Simulation of one dimensional staged DNA tile assembly by the signal-passing hierarchical TAM

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Publication Details

List of Authors: Gefry Barad, Alexandru Amarioarei, Mihaela Paun, Ana Maria Dobre, Corina Itcus, Iris Tusa, Romica Trandafir, Eugen Czeizler
Editors: Imre J. Rudas, Csirik Janos, Carlos Toro, Janos Botzheim, Robert J. Howlett, Lakhmi C. Jain
Publication year: 2019
Journal: Procedia Computer Science
Publisher: Elsevier
Book title: Knowledge-Based and Intelligent Information & Engineering Systems: Proceedings of the 23rd International Conference KES2019
Volume number: 159
Start page: 1918
End page: 1927


The Tile Assembly Model, and its many variants, is one of the most
fundamental algorithmic assembly formalism within DNA nanotechnology.
Most of the research in this field is focused on the complexity of
assembling different shapes and patterns. In many cases, the assembly
process is intrinsically deterministic and the final product is unique,
while the assembly process might evolve through several possible
assembly strategies. In this study we consider the controlled assembly
of one dimensional tile structures according to predefined assembly
graphs. We provide algorithmic approaches for developing such controlled
assembly protocols, using the signal-passing Tile Assembly Model, as
well as probabilistic approaches for investigating the assembly of such
tile-based one-dimensional structures. As a byproduct, we build a
generalized TAS (tile assembly system) which generate specific non-local
non-associative algebraic computations and we assamble n × n squares using only one tile, which is a better efficiency compared to the staged assembly model.

Last updated on 2020-04-04 at 07:26