Literature DB >> 21219152

Coarse-grained simulations of macromolecules: from DNA to nanocomposites.

Juan J de Pablo1.   

Abstract

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.

Entities:  

Mesh:

Substances:

Year:  2011        PMID: 21219152     DOI: 10.1146/annurev-physchem-032210-103458

Source DB:  PubMed          Journal:  Annu Rev Phys Chem        ISSN: 0066-426X            Impact factor:   12.703


  20 in total

1.  A coarse-grain three-site-per-nucleotide model for DNA with explicit ions.

Authors:  Gordon S Freeman; Daniel M Hinckley; Juan J de Pablo
Journal:  J Chem Phys       Date:  2011-10-28       Impact factor: 3.488

2.  Molecular stripping in the NF-κB/IκB/DNA genetic regulatory network.

Authors:  Davit A Potoyan; Weihua Zheng; Elizabeth A Komives; Peter G Wolynes
Journal:  Proc Natl Acad Sci U S A       Date:  2015-12-23       Impact factor: 11.205

3.  Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions.

Authors:  Ya-Zhou Shi; Lei Jin; Feng-Hua Wang; Xiao-Long Zhu; Zhi-Jie Tan
Journal:  Biophys J       Date:  2015-12-15       Impact factor: 4.033

Review 4.  Molecular modeling of nucleic acid structure: energy and sampling.

Authors:  T E Cheatham; B R Brooks; P A Kollman
Journal:  Curr Protoc Nucleic Acid Chem       Date:  2001-05

5.  Molecular modeling of nucleic acid structure: electrostatics and solvation.

Authors:  T E Cheatham; B R Brooks; P A Kollman
Journal:  Curr Protoc Nucleic Acid Chem       Date:  2001-08

6.  Structure and conformational dynamics of scaffolded DNA origami nanoparticles.

Authors:  Keyao Pan; William P Bricker; Sakul Ratanalert; Mark Bathe
Journal:  Nucleic Acids Res       Date:  2017-06-20       Impact factor: 16.971

7.  Switching promotor recognition of phage RNA polymerase in silico along lab-directed evolution path.

Authors:  Chao E; Liqiang Dai; Jin Yu
Journal:  Biophys J       Date:  2022-01-11       Impact factor: 4.033

8.  More than the sum of its parts: coarse-grained peptide-lipid interactions from a simple cross-parametrization.

Authors:  Tristan Bereau; Zun-Jing Wang; Markus Deserno
Journal:  J Chem Phys       Date:  2014-03-21       Impact factor: 3.488

Review 9.  Theoretical frameworks for multiscale modeling and simulation.

Authors:  Huan-Xiang Zhou
Journal:  Curr Opin Struct Biol       Date:  2014-02-01       Impact factor: 6.809

Review 10.  Molecular modeling of nucleic acid structure: energy and sampling.

Authors:  Christina Bergonzo; Rodrigo Galindo-Murillo; Thomas E Cheatham
Journal:  Curr Protoc Nucleic Acid Chem       Date:  2013-10-08
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.