One Dimensional DNA Tiles Self Assembly Model Simulation

Alexandru Amarioarei; Gefry Barad; Eugen Czeizler; Eugen Czeizler; Ana-Maria Dobre; Corina Itcus; Andrei Paun; Mihaela Paun; Romica Trandafir; Iris Tusa

One Dimensional DNA Tiles Self Assembly Model Simulation

Alexandru Amarioarei, Gefry Barad, Eugen Czeizler, Eugen Czeizler, Ana-Maria Dobre, Corina Itcus, Andrei Paun, Mihaela Paun, Romica Trandafir, Iris Tusa

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Research output: Contribution to journal › Article › Scientific › peer-review

4 Citations (Scopus)

Abstract

The TAM (Model Tile Assembly Model) is a mathematical paradigm for modeling DNA self-assembling according to various given shapes, using DNA-tiles (rectangular shape) with sticky ends on each of the four edges that bound together on various shapes desired by the researcher. Although there are various models in the literature, the focus in this manuscript is on a rule based model, specifically the authors present an overview of the one-dimensional hierarchical self-assembly model of DNA tiles. The authors also present the evolution of number of tiles in partial assemblies, the average assembly size and of the number of partial assemblies of sizes 2 through 10 over the total running time. All simulations were run using the NFSim simulator on a preset period of time.

Original language	Undefined/Unknown
Pages (from-to)	399–415
Number of pages	17
Journal	International Journal of Unconventional Computing
Volume	13
Issue number	4/5
Publication status	Published - 2018
MoE publication type	A1 Journal article-refereed

Keywords

Tile assembly model
DNA self assembly
computational modeling

Access to Document

http://urn.fi/URN:NBN:fi-fe2020100882229

AlgoNano: Algorithmic Nanotechnology: Modeling, Design and Automation of Synthetic Self-Assembly Systems (AlgoNano) (Academy of Finland)
Czeizler, E. (Principal Investigator)
01/09/17 → 31/08/21
Project: Research Council of Finland/Other Research Councils

Cite this

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title = "One Dimensional DNA Tiles Self Assembly Model Simulation",

abstract = "The TAM (Model Tile Assembly Model) is a mathematical paradigm for modeling DNA self-assembling according to various given shapes, using DNA-tiles (rectangular shape) with sticky ends on each of the four edges that bound together on various shapes desired by the researcher. Although there are various models in the literature, the focus in this manuscript is on a rule based model, specifically the authors present an overview of the one-dimensional hierarchical self-assembly model of DNA tiles. The authors also present the evolution of number of tiles in partial assemblies, the average assembly size and of the number of partial assemblies of sizes 2 through 10 over the total running time. All simulations were run using the NFSim simulator on a preset period of time.",

keywords = "Tile assembly model, DNA self assembly, computational modeling, Tile assembly model, DNA self assembly, computational modeling, Tile assembly model, DNA self assembly, computational modeling",

author = "Alexandru Amarioarei and Gefry Barad and Eugen Czeizler and Eugen Czeizler and Ana-Maria Dobre and Corina Itcus and Andrei Paun and Mihaela Paun and Romica Trandafir and Iris Tusa",

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language = "Odefinierat/ok{\"a}nt",

volume = "13",

pages = "399–415",

journal = "International Journal of Unconventional Computing",

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TY - JOUR

T1 - One Dimensional DNA Tiles Self Assembly Model Simulation

AU - Amarioarei, Alexandru

AU - Barad, Gefry

AU - Czeizler, Eugen

AU - Dobre, Ana-Maria

AU - Itcus, Corina

AU - Paun, Andrei

AU - Paun, Mihaela

AU - Trandafir, Romica

AU - Tusa, Iris

PY - 2018

Y1 - 2018

N2 - The TAM (Model Tile Assembly Model) is a mathematical paradigm for modeling DNA self-assembling according to various given shapes, using DNA-tiles (rectangular shape) with sticky ends on each of the four edges that bound together on various shapes desired by the researcher. Although there are various models in the literature, the focus in this manuscript is on a rule based model, specifically the authors present an overview of the one-dimensional hierarchical self-assembly model of DNA tiles. The authors also present the evolution of number of tiles in partial assemblies, the average assembly size and of the number of partial assemblies of sizes 2 through 10 over the total running time. All simulations were run using the NFSim simulator on a preset period of time.

AB - The TAM (Model Tile Assembly Model) is a mathematical paradigm for modeling DNA self-assembling according to various given shapes, using DNA-tiles (rectangular shape) with sticky ends on each of the four edges that bound together on various shapes desired by the researcher. Although there are various models in the literature, the focus in this manuscript is on a rule based model, specifically the authors present an overview of the one-dimensional hierarchical self-assembly model of DNA tiles. The authors also present the evolution of number of tiles in partial assemblies, the average assembly size and of the number of partial assemblies of sizes 2 through 10 over the total running time. All simulations were run using the NFSim simulator on a preset period of time.

KW - Tile assembly model

KW - DNA self assembly

KW - computational modeling

KW - Tile assembly model

KW - DNA self assembly

KW - computational modeling

KW - Tile assembly model

KW - DNA self assembly

KW - computational modeling

M3 - Artikel

SN - 1548-7199

VL - 13

SP - 399

EP - 415

JO - International Journal of Unconventional Computing

JF - International Journal of Unconventional Computing

IS - 4/5

ER -

One Dimensional DNA Tiles Self Assembly Model Simulation

Abstract

Keywords

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Projects

AlgoNano: Algorithmic Nanotechnology: Modeling, Design and Automation of Synthetic Self-Assembly Systems (AlgoNano) (Academy of Finland)

Cite this