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Cellular Automata Approaches to Enzymatic Reaction Networks [chapter]

Jörg R. Weimar
2002 Lecture Notes in Computer Science  
Cellular automata simulations for enzymatic reaction networks differ from other models for reaction-diffusion systems, since enzymes and metabolites have very different properties.  ...  Different possible approaches to rule construction are presented and analyzed, and simulations are shown for single reactions and simple enzyme networks.  ...  In this paper I present an approach based on cellular automata for simulating enzymatic reaction networks including diffusive transport.  ... 
doi:10.1007/3-540-45830-1_28 fatcat:35ylztev4zde7ea23urompc6pq

Cellular Automata Modeling of Biomolecular Networks [chapter]

Danail Bonchev
2011 Cellular Automata - Simplicity Behind Complexity  
Each motif's arc i was assumed to correspond to an enzymatic reaction: S(i) + E(i) SE(i) PE(i) P(i) + E(i), and the probabilistic rules used were the ones for enzymatic reactions (See Section 3).  ...  Automata Modeling of Biomolecular Networks 293 www.intechopen.comCellular Automata -Simplicity Behind Complexity www.intechopen.com Cellular Automata Modeling of Biomolecular Networks  ...  Cellular Automata Modeling of Biomolecular Networks, Cellular Automata -Simplicity Behind Complexity, Dr.  ... 
doi:10.5772/15727 fatcat:py4oxnuvp5ayrg7lrmnfut2qku

Enzymes as molecular automata: a stochastic model of self-oscillatory glycolytic cycles in cellular metabolism

Antonio Garcı́a-Olivares, Morris Villarroel, Pedro C Marijuán
2000 Biosystems (Amsterdam. Print)  
The stochastic algorithm, based on Gillespie's method, simulates the master equation associated with any network of enzymatically controlled reactions.  ...  Other possible applications of the stochastic automata approach for different cases of channels, receptors and enzymatic control are suggested.  ...  Acknowledgements Antonio García-Olivares would like to thank Dr Luis Valiñ o, from the LITEC (CSIC) institute, for the facilities provided for the realization of this work.  ... 
doi:10.1016/s0303-2647(00)00078-2 pmid:10880859 fatcat:x6castj6arezlklxhwueghmrxa

Computational methodologies for modelling, analysis and simulation of signalling networks

D. Gilbert, H. Fuss, X. Gu, R. Orton, S. Robinson, V. Vyshemirsky, M. J. Kurth, C. S. Downes, W. Dubitzky
2006 Briefings in Bioinformatics  
We propose a conceptual framework, and discuss the role of signalling networks in three major areas: signal transduction, cellular rhythms and cell-to-cell communication.  ...  This article is a critical review of computational techniques used to model, analyse and simulate signalling networks.  ...  F. has been supported by an EPSRC network grant GR/ S98719/01. R. O. and V. V. have been supported by a DTI 'Post-genomics Beacons' grant.  ... 
doi:10.1093/bib/bbl043 pmid:17116646 fatcat:cf42u6jo6fgq5lp63c22gh4xqe

An improved cellular automata model of enzyme kinetics based on genetic algorithm

Saurajyoti Kar, Kaustuv Nag, Abhishek Dutta, Denis Constales, Tandra Pal
2014 Chemical Engineering Science  
Acknowledgement SK and AD would like to acknowledge Advait Apte, Arizona State University (USA) for his valuable inputs and discussions on the cellular automata model.  ...  For the pseudo-artificial reaction simulations, computational resources (Stevin Supercomputer Infrastructure) and services were used in this work and provided by Ghent University, the Hercules Foundation  ...  Cellular Automata (CA) is one such stochastic approach in which a natural event can be successfully simulated.  ... 
doi:10.1016/j.ces.2013.08.013 fatcat:wmbcxpqturazhaargspn62gaxy

Cellular automata simulation of topological effects on the dynamics of feed-forward motifs

Advait A Apte, John W Cain, Danail G Bonchev, Stephen S Fong
2008 Journal of Biological Engineering  
Results: Feed-forward motif dynamics were studied using cellular automata and compared with differential equation modeling.  ...  The number of cellular automata iterations needed for a 100% conversion of a substrate into a target product was used as an inverse measure of the transformation rate.  ...  Acknowledgements The authors are indebted to Dr. L.B. Kier, VCU, for introducing them to the field of CA modeling.  ... 
doi:10.1186/1754-1611-2-2 pmid:18304325 pmcid:PMC2278126 fatcat:m4sprx2r4bh4bkrpzgfgqm7jeu

A probabilistic cellular automaton for two dimensional contaminant transport simulation in ground water

Jegathambal Palanichamy, Holger Schüttrumpf, Sundarambal Palani
2008 Water Science and Technology  
Genetic algorithms, Neural Networks, and Cellular Automata are the branches of evolutionary computing techniques.  ...  The overview of the Cellular Automata is explained in section 2.  ...  In the second step, the reaction simulation was done using reactive gas Cellular Automata approach.  ... 
doi:10.2166/wst.2008.824 pmid:19092183 fatcat:2hh3ssv7nzezpjb4r2ugkhrcqa

Computational model for monitoring cholesterol metabolism

R. Selvakumar, M. Rashith Muhammad, G. Poornima Devi
2014 Journal of Systems and Synthetic Biology  
The rejection state of this machine shows the inhibition of enzymatic activity in cholesterol synthesis and removal of free fatty acids.  ...  incident due to the respective metabolic disorder.  ...  Acknowledgments Thanks to Ms. M. Faleela Farzana for supporting the algorithm part. Conflict of interest The authors declare no conflict of interest.  ... 
doi:10.1007/s11693-014-9152-8 pmid:26396654 pmcid:PMC4571723 fatcat:v4mlfokyt5ae7e6k4jo6idnnhq

Improving the Timed Automata Approach to Biological Pathway Dynamics [chapter]

Rom Langerak, Jaco van de Pol, Janine N. Post, Stefano Schivo
2017 Lecture Notes in Computer Science  
ANIMO (Analysis of Networks with Interactive MOdeling) was built with the aim to provide biologists with access to the powerful modeling formalism of Timed Automata in a user friendly way.  ...  In this paper we introduce an improved modeling approach that allows us to considerably increase ANIMO's performances, opening the way for the analysis of bigger models.  ...  even if no other automaton is present in the network, and would be able to react to any changes in B, C or D if automata representing those reactants were added to the model.  ... 
doi:10.1007/978-3-319-63121-9_5 fatcat:g5blhkswnndg7icaispdfqoysa

Page 4977 of Mathematical Reviews Vol. , Issue 80M [page]

1980 Mathematical Reviews  
This method is contrasted with the “bottom- up” approach, in which properties of a given cell or well-defined network are analyzed.  ...  Authors’ summary: “We show that the two-factor model, intro- duced by Rosen for biological automata, can be realized at a molecular level by an enzymatic conjugate system.  ... 

Cancer systems biology and modeling: Microscopic scale and multiscale approaches

Ali Masoudi-Nejad, Gholamreza Bidkhori, Saman Hosseini Ashtiani, Ali Najafi, Joseph H. Bozorgmehr, Edwin Wang
2015 Seminars in Cancer Biology  
In this paper, different systems biology modeling techniques such as systems of differential equations, stochastic methods, Boolean networks, Petri nets, cellular automata methods and agent-based systems  ...  , in addition to intracellular and extracellular complex interaction networks.  ...  Cellular automata and agent-based approaches are used as well.  ... 
doi:10.1016/j.semcancer.2014.03.003 pmid:24657638 fatcat:a2trd7ijvbbytbeh3oq4udbbry

A Modeling Framework For Immune-related Diseases

F. Castiglione, S. Motta, F. Pappalardo, M. Pennisi
2012 Mathematical Modelling of Natural Phenomena  
Here we describe this computational framework, developed to perform simulations of different pathologies that are directly or indirectly connected to the immune system.  ...  Later, many other computational models have been proposed each one adding a certain level of sophistication and detail to the description of the system.  ...  Others belong to the class of discrete models known as cellular automata or agent-based.  ... 
doi:10.1051/mmnp/20127304 fatcat:movy5xtcmfhpznlomvdjejdchi

Genome Scale Modeling in Systems Biology: Algorithms and Resources

Ali Najafi, Gholamreza Bidkhori, Joseph Bozorgmehr, Ina Koch, Ali Masoudi-Nejad
2014 Current Genomics  
Consequently, given the complexity of generated experimental data and cellular networks, it is no surprise that researchers have turned to computer simulation and the development of more theory-based approaches  ...  to augment and assist in the development of a fully quantitative understanding of cellular dynamics.  ...  ACKNOWLEDGEMENTS We would like to thank all members of the laboratory of systems biology and bioinformatics (LBB) for their help during course of this study.  ... 
doi:10.2174/1389202915666140319002221 pmid:24822031 pmcid:PMC4009841 fatcat:xh7tgip2yfdq3fe2typ74jlfkq

A General Overview of Formal Languages for Individual-Based Modelling of Ecosystems [article]

Mauricio Toro
2019 arXiv   pre-print
We also discuss, briefly, other approaches such as P systems, cellular automata and Petri nets.  ...  Bortolussi et al. have used sCCP to model bio-mechanical reactions such as an enzymatic reaction [18] . sCCP has also been in system biology [17] and to model prey-predator dynamics [16] .  ...  Cellular automata were proposed by Von Neumann, in 1949 . There are one-, two-and three-dimensional cellular automata.  ... 
arXiv:1901.10820v1 fatcat:2x5nucj7frd5nlfkrp7sszhlf4

Prebiotic Geochemical Automata at the Intersection of Radiolytic Chemistry, Physical Complexity, and Systems Biology

Zachary R. Adam, Albert C. Fahrenbach, Betul Kacar, Masashi Aono
2018 Complexity  
Connectivity across multiple levels imparts the potential to create and maintain far-from-equilibrium chemical conditions and to manifest nonlinear system behaviors best approximated using automata formalisms  ...  The architectural attribute of "information hiding" of energy exchange processes at each object level is shared with stable, multitiered automata such as digital computers.  ...  The authors would like to thank Marta Dueñas Diez and Juan Perez-Mercader for stimulating discussions that led to this paper.  ... 
doi:10.1155/2018/9376183 fatcat:27gs53v3ffcbfaj64tl5t5ezta
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