Stoichiometric network analysis of spontaneous mirror symmetry breaking in chemical reactions

2017 ◽  
Vol 19 (27) ◽  
pp. 17618-17636 ◽  
Author(s):  
David Hochberg ◽  
Rubén D. Bourdon García ◽  
Jesús A. Ágreda Bastidas ◽  
Josep M. Ribó
Keyword(s):  
Network Analysis ◽  
Symmetry Breaking ◽  
Chemical Reactions ◽  
Chemical Reaction ◽  
Mirror Symmetry ◽  
Stoichiometric Network Analysis ◽  
Reaction Schemes

Stoichiometric network analysis (SNA) is used to study spontaneous mirror symmetry breaking in chemical reaction schemes.

scholarly journals Entropic Analysis of Mirror Symmetry Breaking in Chiral Hypercycles

Life ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 28 ◽  
Author(s):  
David Hochberg ◽  
Josep Ribó
Keyword(s):  
Symmetry Breaking ◽  
Entropy Production ◽  
Mirror Symmetry ◽  
Flow Reactor ◽  
Evolutionary Selection ◽  
Replicator System ◽  
Stoichiometric Network Analysis ◽  
Underlying Mechanisms ◽  
The Individual ◽  
Origin Of Homochirality

Replicators are fundamental to the origin of life and evolvability. Biology exhibits homochirality: only one of two enantiomers is used in proteins and nucleic acids. Thermodynamic studies of chemical replicators able to lead to homochirality shed valuable light on the origin of homochirality and life in conformity with the underlying mechanisms and constraints. In line with this framework, enantioselective hypercyclic replicators may lead to spontaneous mirror symmetry breaking (SMSB) without the need for additional heterochiral inhibition reactions, which can be an obstacle for the emergence of evolutionary selection properties. We analyze the entropy production of a two-replicator system subject to homochiral cross-catalysis which can undergo SMSB in an open-flow reactor. The entropy exchange with the environment is provided by the input and output matter flows, and is essential for balancing the entropy production at the non-equilibrium stationary states. The partial entropy contributions, associated with the individual elementary flux modes, as defined by stoichiometric network analysis (SNA), describe how the system’s internal currents evolve, maintaining the balance between entropy production and exchange, while minimizing the entropy production after the symmetry breaking transition. We validate the General Evolution Criterion, stating that the change in the chemical affinities proceeds in a way as to lower the value of the entropy production.

Stoichiometric network analysis of entropy production in chemical reactions

2018 ◽  
Vol 20 (36) ◽  
pp. 23726-23739 ◽  
Author(s):  
David Hochberg ◽  
Josep M. Ribó
Keyword(s):  
Network Analysis ◽  
Entropy Production ◽  
Chemical Reactions ◽  
Open System ◽  
Reaction Networks ◽  
Stoichiometric Network Analysis

SNA extreme currents allow for the evaluation and understanding of entropy production of NESS in open system reaction networks.

2,6-Dibromogallates as a new building block for controlling π-stacking, network formation and mirror symmetry breaking

2021 ◽  
Author(s):  
Ohjin Kwon ◽  
Xiaoqian Cai ◽  
Azhar Saeed ◽  
Feng Liu ◽  
Silvio Poppe ◽  
...  
Keyword(s):  
Symmetry Breaking ◽  
Building Block ◽  
Mirror Symmetry ◽  
Network Formation ◽  
Network Structures ◽  
Π Stacking ◽  
Bicontinuous Cubic ◽  
Substituted 1 ◽  
End Group

Achiral multi-chain (polycatenar) compounds based on the 2,7-diphenyl substituted [1]benzothieno[3,2-b]benzothiophene (BTBT) unit and a 2,6-dibromo-3,4,5-trialkoxybenzoate end group lead to materials forming bicontinuous cubic liquid crystaline phases with helical network structures...

Normal approximations for distributions arising in the stochastic approach to chemical reaction kinetics

1981 ◽  
Vol 18 (01) ◽  
pp. 263-267 ◽  
Author(s):  
F. D. J. Dunstan ◽  
J. F. Reynolds
Keyword(s):  
Reaction Kinetics ◽  
Chemical Reactions ◽  
Chemical Reaction ◽  
Stochastic Approach ◽  
Algebraic Functions ◽  
Chemical Reaction Kinetics ◽  
Normal Approximations ◽  
Formal Solutions

Earlier stochastic analyses of chemical reactions have provided formal solutions which are unsuitable for most purposes in that they are expressed in terms of complex algebraic functions. Normal approximations are derived here for solutions to a variety of reactions. Using these, it is possible to investigate the level at which the classical deterministic solutions become inadequate. This is important in fields such as radioimmunoassay.

scholarly journals Mapping the Space of Chemical Reactions using Attention-Based Neural Networks

2020 ◽  
Author(s):  
Philippe Schwaller ◽  
Daniel Probst ◽  
Alain C. Vaucher ◽  
Vishnu H Nair ◽  
David Kreutter ◽  
...  
Keyword(s):  
Neural Networks ◽  
Reaction Center ◽  
Chemical Reactions ◽  
Chemical Reaction ◽  
Classification Accuracy ◽  
Similarity Searching ◽  
Reaction Space ◽  
Fine Grained ◽  
Visual Clustering ◽  
Better Than

<div><div><div><p>Organic reactions are usually assigned to classes grouping reactions with similar reagents and mechanisms. Reaction classes facilitate communication of complex concepts and efficient navigation through chemical reaction space. However, the classification process is a tedious task, requiring the identification of the corresponding reaction class template via annotation of the number of molecules in the reactions, the reaction center and the distinction between reactants and reagents. In this work, we show that transformer-based models can infer reaction classes from non-annotated, simple text-based representations of chemical reactions. Our best model reaches a classification accuracy of 98.2%. We also show that the learned representations can be used as reaction fingerprints which capture fine-grained differences between reaction classes better than traditional reaction fingerprints. The unprecedented insights into chemical reaction space enabled by our learned fingerprints is illustrated by an interactive reaction atlas providing visual clustering and similarity searching. </p><p><br></p><p>Code: https://github.com/rxn4chemistry/rxnfp</p><p>Tutorials: https://rxn4chemistry.github.io/rxnfp/</p><p>Interactive reaction atlas: https://rxn4chemistry.github.io/rxnfp//tmaps/tmap_ft_10k.html</p></div></div></div>

scholarly journals Mass transfer with complex reversible chemical reactions—I. Single reversible chemical reaction

1989 ◽  
Vol 44 (10) ◽  
pp. 2295-2310 ◽  
Author(s):  
G.F. Versteeg ◽  
J.A.M. Kuipers ◽  
F.P.H. Van Beckum ◽  
W.P.M. Van Swaaij
Keyword(s):  
Mass Transfer ◽  
Chemical Reactions ◽  
Chemical Reaction ◽  
Reversible Chemical Reaction
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