Programmable control of nucleation for algorithmic self-assembly

DOI10.1137/070680266zbMATH Open1205.68497arXivcond-mat/0607317OpenAlexW2077771699MaRDI QIDQ3586192FDOQ3586192

Authors: Rebecca Schulman, Erik Winfree 

Publication date: 6 September 2010

Published in: SIAM Journal on Computing (Search for Journal in Brave)

Abstract: Algorithmic self-assembly, a generalization of crystal growth processes, has been proposed as a mechanism for autonomous DNA computation and for bottom-up fabrication of complex nanostructures. A `program' for growing a desired structure consists of a set of molecular `tiles' designed to have specific binding interactions. A key challenge to making algorithmic self-assembly practical is designing tile set programs that make assembly robust to errors that occur during initiation and growth. One method for the controlled initiation of assembly, often seen in biology, is the use of a seed or catalyst molecule that reduces an otherwise large kinetic barrier to nucleation. Here we show how to program algorithmic self-assembly similarly, such that seeded assembly proceeds quickly but there is an arbitrarily large kinetic barrier to unseeded growth. We demonstrate this technique by introducing a family of tile sets for which we rigorously prove that, under the right physical conditions, linearly increasing the size of the tile set exponentially reduces the rate of spurious nucleation. Simulations of these `zig-zag' tile sets suggest that under plausible experimental conditions, it is possible to grow large seeded crystals in just a few hours such that less than 1 percent of crystals are spuriously nucleated. Simulation results also suggest that zig-zag tile sets could be used for detection of single DNA strands. Together with prior work showing that tile sets can be made robust to errors during properly initiated growth, this work demonstrates that growth of objects via algorithmic self-assembly can proceed both efficiently and with an arbitrarily low error rate, even in a model where local growth rules are probabilistic.

Full work available at URL: https://arxiv.org/abs/cond-mat/0607317

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zbMATH Keywords

algorithmic self-assemblyDNA nanotechnologynucleation theory

Mathematics Subject Classification ID

Analysis of algorithms (68W40) Nonnumerical algorithms (68W05) Statistical mechanics of crystals (82D25)

Cited In (25)

• Search methods for tile sets in patterned DNA self-assembly
• An introduction to tile-based self-assembly and a survey of recent results
• Algorithmic DNA Self-assembly
• Complexity of graph self-assembly in accretive systems and self-destructible systems
• Error suppression mechanisms for DNA tile self-assembly and their simulation
• Producibility in hierarchical self-assembly
• Capabilities and limits of compact error resilience methods for algorithmic self-assembly
• Pictures worth a thousand tiles, a geometrical programming language for self-assembly
• Nearly constant tile complexity for any shape in two-handed tile assembly
• On the effects of hierarchical self-assembly for reducing program-size complexity
• Optimizing tile concentrations to minimize errors and time for DNA tile self-assembly systems
• Tile complexity of approximate squares
• DNA Computing
• Resiliency to multiple nucleation in temperature-1 self-assembly
• Resiliency to multiple nucleation in temperature-1 self-assembly
• Simple evolution of complex crystal species
• Computational modelling of the kinetic tile assembly model using a rule-based approach
• A Self-assembly Model of Time-Dependent Glue Strength
• Complexity of Graph Self-assembly in Accretive Systems and Self-destructible Systems
• Complexity of Compact Proofreading for Self-assembled Patterns
• Computing properties of stable configurations of thermodynamic binding networks
• A brief tour of theoretical tile self-assembly
• On the complexity of graph self-assembly in accretive systems
• Activatable tiles for compact robust programmable molecular assembly and other applications
• Parallelism and time in hierarchical self-assembly

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