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Author Aracena, J.; Demongeot, J.; Fanchon, E.; Montalva, M. pdf  doi
openurl 
  Title On the number of different dynamics in Boolean networks with deterministic update schedules Type Journal Article
  Year 2013 Publication Mathematical Biosciences Abbreviated Journal Math. Biosci.  
  Volume 242 Issue 2 Pages 188-194  
  Keywords Boolean network; Update schedule; Update digraph; Dynamics  
  Abstract Deterministic Boolean networks are a type of discrete dynamical systems widely used in the modeling of genetic networks. The dynamics of such systems is characterized by the local activation functions and the update schedule, i.e., the order in which the nodes are updated. In this paper, we address the problem of knowing the different dynamics of a Boolean network when the update schedule is changed. We begin by proving that the problem of the existence of a pair of update schedules with different dynamics is NP-complete. However, we show that certain structural properties of the interaction digraph are sufficient for guaranteeing distinct dynamics of a network. In [1] the authors define equivalence classes which have the property that all the update schedules of a given class yield the same dynamics. In order to determine the dynamics associated to a network, we develop an algorithm to efficiently enumerate the above equivalence classes by selecting a representative update schedule for each class with a minimum number of blocks. Finally, we run this algorithm on the well known Arabidopsis thaliana network to determine the full spectrum of its different dynamics. (C) 2013 Elsevier Inc. All rights reserved.  
  Address Univ Concepcion, CI2MA, Concepcion, Chile, Email: jaracena@ing-mat.udec.cl;  
  Corporate Author Thesis  
  Publisher Elsevier Science Inc Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0025-5564 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000317164700008 Approved no  
  Call Number UAI @ eduardo.moreno @ Serial 275  
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Author Aracena, J.; Demongeot, J.; Fanchon, E.; Montalva, M. pdf  doi
openurl 
  Title On the number of update digraphs and its relation with the feedback arc sets and tournaments Type Journal Article
  Year 2013 Publication Discrete Applied Mathematics Abbreviated Journal Discret Appl. Math.  
  Volume 161 Issue 10-11 Pages 1345-1355  
  Keywords Update digraph; Feedback arc set; Tournament; Update schedule  
  Abstract An update digraph corresponds to a labeled digraph that indicates a relative order of its nodes introduced to define equivalence classes of deterministic update schedules yielding the same dynamical behavior of a Boolean network. In Aracena et al. [1], the authors exhibited relationships between update digraphs and the feedback arc sets of a given digraph G. In this paper, we delve into the study of these relations. Specifically, we show differences and similarities between both sets through increasing and decreasing monotony properties in terms of their structural characteristics. Besides, we prove that these sets are equivalent if and only if all the digraph circuits are cycles. On the other hand, we characterize the minimal feedback arc sets of a given digraph in terms of their associated update digraphs. In particular, for complete digraphs, this characterization shows a close relation with acyclic tournaments. For the latter, we show that the size of the associated equivalence classes is a power of two. Finally, we determine exactly the number of update digraphs associated to digraphs containing a tournament. (C) 2013 Elsevier B.V. All rights reserved.  
  Address Univ Concepcion, CI2 MA & Dept Ingn Matemat, Concepcion, Chile, Email: jaracena@ing-mat.udec.cl;  
  Corporate Author Thesis  
  Publisher Elsevier Science Bv Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0166-218x ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000319029300005 Approved no  
  Call Number UAI @ eduardo.moreno @ Serial 282  
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Author Perrot, K.; Montalva-Medel, M.; de Oliveira, P.P.B.; Ruivo, E.L.P. doi  openurl
  Title Maximum sensitivity to update schedules of elementary cellular automata over periodic configurations Type Journal Article
  Year 2020 Publication Natural Computing Abbreviated Journal Nat. Comput.  
  Volume 19 Issue 1 Pages 51-90  
  Keywords Synchronism sensitivity; Elementary cellular automata; Update digraph  
  Abstract This work is a thoughtful extension of the ideas sketched in Montalva et al. (AUTOMATA 2017 exploratory papers proceedings, 2017), aiming at classifying elementary cellular automata (ECA) according to their maximal one-step sensitivity to changes in the schedule of cells update. It provides a complete classification of the ECA rule space for all period sizes n[ 9 and, together with the classification for all period sizes n <= 9 presented in Montalva et al. (Chaos Solitons Fractals 113:209-220, 2018), closes this problem and opens further questionings. Most of the 256 ECA rule's sensitivity is proved or disproved to be maximum thanks to an automatic application of basic methods. We formalize meticulous case disjunctions that lead to the results, and patch failing cases for some rules with simple arguments. This gives new insights on the dynamics of ECA rules depending on the proof method employed, as for the last rules 45 and 105 requiring o0011THORN induction patterns.  
  Address [Perrot, Kevin] Univ, Aix Marseille Univ.,Toulon,CNRS,UMR 7020, Marseille, France, Email: kevin.perrot@lis-lab.fr  
  Corporate Author Thesis  
  Publisher Springer Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1567-7818 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000517129300006 Approved no  
  Call Number UAI @ eduardo.moreno @ Serial 1162  
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Author Ruivo, E.L.P.; Montalva-Medel, M.; de Oliveira, P.P.B.; Perrot, K. pdf  doi
openurl 
  Title Characterisation of the elementary cellular automata in terms of their maximum sensitivity to all possible asynchronous updates Type Journal Article
  Year 2018 Publication Chaos Solitons & Fractals Abbreviated Journal Chaos Solitons Fractals  
  Volume 113 Issue Pages 209-220  
  Keywords Cellular automaton; Asynchronous update; Update digraph; Discrete dynamics; One-step maximum sensitivity  
  Abstract Cellular automata are fully-discrete dynamical systems with global behaviour depending upon their locally specified state transitions. They have been extensively studied as models of complex systems as well as objects of mathematical and computational interest. Classically, the local rule of a cellular automaton is iterated synchronously over the entire configuration. However, the question of how asynchronous updates change the behaviour of a cellular automaton has become a major issue in recent years. Here, we analyse the elementary cellular automata rule space in terms of how many different one-step trajectories a rule would entail when taking into account all possible deterministic ways of updating the rule, for one time step, over all possible initial configurations. More precisely, we provide a characterisation of the elementary cellular automata, by means of their one-step maximum sensitivity to all possible update schedules, that is, the property that any change in the update schedule causes the rule's one-step trajectories also to change after one iteration. Although the one-step maximum sensitivity does not imply that the remainder of the time-evolutions will be distinct, it is a necessary condition for that. (C) 2018 Elsevier Ltd. All rights reserved.  
  Address [Ruivo, Eurico L. P.; de Oliveira, Pedro P. B.] Univ Presbiteriana Mackenzie, Fac Comp & Informat, Sao Paulo, SP, Brazil, Email: eurico.ruivo@mackenzie.br  
  Corporate Author Thesis  
  Publisher Pergamon-Elsevier Science Ltd Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0960-0779 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000442101600024 Approved no  
  Call Number UAI @ eduardo.moreno @ Serial 910  
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