scholarly journals Verifying Chemical Reaction Network Implementations: A Bisimulation Approach

2016 ◽  
pp. 114-134 ◽  
Author(s):  
Robert F. Johnson ◽  
Qing Dong ◽  
Erik Winfree
Keyword(s):  
Chemical Reaction ◽  
Reaction Network ◽  
Chemical Reaction Network

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

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 Artificial chemical reaction network of molecular automata.

2001 ◽  
Vol 41 (supplement) ◽  
pp. S73
Author(s):  
T. Ushikubo ◽  
M. Sasai
Keyword(s):  
Chemical Reaction ◽  
Reaction Network ◽  
Chemical Reaction Network

scholarly journals Yield prediction in parallel homogeneous assembly

Soft Matter ◽  
2017 ◽  
Vol 13 (41) ◽  
pp. 7595-7608 ◽  
Author(s):  
Dhananjay Ipparthi ◽  
Andrew Winslow ◽  
Metin Sitti ◽  
Marco Dorigo ◽  
Massimo Mastrangeli
Keyword(s):  
Chemical Reaction ◽  
Reaction Network ◽  
Chemical Reaction Network ◽  
Yield Prediction ◽  
Parallel Assembly

The parallel assembly of 2D target structures from homogeneous macroscopic components is studied experimentally and through a chemical reaction network-based model, highlighting the incompatible substructures problem.

Sign in / Sign up

Export Citation Format

Share Document