An introduction to tile-based self-assembly and a survey of recent results

MJ Patitz - Natural Computing, 2014 - Springer
We first give an introduction to the field of tile-based self-assembly, focusing primarily on
theoretical models and their algorithmic nature. We start with a description of Winfree's …

Intrinsic universality and the computational power of self-assembly

D Woods - … Transactions of the Royal Society A …, 2015 - royalsocietypublishing.org
Molecular self-assembly, the formation of large structures by small pieces of matter sticking
together according to simple local interactions, is a ubiquitous phenomenon. A challenging …

Theory of algorithmic self-assembly

D Doty - Communications of the ACM, 2012 - dl.acm.org
Theory of algorithmic self-assembly Page 1 78 communications of the acm | december 2012 |
vol. 55 | no. 12 review articles PHO T O g RAPH B Y ZUBEIR TAI seLF-asseMBLY is the process …

Active self-assembly of algorithmic shapes and patterns in polylogarithmic time

D Woods, HL Chen, S Goodfriend, N Dabby… - Proceedings of the 4th …, 2013 - dl.acm.org
We describe a computational model for studying the complexity of self-assembled structures
with active molecular components. Our model captures notions of growth and movement …

Intrinsic universality in tile self-assembly requires cooperation

PE Meunier, MJ Patitz, SM Summers, G Theyssier… - Proceedings of the twenty …, 2014 - SIAM
We prove a negative result on the power of a model of algorithmic self-assembly for which
finding general techniques and results has been notoriously difficult. Specifically, we prove …

The non-cooperative tile assembly model is not intrinsically universal or capable of bounded Turing machine simulation

PÉ Meunier, D Woods - proceedings of the 49th annual ACM SIGACT …, 2017 - dl.acm.org
The field of algorithmic self-assembly is concerned with the computational and expressive
power of nanoscale self-assembling molecular systems. In the well-studied cooperative, or …

The two-handed tile assembly model is not intrinsically universal

ED Demaine, MJ Patitz, TA Rogers, RT Schweller… - Algorithmica, 2016 - Springer
Abstract The Two-Handed Tile Assembly Model (2HAM) is a model of algorithmic self-
assembly in which large structures, or assemblies of tiles, are grown by the binding of …

Non-explosivity of stochastically modeled reaction networks that are complex balanced

DF Anderson, D Cappelletti, M Koyama… - Bulletin of mathematical …, 2018 - Springer
We consider stochastically modeled reaction networks and prove that if a constant solution
to the Kolmogorov forward equation decays fast enough relatively to the transition rates …

Universal computation with arbitrary polyomino tiles in non-cooperative self-assembly

SP Fekete, J Hendricks, MJ Patitz, TA Rogers… - Proceedings of the …, 2014 - SIAM
In this paper we explore the power of geometry to overcome the limitations of non-
cooperative self-assembly. We define a generalization of the abstract Tile Assembly Model …

Oritatami: a computational model for molecular co-transcriptional folding

C Geary, PÉ Meunier, N Schabanel, S Seki - International Journal of …, 2019 - mdpi.com
We introduce and study the computational power of Oritatami, a theoretical model that
explores greedy molecular folding, whereby a molecular strand begins to fold before its …