Controlling Fragment Competition on Pathways to Addressable Self-Assembly
arXiv:1912.00961 · doi:10.1021/acs.jpcb.8b08096
Abstract
Addressable self-assembly is the formation of a target structure from a set of unique molecular or colloidal building-blocks, each of which occupies a defined location in the target. The requirement that each type of building-block appears exactly once in each copy of the target introduces severe restrictions on the combinations of particles and on the pathways that lead to successful self-assembly. These restrictions can limit the efficiency of self-assembly and the final yield of the product. In particular, partially formed fragments may compete with each other if their compositions overlap, since they cannot be combined. Here, we introduce a "completability" algorithm to quantify competition between self-assembling fragments and use it to deduce general principles for suppressing the effects of fragment incompatibility in the self-assembly of small addressable clusters. Competition originates from loops in the bonding network of the target structure, but loops may be needed to provide structural rigidity and thermodynamic stability. An optimal compromise can be achieved by careful choice of bonding networks and by promoting semi-hierarchical pathways that rule out competition between early fragments. These concepts are illustrated in simulations of self-assembly in two contrasting addressable targets of 20 unique components each.
arXiv comment35 pages (preprint style), 12 figures
References in corpus (16)
- Avoiding unphysical kinetic traps in Monte Carlo simulations of strongly attractive particles
- Controlling crystallization and its absence: Proteins, colloids and patchy models
- The role of collective motion in examples of coarsening and self-assembly
- Rational design of self-assembly pathways for complex multicomponent structures
- Vacancy-stabilized crystalline order in hard cubes
- DNA-Programmed Mesoscopic Architecture
- Numerical evidence for nucleated self-assembly of DNA brick structures
- The self-assembly and evolution of homomeric protein complexes
- Monodisperse self-assembly in a model with protein-like interactions
- Self-assembly of monodisperse clusters: Dependence on target geometry
- Extracting bulk properties of self-assembling systems from small simulations
- Theoretical prediction of free-energy landscapes for complex self-assembly
- Do hierarchical structures assemble best via hierarchical pathways?
- Direct observation and rational design of nucleation behavior in addressable self-assembly
- Design Strategies for Self-Assembly of Discrete Targets
- Optimising self-assembly through time-dependent interactions