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Cellular Automata Approaches to Enzymatic Reaction Networks
[chapter]
2002
Lecture Notes in Computer Science
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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]
2011
Cellular Automata - Simplicity Behind Complexity
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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
2000
Biosystems (Amsterdam. Print)
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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
2006
Briefings in Bioinformatics
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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
2014
Chemical Engineering Science
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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
2008
Journal of Biological Engineering
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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
2008
Water Science and Technology
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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
2014
Journal of Systems and Synthetic Biology
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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]
2017
Lecture Notes in Computer Science
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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
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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
2015
Seminars in Cancer Biology
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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
2012
Mathematical Modelling of Natural Phenomena
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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
2014
Current Genomics
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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]
2019
arXiv
pre-print
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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
2018
Complexity
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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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