The Statistical Mechanics of Dynamic Pathways to Self-Assembly

Whitelam, Stephen; Jack, Robert L.

doi:10.1146/annurev-physchem-040214-121215

Cited by 193 publications

(249 citation statements)

References 163 publications

(266 reference statements)

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“…We leave the extensions to more complex kinetic models [41][42][43] such as hierarchical assembly to future work. Our framework and results have precedence in earlier work on the impact of concentrations in specific models of micelles 44 , polymer condensation 39 and protein complexes 37 .…”

Section: Discussionmentioning

confidence: 99%

Undesired usage and the robust self-assembly of heterogeneous structures

2015

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Inspired by multiprotein complexes in biology and recent successes in synthetic DNA tile and colloidal self-assembly, we study the spontaneous assembly of structures made of many kinds of components. The major challenge with achieving high assembly yield is eliminating incomplete or incorrectly bound structures. Here, we find that such undesired structures rapidly degrade yield with increasing structural size and complexity in diverse models of assembly, if component concentrations reflect the composition (that is, stoichiometry) of the desired structure. But this yield catastrophe can be mitigated by using highly nonstoichiometric concentrations. Our results support a general principle of 'undesired usage'-concentrations of components should be chosen to account for how they are 'used' by undesired structures and not just by the desired structure. This principle could improve synthetic assembly methods, but also raises new questions about expression levels of proteins that form biological complexes such as the ribosome.

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Section: Discussionmentioning

confidence: 99%

Undesired usage and the robust self-assembly of heterogeneous structures

2015

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“…Our findings imply that controlled self-assembly of 3D addressable structures is unlikely to be achieved straightforwardly using subunits with coordination numbers higher than 4. In higher-coordinated structures, which are well described by CNT, it would be necessary to go to high supersaturation to find a surmountable nucleation barrier; however, such an approach is likely to fail due to kinetic trapping (17). However, in DNA-brick structures, the nucleation barrier is surmountable at low supersaturation and is relatively insensitive to the size of the target structure (Fig.…”

Section: Coordination Number Controls the Nucleation Barriermentioning

confidence: 99%

Rational design of self-assembly pathways for complex multicomponent structures

Jacobs

Reinhardt

Frenkel

2015

Proc. Natl. Acad. Sci. U.S.A.

108

142

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The field of complex self-assembly is moving toward the design of multiparticle structures consisting of thousands of distinct building blocks. To exploit the potential benefits of structures with such "addressable complexity," we need to understand the factors that optimize the yield and the kinetics of self-assembly. Here we use a simple theoretical method to explain the key features responsible for the unexpected success of DNA-brick experiments, which are currently the only demonstration of reliable self-assembly with such a large number of components. Simulations confirm that our theory accurately predicts the narrow temperature window in which error-free assembly can occur. Even more strikingly, our theory predicts that correct assembly of the complete structure may require a time-dependent experimental protocol. Furthermore, we predict that low coordination numbers result in nonclassical nucleation behavior, which we find to be essential for achieving optimal nucleation kinetics under mild growth conditions. We also show that, rather surprisingly, the use of heterogeneous bond energies improves the nucleation kinetics and in fact appears to be necessary for assembling certain intricate 3D structures. This observation makes it possible to sculpt nucleation pathways by tuning the distribution of interaction strengths. These insights not only suggest how to improve the design of structures based on DNA bricks, but also point the way toward the creation of a much wider class of chemical or colloidal structures with addressable complexity.self-assembly | free-energy landscapes | nucleation | DNA nanotechnology R ecent experiments with short pieces of single-stranded DNA (1, 2) have shown that it is possible to assemble well-defined molecular superstructures from a single solution with more than merely a handful of distinct building blocks. These experiments use complementary DNA sequences to encode an addressable structure (3) in which each distinct single-stranded "brick" belongs in a specific location within the target assembly. A remarkable feature of these experiments is that even without careful control of the subunit stoichiometry or optimization of the DNA sequences, a large number of 2-and 3D designed structures with thousands of subunits assemble reliably (1, 2, 4, 5). The success of this approach is astounding given the many ways in which the assembly of an addressable structure could potentially go wrong (6-8).Any attempt to optimize the assembly yield or to create even more complex structures should be based on a better understanding of the mechanism by which DNA bricks manage to self-assemble robustly. The existence of a sizable nucleation barrier, as originally proposed in refs. 1, 2, would remedy two possible sources of error that were previously thought to limit the successful assembly of multicomponent nanostructures: the depletion of free monomers and the uncontrolled aggregation of partially formed structures. Slowing the rate of nucleation would suppress competition among multiple nucleatio...

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“…For the success of programmed self-assembly into a target structure, the microscale colloidal particles need to negotiate the so-called kinetic traps, which arise from the presence of metastable "wrong" structures in the free-energy landscape. 39 Reversible association allows for facile annealing of defects, and hence removal of kinetic traps. Such reversibility is best achieved here at the expense of relatively weak thermodynamic driving forces for the second stage of assembly.…”

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confidence: 99%

Programming hierarchical self-assembly of colloids: matching stability and accessibility

Morphew

Chakrabarti

2018

Nanoscale

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Encoding hierarchical self-assembly in colloidal building blocks is a promising bottom-up route to high-level structural complexity often observed in biological materials. However, harnessing this promise faces the grand challenge of bridging hierarchies of multiple length-and time-scales, associated with structure and dynamics respectively along the self-assembly pathway. Here we report on a case study, which examines the kinetic accessibility of a series of hollow spherical structures with a two-level structural hierarchy self-assembled from charge-stabilized colloidal magnetic particles. By means of a variety of computational methods, we find that for a staged assembly pathway, the structure, which derives the strongest energetic stability from the first stage of assembly and the weakest from the second stage, is most kinetically accessible. Such a striking correspondence between energetics and kinetics for optimal design principles should have general implications for programming hierarchical self-assembly pathways for nano-and micro-particles, while matching stability and accessibility.Self-assembly of colloidal particles offers tremendous opportunities for fabricating three-dimensional structures in a bottom-up approach due to the scope for tuning the interparticle interactions.1,2 Recent advances in the synthesis of complex colloidal particles have made a wide variety of nanoand micro-scale building blocks available. Many of these colloidal building blocks involve anisotropic interparticle interactions, often due to either anisotropic shape or heterogeneous surface chemistry. 2-5 These novel colloidal particles offer rich avenues for programming colloidal self-assembly.6,7Hierarchical self-assembly of nano-and micro-particles is emerging as an attractive route to structural organization at a higher level, spanning multiple length scales. 8,9 Notably, the hierarchical self-assembly of mono-disperse colloidal octapodshaped nanocrystals resulted in a three-dimensional superlattice via the formation of linear chains of interlocked octapods. 10 The assembly of binary and ternary patchy nanoparticles produced supracolloidal ordered structures in a hierarchical scheme. 11 The 'patchiness' of colloidal triblock spherical particles was exploited to encode staged self-assembly triggered by stepwise changes of the ionic strength of the medium. 12 A computational study demonstrated an alternative scheme for patchiness without engineered surfaces en route to a variety of complex superstructures via hierarchical selfassembly. 13 A theoretical analysis was presented for programming self-assembly of octopus nanoparticles, which themselves may be self-assembled, into a target nanostructure.

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The Statistical Mechanics of Dynamic Pathways to Self-Assembly

Cited by 193 publications

References 163 publications

Undesired usage and the robust self-assembly of heterogeneous structures

Undesired usage and the robust self-assembly of heterogeneous structures

Rational design of self-assembly pathways for complex multicomponent structures

Programming hierarchical self-assembly of colloids: matching stability and accessibility

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