Universal Computation and Optimal Construction in the Chemical Reaction Network-Controlled Tile Assembly Model

2015 ◽  
pp. 34-54 ◽  
Author(s):  
Nicholas Schiefer ◽  
Erik Winfree
Keyword(s):  
Chemical Reaction ◽  
Reaction Network ◽  
Chemical Reaction Network ◽  
Assembly Model ◽  
Tile Assembly Model ◽  
Universal Computation ◽  
Tile Assembly ◽  
Optimal Construction

Synthesis and Breakdown of the Universal Precursors to Biological Metabolism Promoted by Ferrous Iron

2018 ◽  
Author(s):  
Kamila B. Muchowska ◽  
Sreejith Jayasree VARMA ◽  
Joseph Moran
Keyword(s):  
Amino Acids ◽  
Chemical Reaction ◽  
Metabolic Pathways ◽  
Ferrous Iron ◽  
Reaction Network ◽  
Tca Cycle ◽  
Chemical Reaction Network ◽  
Metabolic Precursors ◽  
Tca Cycle Intermediates

How core biological metabolism initiated and why it uses the intermediates, reactions and pathways that it does remains unclear. Life builds its molecules from CO<sub>2 </sub>and breaks them down to CO<sub>2 </sub>again through the intermediacy of just five metabolites that act as the hubs of biochemistry. Here, we describe a purely chemical reaction network promoted by Fe<sup>2+ </sup>in which aqueous pyruvate and glyoxylate, two products of abiotic CO<sub>2 </sub>reduction, build up nine of the eleven TCA cycle intermediates, including all five universal metabolic precursors. The intermediates simultaneously break down to CO<sub>2 </sub>in a life-like regime resembling biological anabolism and catabolism. Introduction of hydroxylamine and Fe<sup>0 </sup>produces four biological amino acids. The network significantly overlaps the TCA/rTCA and glyoxylate cycles and may represent a prebiotic precursor to these core metabolic pathways.

scholarly journals Modular verification of chemical reaction network encodings via serializability analysis

2016 ◽  
Vol 632 ◽  
pp. 21-42 ◽  
Author(s):  
Matthew R. Lakin ◽  
Darko Stefanovic ◽  
Andrew Phillips
Keyword(s):  
Chemical Reaction ◽  
Reaction Network ◽  
Chemical Reaction Network ◽  
Modular Verification

scholarly journals The Two-Handed Tile Assembly Model Is Not Intrinsically Universal

2013 ◽  
pp. 400-412 ◽  
Author(s):  
Erik D. Demaine ◽  
Matthew J. Patitz ◽  
Trent A. Rogers ◽  
Robert T. Schweller ◽  
Scott M. Summers ◽  
...  
Keyword(s):  
Assembly Model ◽  
Tile Assembly Model ◽  
Tile Assembly

Fractal Dimension of Assemblies in the Abstract Tile Assembly Model

2021 ◽  
pp. 116-130
Author(s):  
Daniel Hader ◽  
Matthew J. Patitz ◽  
Scott M. Summers
Keyword(s):  
Fractal Dimension ◽  
Assembly Model ◽  
Tile Assembly Model ◽  
Tile Assembly

scholarly journals Exponential replication of patterns in the signal tile assembly model

2014 ◽  
Vol 14 (2) ◽  
pp. 265-278 ◽  
Author(s):  
Alexandra Keenan ◽  
Robert Schweller ◽  
Xingsi Zhong
Keyword(s):  
Assembly Model ◽  
Tile Assembly Model ◽  
Tile Assembly

IDENTIFYING CHEMICAL REACTION NETWORK MODELS

2007 ◽  
Vol 40 (5) ◽  
pp. 225-230 ◽  
Author(s):  
S.C. Burnham ◽  
M.J. Willis ◽  
A.R Wright
Keyword(s):  
Chemical Reaction ◽  
Reaction Network ◽  
Network Models ◽  
Chemical Reaction Network

scholarly journals Hierarchical self assembly of patterns from the Robinson tilings: DNA tile design in an enhanced Tile Assembly Model

2011 ◽  
Vol 11 (2) ◽  
pp. 323-338 ◽  
Author(s):  
Jennifer E. Padilla ◽  
Wenyan Liu ◽  
Nadrian C. Seeman
Keyword(s):  
Self Assembly ◽  
Assembly Model ◽  
Tile Assembly Model ◽  
Tile Assembly
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