Literature DB >> 25591330

Communication: theoretical prediction of free-energy landscapes for complex self-assembly.

William M Jacobs1, Aleks Reinhardt1, Daan Frenkel1.   

Abstract

We present a technique for calculating free-energy profiles for the nucleation of multicomponent structures that contain as many species as building blocks. We find that a key factor is the topology of the graph describing the connectivity of the target assembly. By considering the designed interactions separately from weaker, incidental interactions, our approach yields predictions for the equilibrium yield and nucleation barriers. These predictions are in good agreement with corresponding Monte Carlo simulations. We show that a few fundamental properties of the connectivity graph determine the most prominent features of the assembly thermodynamics. Surprisingly, we find that polydispersity in the strengths of the designed interactions stabilizes intermediate structures and can be used to sculpt the free-energy landscape for self-assembly. Finally, we demonstrate that weak incidental interactions can preclude assembly at equilibrium due to the combinatorial possibilities for incorrect association.

Year:  2015        PMID: 25591330     DOI: 10.1063/1.4905670

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  10 in total

1.  Rational design of self-assembly pathways for complex multicomponent structures.

Authors:  William M Jacobs; Aleks Reinhardt; Daan Frenkel
Journal:  Proc Natl Acad Sci U S A       Date:  2015-05-04       Impact factor: 11.205

2.  Information capacity of specific interactions.

Authors:  Miriam H Huntley; Arvind Murugan; Michael P Brenner
Journal:  Proc Natl Acad Sci U S A       Date:  2016-05-06       Impact factor: 11.205

3.  Folding Proteins One Loop at a Time.

Authors:  Daan Frenkel
Journal:  Biophys J       Date:  2016-09-06       Impact factor: 4.033

4.  Eye patches: Protein assembly of index-gradient squid lenses.

Authors:  J Cai; J P Townsend; T C Dodson; P A Heiney; A M Sweeney
Journal:  Science       Date:  2017-08-11       Impact factor: 47.728

5.  State-space reduction and equivalence class sampling for a molecular self-assembly model.

Authors:  Daniel M Packwood; Patrick Han; Taro Hitosugi
Journal:  R Soc Open Sci       Date:  2016-07-20       Impact factor: 2.963

6.  Structure-Based Prediction of Protein-Folding Transition Paths.

Authors:  William M Jacobs; Eugene I Shakhnovich
Journal:  Biophys J       Date:  2016-09-06       Impact factor: 4.033

Review 7.  The Art of Designing DNA Nanostructures with CAD Software.

Authors:  Martin Glaser; Sourav Deb; Florian Seier; Amay Agrawal; Tim Liedl; Shawn Douglas; Manish K Gupta; David M Smith
Journal:  Molecules       Date:  2021-04-15       Impact factor: 4.411

8.  Temperature protocols to guide selective self-assembly of competing structures.

Authors:  Arunkumar Bupathy; Daan Frenkel; Srikanth Sastry
Journal:  Proc Natl Acad Sci U S A       Date:  2022-02-22       Impact factor: 12.779

9.  Anatomy and formation mechanisms of early amyloid-β oligomers with lateral branching: graph network analysis on large-scale simulations.

Authors:  Miao Yuan; Xuan Tang; Wei Han
Journal:  Chem Sci       Date:  2022-02-08       Impact factor: 9.825

10.  Direct observation and rational design of nucleation behavior in addressable self-assembly.

Authors:  Martin Sajfutdinow; William M Jacobs; Aleks Reinhardt; Christoph Schneider; David M Smith
Journal:  Proc Natl Acad Sci U S A       Date:  2018-06-11       Impact factor: 11.205

  10 in total

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