Constrained stoichiometric network analysis

2018 ◽  
Vol 20 (15) ◽  
pp. 9910-9921 ◽  
Author(s):  
Vuk Radojković ◽  
Igor Schreiber
Keyword(s):  
Hopf Bifurcation ◽  
Network Analysis ◽  
Linear Optimization ◽  
Reaction Network ◽  
Rate Coefficients ◽  
Bz Reaction ◽  
Stoichiometric Network Analysis

BZ reaction network – rate coefficients of reactions 11–14 were found by convex linear optimization at Hopf bifurcation.

scholarly journals Model of the nonlinear reaction system with autocatalysis and autoinhibition: Stability of dynamic states

2012 ◽  
Vol 66 (5) ◽  
pp. 637-646 ◽  
Author(s):  
Stevan Macesic ◽  
Zeljko Cupic ◽  
Ljiljana Kolar-Anic
Keyword(s):  
Sensitivity Analysis ◽  
Hopf Bifurcation ◽  
Network Analysis ◽  
Self Regulation ◽  
Reaction System ◽  
Model System ◽  
Economic Systems ◽  
Nonlinear Reaction ◽  
Stoichiometric Network Analysis ◽  
Theoretical Analyses

Self-regulation, achieved through positive (autocatalytic) or negative (autoinhibitory) feedback is commonly encountered in natural, technological and economic systems. The dynamic behavior of such systems is often complex and cannot be easily predicted, necessitating mathematical modelling and theoretical analyses. The aim of this work is to analyze the dynamics of a minimal model system with autocatalytic and autoinhibitory steps coupled through the same species, in order to understand under which critical condition the system loses stability and passes through an Andronov-Hopf bifurcation. The analysis used was improved stoichiometric network analysis (SNA) in combination with bifurcation and sensitivity analysis.

scholarly journals Current rates and reaction rates in the Stoichiometric Network Analysis (SNA)

2014 ◽  
Vol 13 (1) ◽  
Author(s):  
Stevan R. Maćešić ◽  
Željko D. Čupić ◽  
Slavica M. Blagojević ◽  
Nataša D. Pejić ◽  
Slobodan R. Anić ◽  
...  
Keyword(s):  
Network Analysis ◽  
Reaction Rates ◽  
Point Of View ◽  
Experimental Point ◽  
Instability Condition ◽  
Bz Reaction ◽  
Stoichiometric Network Analysis

AbstractIn stoichiometric network analysis (SNA) the instability condition is calculated by the current rates. Recently, we have shown that in the final result the current rates can be substituted by reaction rates, which is a more appropriate value for the examination of instability from experimental point of view. Here, we elaborate the problem of whether the current rates are necessary parameters in the calculation, with the aim of obtaining the region of instability. All calculations are performed on a model for Belousov-Zhabotinsky (BZ) reaction, which has not been examined by SNA.

scholarly journals Cover Feature: Reaction Network Analysis of the Ruthenium‐Catalyzed Reduction of Carbon Dioxide to Dimethoxymethane (ChemCatChem 12/2021)

ChemCatChem ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2746-2746
Author(s):  
Max Leopold ◽  
Max Siebert ◽  
Alexander F. Siegle ◽  
Oliver Trapp
Keyword(s):  
Carbon Dioxide ◽  
Network Analysis ◽  
Reaction Network

scholarly journals Carcinogenesis and Chemotherapy Viewed from the Perspective of Stoichiometric Network Analysis (SNA): What Can the Biological System of the Elements Contribute to an Understanding of Tumour Induction by Elemental Chemical Noxae (e.g., Ni2+, Cd2+) and to an Understanding of Chemotherapy?

2003 ◽  
Vol 3 ◽  
pp. 319-341 ◽  
Author(s):  
Stefan Franzle ◽  
Bernd Markert
Keyword(s):  
Network Analysis ◽  
Biological System ◽  
Cell Biology ◽  
Essential Feature ◽  
Comprehensive Treatment ◽  
Biological Processes ◽  
Tumour Induction ◽  
Stoichiometric Network Analysis ◽  
Autocatalytic Networks

The biological application of stoichiometric network analysis (SNA) permits an understanding of tumour induction, carcinogenesis, and chemotherapy. Starting from the Biological System of the Elements, which provides a comprehensive treatment of the functions and distributions of chemical (trace) elements in biology, an attempt is made to interrelate the essential feature of biology and — regrettably — of tumour genesis by superimposing SNA reasoning on common features of all crucial biological processes. For this purpose, aspects, effects and drawbacks of autocatalysis (identical reproduction which can occur either under control or without control [in tumours]) are linked with the known facts about element distributions in living beings and about interference of metals with tumours (in terms of both chemotherapy and carcinogenesis). The essential role of autocatalysis in biology and the drawbacks of either controlled or spontaneous cell division can be used to understand crucial aspects of carcinogenesis and chemotherapy because SNA describes and predicts effects of autocatalysis, including phase effects that may be due to some kind of intervention. The SNA-based classifications of autocatalytic networks in cell biology are outlined here to identify new approaches to chemotherapy.

L1 Regularization-Based Model Reduction of Complex Chemistry Molecular Dynamics for Statistical Learning of Kinetic Monte Carlo Models

MRS Advances ◽  
2016 ◽  
Vol 1 (24) ◽  
pp. 1767-1772 ◽  
Author(s):  
Qian Yang ◽  
Carlos A. Sing-Long ◽  
Evan J. Reed
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Kinetic Monte Carlo ◽  
A Priori ◽  
Reaction Network ◽  
Md Simulations ◽  
Rate Coefficients ◽  
Elementary Reactions ◽  
L1 Regularization ◽  
Complex Chemistry

ABSTRACTKinetic Monte Carlo (KMC) methods have been a successful technique for accelerating time scales and increasing system sizes beyond those achievable with fully atomistic simulations. However, a requirement for its success is a priori knowledge of all relevant reaction pathways and their rate coefficients. This can be difficult for systems with complex chemistry, such as shock-compressed materials at high temperatures and pressures or phenolic spacecraft heat shields undergoing pyrolysis, which can consist of hundreds of molecular species and thousands of distinct reactions. In this work, we develop a method for first estimating a KMC model composed of elementary reactions and rate coefficients by using large datasets derived from a few molecular dynamics (MD) simulations of shock compressed liquid methane, and then using L1 regularization to reduce the estimated chemical reaction network. We find that the full network of 2613 reactions can be reduced by 89% while incurring approximately 9% error in the dominant species (CH4) population. We find that the degree of sparsity achievable decreases when similar accuracy is required for additional populations of species.

The formation of p-toluic acid from coumalic acid: a reaction network analysis

2017 ◽  
Vol 19 (14) ◽  
pp. 3263-3271 ◽  
Author(s):  
Toni Pfennig ◽  
Robert L. Johnson ◽  
Brent H. Shanks
Keyword(s):  
Network Analysis ◽  
Polyethylene Terephthalate ◽  
Terephthalic Acid ◽  
Alternative Pathway ◽  
Reaction Network ◽  
Diels Alder

Diels–Alder cycloaddition of biomass-derived 2-pyrone coumalic acid (CMA) with propylene provides an alternative pathway to produce toluic acid (TA), a precursor to terephthalic acid (TPA) which is a key component in the manufacture of polyethylene terephthalate (PET).

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