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 …

[PDF][PDF] Oritatami systems assemble shapes no less complex than tile assembly model (aTAM)

D Pchelina, N Schabanel, S Seki… - … on Theoretical Aspects …, 2022 - drops.dagstuhl.de
Different models have been proposed to understand natural phenomena at the molecular
scale from a computational point of view. Oritatami systems are a model of molecular co …

Towards composable computations by RNA co-transcriptional folding: A proof-of-concept demonstration of nested loops in oritatami

SZ Fazekas, N Iwano, Y Kihara, R Matsuoka… - Theoretical Computer …, 2024 - Elsevier
Gliders have been underpinning various computations in oritatami, a model of computation
by letting an RNA sequence fold while being synthesized (transcribed). It has proven quite …

On algorithmic self-assembly of squares by co-transcriptional folding

SZ Fazekas, H Kim, R Matsuoka, S Seki… - … on Algorithms and …, 2022 - drops.dagstuhl.de
Algorithms play a primary role in programming an orchestrated self-assembly of shapes into
molecules. In this paper, we study the algorithmic self-assembly of squares by RNA co …

Simple intrinsic simulation of cellular automata in oritatami molecular folding model

D Pchelina, N Schabanel, S Seki, Y Ubukata - Latin American Symposium …, 2020 - Springer
The Oritatami model was introduced by Geary et al.(2016) to study the computational
potential of RNA cotranscriptional folding as first shown in wet-lab experiments by Geary et …

Programmable single-stranded architectures for computing

Y Kihara, S Seki - Natural Computing, 2023 - Springer
Oritatami is a mathematical model of co-transcriptional folding, a phenomenon in which,
while being synthesized (transcribed) sequentially, an RNA sequence folds upon itself into …

Counting infinitely by oritatami co-transcriptional folding

K Maruyama, S Seki - Natural Computing, 2021 - Springer
A fixed bit-width counter was proposed as a proof-of-concept demonstration of the oritatami
model of cotranscriptional folding [Geary et al., Proc. MFCS 2016, LIPIcs 58, 43: 1-43: 14] …

Ok: A Kinetic Model for Locally Reconfigurable Molecular Systems

P Marcus, N Schabanel, S Seki - Visions of DNA Nanotechnology at 40 for …, 2023 - Springer
Oritatami is a formal model of RNA co-transcriptional folding, in which an RNA sequence
(transcript) folds upon itself while being synthesized (transcribed) out of its DNA template …

On turedo hierarchies and intrinsic universality

S Nalin, G Theyssier - arXiv preprint arXiv:2205.04103, 2022 - arxiv.org
This paper is about turedos, which are Turing machine whose head can move in the plane
(or in a higher-dimensional space) but only in a selfavoiding way, by putting marks (letters) …

Impossibility of strict assembly of infinite fractals by oritatami

YS Han, H Kim - Natural Computing, 2021 - Springer
RNA cotranscriptional folding is the phenomenon in which an RNA transcript folds upon
itself while being synthesized out of a gene. The oritatami system is a computation model of …