Coarse-Grained Simulations of Macromolecules: From DNA to Nanocomposites

被引:96
|
作者
de Pablo, Juan J. [1 ]
机构
[1] Univ Wisconsin, Dept Chem & Biol Engn, Madison, WI 53706 USA
关键词
molecular simulations; polymers; copolymers; nanoparticles; MOLECULAR-DYNAMICS SIMULATION; MONTE-CARLO SIMULATIONS; POLYMER-NANOCOMPOSITE; TOPOLOGICAL ANALYSIS; COMPUTER-SIMULATION; ENTANGLED POLYMERS; BLOCK-COPOLYMERS; SINGLE-CHAIN; MODEL; BEHAVIOR;
D O I
10.1146/annurev-physchem-032210-103458
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
This review discusses multiscale modeling and simulations of macromolecules and macromolecular systems in the context of two specific examples. In the first, recent attempts to develop coarse-grained representations of DNA are reviewed, and a discussion of recent predictions of such models is presented particularly in the context of DNA melting and rehybridization. The second example considers polymer nanocomposites; a review of recent simulations is presented, with an emphasis on the description of entanglements in such systems and new methods for the study of the segregation of nanoparticles that arises in copolymers, in which composition heterogeneity can be used to control nanoparticle position and develop an increased understanding of nanoparticle-polymer interactions.
引用
收藏
页码:555 / 574
页数:20
相关论文
共 50 条
  • [1] Coarse-grained simulations of DNA overstretching
    Romano, Flavio
    Chakraborty, Debayan
    Doye, Jonathan P. K.
    Ouldridge, Thomas E.
    Louis, Ard A.
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2013, 138 (08):
  • [2] Coarse-grained models for macromolecules
    Yethiraj, Arun
    [J]. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2013, 246
  • [3] Coarse-Grained Simulations of Penetrant Transport in Polymer Nanocomposites
    Pryamitsyn, Victor
    Hanson, Benjamin
    Ganesan, Venkat
    [J]. MACROMOLECULES, 2011, 44 (24) : 9839 - 9851
  • [4] Coarse-Grained Simulations of RNA and DNA Duplexes
    Cragnolini, Tristan
    Derreumaux, Philippe
    Pasquali, Samuela
    [J]. JOURNAL OF PHYSICAL CHEMISTRY B, 2013, 117 (27): : 8047 - 8060
  • [5] Atomistic and coarse-grained simulations of histones, Nuclesomes and DNA
    Papoian, Garegin
    Winogradoff, David
    Zhao, Haiqing
    Echeverria, Ignacia
    Dalal, Yamini
    [J]. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2015, 249
  • [6] DNA elasticity from coarse-grained simulations: The effect of groove asymmetry
    Skoruppa, Enrico
    Laleman, Michiel
    Nomidis, Stefanos K.
    Carlon, Enrico
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2017, 146 (21):
  • [7] A polarizable coarse-grained water model for coarse-grained proteins simulations
    Ha-Duong, Tap
    Basdevant, Nathalie
    Borgis, Daniel
    [J]. CHEMICAL PHYSICS LETTERS, 2009, 468 (1-3) : 79 - 82
  • [8] Classical, Coarse-Grained, and Reactive Molecular Dynamics Simulations on Polymer Nanocomposites
    Inseok Jeon
    Taeyoung Yun
    Seunghwa Yang
    [J]. Multiscale Science and Engineering, 2022, 4 (4) : 161 - 178
  • [9] Coarse-Grained and Atomistic MD Simulations of RNA and DNA Folding
    Leuchter, Jessica D.
    Green, Adam T.
    Gilyard, Julian
    Rambarat, Cecilia G.
    Cho, Samuel S.
    [J]. ISRAEL JOURNAL OF CHEMISTRY, 2014, 54 (8-9) : 1152 - 1164
  • [10] Novel Coarse-Grained Model for Molecular Dynamics Simulations of DNA
    Karolak, Aleksandra
    van der Vaart, Arjan
    [J]. BIOPHYSICAL JOURNAL, 2014, 106 (02) : 804A - 804A