2.  Multiscale modeling of nucleosome dynamics.

Authors:  Shantanu Sharma; Feng Ding; Nikolay V Dokholyan
Journal:  Biophys J       Date:  2006-12-01       Impact factor: 4.033

3.  Coarse-grained peptide modeling using a systematic multiscale approach.

Authors:  Jian Zhou; Ian F Thorpe; Sergey Izvekov; Gregory A Voth
Journal:  Biophys J       Date:  2007-03-30       Impact factor: 4.033

4.  Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model.

Authors:  Chia-En Chang; Tongye Shen; Joanna Trylska; Valentina Tozzini; J Andrew McCammon
Journal:  Biophys J       Date:  2006-03-13       Impact factor: 4.033

5.  Molecular renormalization group coarse-graining of polymer chains: application to double-stranded DNA.

Authors:  Alexey Savelyev; Garegin A Papoian
Journal:  Biophys J       Date:  2009-05-20       Impact factor: 4.033

6.  Energy Renormalization for Coarse-Graining the Dynamics of a Model Glass-Forming Liquid.

Authors:  Wenjie Xia; Jake Song; Nitin K Hansoge; Frederick R Phelan; Sinan Keten; Jack F Douglas
Journal:  J Phys Chem B       Date:  2018-02-05       Impact factor: 2.991

Review 7.  Emerging applications of stimuli-responsive polymer materials.

Authors:  Martien A Cohen Stuart; Wilhelm T S Huck; Jan Genzer; Marcus Müller; Christopher Ober; Manfred Stamm; Gleb B Sukhorukov; Igal Szleifer; Vladimir V Tsukruk; Marek Urban; Françoise Winnik; Stefan Zauscher; Igor Luzinov; Sergiy Minko
Journal:  Nat Mater       Date:  2010-01-22       Impact factor: 43.841

8.  Development of a coarse-grained α-chitin model on the basis of MARTINI forcefield.

Authors:  Zechuan Yu; Denvid Lau
Journal:  J Mol Model       Date:  2015-04-26       Impact factor: 1.810

Review 9.  Coarse grained molecular dynamics simulations of transmembrane protein-lipid systems.

Authors:  Peter Spijker; Bram van Hoof; Michel Debertrand; Albert J Markvoort; Nagarajan Vaidehi; Peter A J Hilbers
Journal:  Int J Mol Sci       Date:  2010-06-09       Impact factor: 5.923

Review 10.  Combined molecular algorithms for the generation, equilibration and topological analysis of entangled polymers: methodology and performance.

Authors:  Nikos Ch Karayiannis; Martin Kröger
Journal:  Int J Mol Sci       Date:  2009-11-23       Impact factor: 6.208

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