Literature DB >> 23227104

The role of collective motion in examples of coarsening and self-assembly.

Stephen Whitelam1, Edward H Feng, Michael F Hagan, Phillip L Geissler.   

Abstract

The simplest prescription for building a patterned structure from its constituents is to add particles, one at a time, to an appropriate template. However, self-organizing molecular and colloidal systems in nature can evolve in much more hierarchical ways. Specifically, constituents (or clusters of constituents) may aggregate to form clusters (or clusters of clusters) that serve as building blocks for later stages of assembly. Here we evaluate the character and consequences of such collective motion in a set of prototypical assembly processes. We do so using computer simulations in which a system's capacity for hierarchical dynamics can be controlled systematically. By explicitly allowing or suppressing collective motion, we quantify its effects. We find that coarsening within a two dimensional attractive lattice gas (and an analogous off-lattice model in three dimensions) is naturally dominated by collective motion over a broad range of temperatures and densities. Under such circumstances, cluster mobility inhibits the development of uniform coexisting phases, especially when macroscopic segregation is strongly favored by thermodynamics. By contrast, the assembly of model viral capsids is not frustrated but is instead facilitated by collective moves, which promote the orderly binding of intermediates consisting of several monomers.

Entities:  

Year:  2008        PMID: 23227104      PMCID: PMC3516813          DOI: 10.1039/b810031d

Source DB:  PubMed          Journal:  Soft Matter        ISSN: 1744-683X            Impact factor:   3.679


  22 in total

1.  Colloidal nanocrystal shape and size control: the case of cobalt.

Authors:  V F Puntes; K M Krishnan; A P Alivisatos
Journal:  Science       Date:  2001-03-16       Impact factor: 47.728

2.  Self-assembly at all scales.

Authors:  George M Whitesides; Bartosz Grzybowski
Journal:  Science       Date:  2002-03-29       Impact factor: 47.728

3.  Collective Monte Carlo updating for spin systems.

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Journal:  Phys Rev Lett       Date:  1989-01-23       Impact factor: 9.161

4.  Nonuniversal critical dynamics in Monte Carlo simulations.

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Journal:  Phys Rev Lett       Date:  1987-01-12       Impact factor: 9.161

5.  Simulation study of the contribution of oligomer/oligomer binding to capsid assembly kinetics.

Authors:  Tiequan Zhang; Russell Schwartz
Journal:  Biophys J       Date:  2005-10-07       Impact factor: 4.033

6.  Self-assembly of polymer-tethered nanorods.

Authors:  Mark A Horsch; Zhenli Zhang; Sharon C Glotzer
Journal:  Phys Rev Lett       Date:  2005-07-29       Impact factor: 9.161

7.  RECONSTITUTION OF ACTIVE TOBACCO MOSAIC VIRUS FROM ITS INACTIVE PROTEIN AND NUCLEIC ACID COMPONENTS.

Authors:  H Fraenkel-Conrat; R C Williams
Journal:  Proc Natl Acad Sci U S A       Date:  1955-10-15       Impact factor: 11.205

8.  Colloids with key-lock interactions: nonexponential relaxation, aging, and anomalous diffusion.

Authors:  Nicholas A Licata; Alexei V Tkachenko
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2007-10-25

9.  Avoiding unphysical kinetic traps in Monte Carlo simulations of strongly attractive particles.

Authors:  Stephen Whitelam; Phillip L Geissler
Journal:  J Chem Phys       Date:  2007-10-21       Impact factor: 3.488

10.  Chaperonin filaments: the archaeal cytoskeleton?

Authors:  J D Trent; H K Kagawa; T Yaoi; E Olle; N J Zaluzec
Journal:  Proc Natl Acad Sci U S A       Date:  1997-05-13       Impact factor: 11.205

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  22 in total

1.  Hierarchical Order Parameters for Macromolecular Assembly Simulations I: Construction and Dynamical Properties of Order Parameters.

Authors:  Abhishek Singharoy; Yuriy Sereda; Peter J Ortoleva
Journal:  J Chem Theory Comput       Date:  2012-03-13       Impact factor: 6.006

2.  Understanding the concentration dependence of viral capsid assembly kinetics--the origin of the lag time and identifying the critical nucleus size.

Authors:  Michael F Hagan; Oren M Elrad
Journal:  Biophys J       Date:  2010-03-17       Impact factor: 4.033

3.  Mechanisms of capsid assembly around a polymer.

Authors:  Aleksandr Kivenson; Michael F Hagan
Journal:  Biophys J       Date:  2010-07-21       Impact factor: 4.033

4.  An improved coarse-grained model of solvation and the hydrophobic effect.

Authors:  Patrick Varilly; Amish J Patel; David Chandler
Journal:  J Chem Phys       Date:  2011-02-21       Impact factor: 3.488

5.  Mechanisms of kinetic trapping in self-assembly and phase transformation.

Authors:  Michael F Hagan; Oren M Elrad; Robert L Jack
Journal:  J Chem Phys       Date:  2011-09-14       Impact factor: 3.488

6.  Monte Carlo simulation of kinetically slowed down phase separation.

Authors:  Štěpán Růžička; Michael P Allen
Journal:  Eur Phys J E Soft Matter       Date:  2015-06-30       Impact factor: 1.890

7.  Modelling toehold-mediated RNA strand displacement.

Authors:  Petr Šulc; Thomas E Ouldridge; Flavio Romano; Jonathan P K Doye; Ard A Louis
Journal:  Biophys J       Date:  2015-03-10       Impact factor: 4.033

8.  How to simulate patchy particles.

Authors:  Lorenzo Rovigatti; John Russo; Flavio Romano
Journal:  Eur Phys J E Soft Matter       Date:  2018-05-14       Impact factor: 1.890

9.  Hierarchical Multiscale Modeling of Macromolecules and their Assemblies.

Authors:  P Ortoleva; A Singharoy; S Pankavich
Journal:  Soft Matter       Date:  2013-04-28       Impact factor: 3.679

10.  DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization.

Authors:  John S Schreck; Thomas E Ouldridge; Flavio Romano; Petr Šulc; Liam P Shaw; Ard A Louis; Jonathan P K Doye
Journal:  Nucleic Acids Res       Date:  2015-06-08       Impact factor: 16.971

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