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A simple proof of the Adams type inequalities in $ {\mathbb R}^{2m} $
On the effects of firing memory in the dynamics of conjunctive networks
1. | Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Diagonal las Torres 2650, Peñalolen, Santiago, Chile, and, Unconventional Computing Laboratory, University of the West of England, Bristol, UK |
2. | Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Diagonal las Torres 2650, Peñalolen, Santiago, Chile |
3. | Departamento de Ingeniería Matemática, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Beauchef 851, Torre Norte, Piso 5, Santiago, Chile, and, Aix Marseille Univ, Université de Toulon, CNRS, LIS, Marseille, France |
A boolean network is a map $ F:\{0,1\}^n \to \{0,1\}^n $ that defines a discrete dynamical system by the subsequent iterations of $ F $. Nevertheless, it is thought that this definition is not always reliable in the context of applications, especially in biology. Concerning this issue, models based in the concept of adding asynchronicity to the dynamics were propose. Particularly, we are interested in a approach based in the concept of delay. We focus in a specific type of delay called firing memory and it effects in the dynamics of symmetric (non-directed) conjunctive networks. We find, in the caseis in which the implementation of the delay is not uniform, that all the complexity of the dynamics is somehow encapsulated in the component in which the delay has effect. Thus, we show, in the homogeneous case, that it is possible to exhibit attractors of non-polynomial period. In addition, we study the prediction problem consisting in, given an initial condition, determinate if a fixed coordinate will eventually change its state. We find again that in the non-homogeneous case all the complexity is determined by the component that is affected by the delay and we conclude in the homogeneous case that this problem is PSPACE-complete.
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J. Aracena, E. Goles, A. Moreira and L. Salinas,
On the robustness of update schedules in Boolean networks, Biosystems, 97 (2009), 1-8.
doi: 10.1016/j.biosystems.2009.03.006. |
[3] |
J. Aracena, A. Richard and L. Salinas,
Fixed points in conjunctive networks and maximal independent sets in graph contractions, J. Comput. System Sci., 88 (2017), 145-163.
doi: 10.1016/j.jcss.2017.03.016. |
[4] |
S. Arora and B. Barak, Computational Complexity: A Modern Approach, Cambridge University Press, Cambridge, 2009.
doi: 10.1017/CBO9780511804090.![]() ![]() |
[5] |
G. Bernot, J.-P. Comet, A. Richard and J. Guespin,
Application of formal methods to biological regulatory networks: Extending Thomas' asynchronous logical approach with temporal logic, J. Theoret. Biol., 229 (2004), 339-347.
doi: 10.1016/j.jtbi.2004.04.003. |
[6] |
J. Demongeot, A. Elena and S. Sené,
Robustness in regulatory networks: A multi-disciplinary approach, Acta Biotheoretica, 56 (2008), 27-49.
doi: 10.1007/s10441-008-9029-x. |
[7] |
J. Fromentin, D. Eveillard and O. Roux, Hybrid modeling of biological networks: Mixing temporal and qualitative biological properties, BMC Systems Biology, 4 (2010), 79.
doi: 10.1186/1752-0509-4-79. |
[8] |
Z. Gao, X. Chen and T. BaÅŸar,
Controllability of conjunctive Boolean networks with application to gene regulation, IEEE Trans. Control Netw. Syst., 5 (2018), 770-781.
doi: 10.1109/TCNS.2017.2746345. |
[9] |
E. Goles, F. Lobos, G. A. Ruz and S. Sené,
Attractor landscapes in Boolean networks with firing memory: A theoretical study applied to genetic networks, Nat. Comput., 19 (2020), 295-319.
doi: 10.1007/s11047-020-09789-0. |
[10] |
E. Goles and P. Montealegre,
Computational complexity of threshold automata networks under different updating schemes, Theoret. Comput. Sci., 559 (2014), 3-19.
doi: 10.1016/j.tcs.2014.09.010. |
[11] |
E. Goles, P. Montealegre, V. Salo and I. Törmä,
PSPACE-completeness of majority automata networks, Theoret. Comput. Sci., 609 (2016), 118-128.
doi: 10.1016/j.tcs.2015.09.014. |
[12] |
E. Goles and M. Noual,
Disjunctive networks and update schedules, Adv. in Appl. Math., 48 (2012), 646-662.
doi: 10.1016/j.aam.2011.11.009. |
[13] |
E. Goles and L. Salinas,
Comparison between parallel and serial dynamics of Boolean networks, Theoret. Comput. Sci., 396 (2008), 247-253.
doi: 10.1016/j.tcs.2007.09.008. |
[14] |
E. Goles-Chacc, F. Fogelman-Soulié and D. Pellegrin,
Decreasing energy functions as a tool for studying threshold networks, Discrete Appl. Math., 12 (1985), 261-277.
doi: 10.1016/0166-218X(85)90029-0. |
[15] |
A. Graudenzi and R. Serra, A new model of genetic network: The Gene Protein Boolean network, Artificial Life and Evolutionary Computation, World Sci. Publ., Hackensack, NJ, (2010), 283-291.
doi: 10.1142/9789814287456_0025. |
[16] |
A. Graudenzi, R. Serra, M. Villani, A. Colacci and S. A. Kauffman,
Robustness analysis of a Boolean model of gene regulatory network with memory, J. Comput. Biol., 18 (2011), 559-577.
doi: 10.1089/cmb.2010.0224. |
[17] |
A. Graudenzi, R. Serra, M. Villani, C. Damiani, A. Colacci and S. A. Kauffman,
Dynamical properties of a Boolean model of gene regulatory network with memory, J. Comput. Biol., 18 (2011), 1291-1303.
doi: 10.1089/cmb.2010.0069. |
[18] |
B. M. Gummow, J. O. Scheys, V. R. Cancelli and G. D. Hammer, Reciprocal regulation of a glucocorticoid receptor-steroidogenic factor-1 transcription complex on the Dax-1 promoter by glucocorticoids and adrenocorticotropic hormone in the adrenal cortex, Molecular Endocrinology, 20 (2006), 2711-2723. Google Scholar |
[19] |
G. H. Hardy and E. M. Wright, An Introduction to the Theory of Numbers, Fifth edition. The Clarendon Press, Oxford University Press, New York, 1979.
![]() |
[20] |
B. Host, A. Maass and S. Martínez,
Uniform Bernoulli measure in dynamics of permutative cellular automata with algebraic local rules, Discrete Contin. Dyn. Syst., 9 (2003), 1423-1446.
doi: 10.3934/dcds.2003.9.1423. |
[21] |
A. S. Jarrah, R. Laubenbacher and A. Veliz-Cuba,
The dynamics of conjunctive and disjunctive Boolean network models, Bull. Math. Biol., 72 (2010), 1425-1447.
doi: 10.1007/s11538-010-9501-z. |
[22] |
S. Kauffman, The large scale structure and dynamics of gene control circuits: An ensemble approach, Journal of Theoretical Biology, 44 (1974), 167-190. Google Scholar |
[23] |
S. A. Kauffman,
Metabolic stability and epigenesis in randomly constructed genetic nets, Journal of Theoretical Biology, 22 (1969), 437-467.
doi: 10.1016/0022-5193(69)90015-0. |
[24] |
M. A. Kiwi, R. Ndoundam, M. Tchuente and E. Goles,
No polynomial bound for the period of the parallel chip firing game on graphs, Theoret. Comput. Sci., 136 (1994), 527-532.
doi: 10.1016/0304-3975(94)00131-2. |
[25] |
D. H. Nguyen and P. D'haeseleer, Deciphering principles of transcription regulation in eukaryotic genomes, Molecular Systems Biology, 2 (2006).
doi: 10.1038/msb4100054. |
[26] |
É. Remy, P. Ruet and D. Thieffry,
Positive or negative regulatory circuit inference from multilevel dynamics, Notes Control Inf. Sci., 341 (2006), 263-270.
|
[27] |
F. Ren and J. Cao,
Asymptotic and robust stability of genetic regulatory networks with time-varying delays, Neurocomputing, 71 (2008), 834-842.
doi: 10.1016/j.neucom.2007.03.011. |
[28] |
T. Ribeiro, M. Magnin, K. Inoue and C. Sakama, Learning delayed influences of biological systems, Frontiers in Bioengineering and Biotechnology, 2 (2015), 81.
doi: 10.3389/fbioe.2014.00081. |
[29] |
F. Robert, Discrete Iterations: A Metric Study, Springer Series in Computational Mathematics, 6. Springer-Verlag, Berlin, 1986.
doi: 10.1007/978-3-642-61607-5. |
[30] |
M. Sobottka,
Right-permutative cellular automata on topological Markov chains, Discrete Contin. Dyn. Syst., 20 (2008), 1095-1109.
doi: 10.3934/dcds.2008.20.1095. |
[31] |
T. K. Subrahmonian Moothathu,
Homogeneity of surjective cellular automata, Discrete Contin. Dyn. Syst., 13 (2005), 195-202.
doi: 10.3934/dcds.2005.13.195. |
[32] |
R. Thomas, Boolean formalization of genetic control circuits, Journal of Theoretical Biology, 42 (1973), 563-585. Google Scholar |
[33] |
R. Thomas,
Regulatory networks seen as asynchronous automata: A Logical description, Journal of Theoretical Biology, 153 (1991), 1-23.
doi: 10.1016/S0022-5193(05)80350-9. |
[34] |
R. Thomas, D. Thieffry and M. Kaufman, Dynamical behaviour of biological regulatory networks-i. biological role of feedback loops and practical use of the concept of the loop-characteristic state, Bulletin of Mathematical Biology, 57 (1995), 247-276. Google Scholar |
show all references
References:
[1] |
J. Ahmad, O. Roux, G. Bernot, J.-P. Comet and A. Richard,
Analysing formal models of genetic regulatory networks with delays, International Journal of Bioinformatics Research and Applications, 4 (2008), 240-262.
doi: 10.1504/IJBRA.2008.019573. |
[2] |
J. Aracena, E. Goles, A. Moreira and L. Salinas,
On the robustness of update schedules in Boolean networks, Biosystems, 97 (2009), 1-8.
doi: 10.1016/j.biosystems.2009.03.006. |
[3] |
J. Aracena, A. Richard and L. Salinas,
Fixed points in conjunctive networks and maximal independent sets in graph contractions, J. Comput. System Sci., 88 (2017), 145-163.
doi: 10.1016/j.jcss.2017.03.016. |
[4] |
S. Arora and B. Barak, Computational Complexity: A Modern Approach, Cambridge University Press, Cambridge, 2009.
doi: 10.1017/CBO9780511804090.![]() ![]() |
[5] |
G. Bernot, J.-P. Comet, A. Richard and J. Guespin,
Application of formal methods to biological regulatory networks: Extending Thomas' asynchronous logical approach with temporal logic, J. Theoret. Biol., 229 (2004), 339-347.
doi: 10.1016/j.jtbi.2004.04.003. |
[6] |
J. Demongeot, A. Elena and S. Sené,
Robustness in regulatory networks: A multi-disciplinary approach, Acta Biotheoretica, 56 (2008), 27-49.
doi: 10.1007/s10441-008-9029-x. |
[7] |
J. Fromentin, D. Eveillard and O. Roux, Hybrid modeling of biological networks: Mixing temporal and qualitative biological properties, BMC Systems Biology, 4 (2010), 79.
doi: 10.1186/1752-0509-4-79. |
[8] |
Z. Gao, X. Chen and T. BaÅŸar,
Controllability of conjunctive Boolean networks with application to gene regulation, IEEE Trans. Control Netw. Syst., 5 (2018), 770-781.
doi: 10.1109/TCNS.2017.2746345. |
[9] |
E. Goles, F. Lobos, G. A. Ruz and S. Sené,
Attractor landscapes in Boolean networks with firing memory: A theoretical study applied to genetic networks, Nat. Comput., 19 (2020), 295-319.
doi: 10.1007/s11047-020-09789-0. |
[10] |
E. Goles and P. Montealegre,
Computational complexity of threshold automata networks under different updating schemes, Theoret. Comput. Sci., 559 (2014), 3-19.
doi: 10.1016/j.tcs.2014.09.010. |
[11] |
E. Goles, P. Montealegre, V. Salo and I. Törmä,
PSPACE-completeness of majority automata networks, Theoret. Comput. Sci., 609 (2016), 118-128.
doi: 10.1016/j.tcs.2015.09.014. |
[12] |
E. Goles and M. Noual,
Disjunctive networks and update schedules, Adv. in Appl. Math., 48 (2012), 646-662.
doi: 10.1016/j.aam.2011.11.009. |
[13] |
E. Goles and L. Salinas,
Comparison between parallel and serial dynamics of Boolean networks, Theoret. Comput. Sci., 396 (2008), 247-253.
doi: 10.1016/j.tcs.2007.09.008. |
[14] |
E. Goles-Chacc, F. Fogelman-Soulié and D. Pellegrin,
Decreasing energy functions as a tool for studying threshold networks, Discrete Appl. Math., 12 (1985), 261-277.
doi: 10.1016/0166-218X(85)90029-0. |
[15] |
A. Graudenzi and R. Serra, A new model of genetic network: The Gene Protein Boolean network, Artificial Life and Evolutionary Computation, World Sci. Publ., Hackensack, NJ, (2010), 283-291.
doi: 10.1142/9789814287456_0025. |
[16] |
A. Graudenzi, R. Serra, M. Villani, A. Colacci and S. A. Kauffman,
Robustness analysis of a Boolean model of gene regulatory network with memory, J. Comput. Biol., 18 (2011), 559-577.
doi: 10.1089/cmb.2010.0224. |
[17] |
A. Graudenzi, R. Serra, M. Villani, C. Damiani, A. Colacci and S. A. Kauffman,
Dynamical properties of a Boolean model of gene regulatory network with memory, J. Comput. Biol., 18 (2011), 1291-1303.
doi: 10.1089/cmb.2010.0069. |
[18] |
B. M. Gummow, J. O. Scheys, V. R. Cancelli and G. D. Hammer, Reciprocal regulation of a glucocorticoid receptor-steroidogenic factor-1 transcription complex on the Dax-1 promoter by glucocorticoids and adrenocorticotropic hormone in the adrenal cortex, Molecular Endocrinology, 20 (2006), 2711-2723. Google Scholar |
[19] |
G. H. Hardy and E. M. Wright, An Introduction to the Theory of Numbers, Fifth edition. The Clarendon Press, Oxford University Press, New York, 1979.
![]() |
[20] |
B. Host, A. Maass and S. Martínez,
Uniform Bernoulli measure in dynamics of permutative cellular automata with algebraic local rules, Discrete Contin. Dyn. Syst., 9 (2003), 1423-1446.
doi: 10.3934/dcds.2003.9.1423. |
[21] |
A. S. Jarrah, R. Laubenbacher and A. Veliz-Cuba,
The dynamics of conjunctive and disjunctive Boolean network models, Bull. Math. Biol., 72 (2010), 1425-1447.
doi: 10.1007/s11538-010-9501-z. |
[22] |
S. Kauffman, The large scale structure and dynamics of gene control circuits: An ensemble approach, Journal of Theoretical Biology, 44 (1974), 167-190. Google Scholar |
[23] |
S. A. Kauffman,
Metabolic stability and epigenesis in randomly constructed genetic nets, Journal of Theoretical Biology, 22 (1969), 437-467.
doi: 10.1016/0022-5193(69)90015-0. |
[24] |
M. A. Kiwi, R. Ndoundam, M. Tchuente and E. Goles,
No polynomial bound for the period of the parallel chip firing game on graphs, Theoret. Comput. Sci., 136 (1994), 527-532.
doi: 10.1016/0304-3975(94)00131-2. |
[25] |
D. H. Nguyen and P. D'haeseleer, Deciphering principles of transcription regulation in eukaryotic genomes, Molecular Systems Biology, 2 (2006).
doi: 10.1038/msb4100054. |
[26] |
É. Remy, P. Ruet and D. Thieffry,
Positive or negative regulatory circuit inference from multilevel dynamics, Notes Control Inf. Sci., 341 (2006), 263-270.
|
[27] |
F. Ren and J. Cao,
Asymptotic and robust stability of genetic regulatory networks with time-varying delays, Neurocomputing, 71 (2008), 834-842.
doi: 10.1016/j.neucom.2007.03.011. |
[28] |
T. Ribeiro, M. Magnin, K. Inoue and C. Sakama, Learning delayed influences of biological systems, Frontiers in Bioengineering and Biotechnology, 2 (2015), 81.
doi: 10.3389/fbioe.2014.00081. |
[29] |
F. Robert, Discrete Iterations: A Metric Study, Springer Series in Computational Mathematics, 6. Springer-Verlag, Berlin, 1986.
doi: 10.1007/978-3-642-61607-5. |
[30] |
M. Sobottka,
Right-permutative cellular automata on topological Markov chains, Discrete Contin. Dyn. Syst., 20 (2008), 1095-1109.
doi: 10.3934/dcds.2008.20.1095. |
[31] |
T. K. Subrahmonian Moothathu,
Homogeneity of surjective cellular automata, Discrete Contin. Dyn. Syst., 13 (2005), 195-202.
doi: 10.3934/dcds.2005.13.195. |
[32] |
R. Thomas, Boolean formalization of genetic control circuits, Journal of Theoretical Biology, 42 (1973), 563-585. Google Scholar |
[33] |
R. Thomas,
Regulatory networks seen as asynchronous automata: A Logical description, Journal of Theoretical Biology, 153 (1991), 1-23.
doi: 10.1016/S0022-5193(05)80350-9. |
[34] |
R. Thomas, D. Thieffry and M. Kaufman, Dynamical behaviour of biological regulatory networks-i. biological role of feedback loops and practical use of the concept of the loop-characteristic state, Bulletin of Mathematical Biology, 57 (1995), 247-276. Google Scholar |















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