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bioRxiv · 10.1101/2021.04.01.437956

The Time Complexity of Self-Assembly

Gartner, F. M.·Graf, I. R.·Frey, E.
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Abstract

Time efficiency of self-assembly is crucial for many biological processes. Moreover, with the advances of nanotechnology, time efficiency in artificial self-assembly becomes ever more important. While structural determinants and the final assembly yield are increasingly well understood, kinetic aspects concerning the time efficiency, however, remain much more elusive. In computer science, the concept of time complexity is used to characterize the efficiency of an algorithm and describes how the algorithms runtime depends on the size of the input data. Here we characterize the time complexity of non-equilibrium self-assembly processes by exploring how the time required to realize a certain, substantial yield of a given target structure scales with its size. We identify distinct classes of assembly scenarios, i.e. algorithms to accomplish this task, and show that they exhibit drastically different degrees of complexity. Our analysis enables us to identify optimal control strategies for non-equilibrium self-assembly processes. Furthermore, we suggest an efficient irreversible scheme for the artificial self-assembly of nanostructures, which complements the state-of-the-art approach using reversible binding reactions and requires no fine-tuning of binding energies.

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Gartner, F. M., Graf, I. R., Frey, E.. 2021-04-01. The Time Complexity of Self-Assembly. https://doi.org/10.1101/2021.04.01.437956

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