Controllability of Conjunctive Boolean Networks With Application to Gene Regulation

A Boolean network is a finite-state discrete-time dynamical system. At each step, each variable takes a value from a binary set. The value update rule for each variable is a local function which depends only on a selected subset of variables. Boolean networks have been used in modeling gene regulatory networks. In this paper, we focus on a special class of Boolean networks, namely, the conjunctive Boolean networks (CBNs), whose value update rule is comprised of only logic AND operations. It is known that any trajectory of a Boolean network will enter a periodic orbit. Periodic orbits of a CBN have been completely understood. In this paper, we investigate the orbit-controllability and state-controllability of a CBN: We ask the question of how one can steer a CBN to enter any periodic orbit or to reach any final state, from any initial state. We establish necessary and sufficient conditions for a CBN to be orbit-controllable and state-controllable. Furthermore, explicit control laws are presented along the analysis.

[1]  Michael Margaliot,et al.  Controllability of Boolean control networks via the Perron-Frobenius theory , 2012, Autom..

[2]  S. Bornholdt,et al.  Boolean Network Model Predicts Cell Cycle Sequence of Fission Yeast , 2007, PloS one.

[3]  Eric Goles Ch.,et al.  On the preservation of limit cycles in Boolean networks under different updating schemes , 2013, ECAL.

[4]  Tamer Basar,et al.  Orbit-controlling sets for conjunctive Boolean networks , 2017, 2017 American Control Conference (ACC).

[5]  Andrzej Lingas,et al.  Towards an Almost Quadratic Lower Bound on the Monotone Circuit Complexity of the Boolean Convolution , 2017, TAMC.

[6]  J J Hopfield,et al.  Neural networks and physical systems with emergent collective computational abilities. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[7]  Tamer Basar,et al.  Asymptotic behavior of a reduced conjunctive Boolean network , 2017, 2017 IEEE 56th Annual Conference on Decision and Control (CDC).

[8]  D. Cheng,et al.  Analysis and control of Boolean networks: A semi-tensor product approach , 2010, 2009 7th Asian Control Conference.

[9]  Justin D. Vrana,et al.  Optogenetic control of cell function using engineered photoreceptors , 2013, Biology of the cell.

[10]  Abdul Salam Jarrah,et al.  The effect of negative feedback loops on the dynamics of boolean networks. , 2007, Biophysical journal.

[11]  P. Stragier,et al.  Processing of a sporulation sigma factor in Bacillus subtilis: How morphological structure could control gene expression , 1988, Cell.

[12]  Fedor V. Fomin,et al.  Finding Induced Subgraphs via Minimal Triangulations , 2009, STACS.

[13]  François Robert,et al.  Discrete iterations - a metric study , 1986, Springer series in computational mathematics.

[14]  Richard M. Karp,et al.  Reducibility Among Combinatorial Problems , 1972, 50 Years of Integer Programming.

[15]  Tamer Basar,et al.  Periodic behavior of a diffusion model over directed graphs , 2016, 2016 IEEE 55th Conference on Decision and Control (CDC).

[16]  W. Brown,et al.  Translation: DNA to mRNA to Protein , 2008 .

[17]  Jianquan Lu,et al.  Some necessary and sufficient conditions for the output controllability of temporal Boolean control networks , 2014 .

[18]  S. Kauffman Homeostasis and Differentiation in Random Genetic Control Networks , 1969, Nature.

[19]  Chunjiang Qian,et al.  State feedback control design for Boolean networks , 2016, BMC Systems Biology.

[20]  Xudong Chen,et al.  State-controlling Sets for Conjunctive Boolean Networks , 2017 .

[21]  Farren J. Isaacs,et al.  Computational studies of gene regulatory networks: in numero molecular biology , 2001, Nature Reviews Genetics.

[22]  Bernd Sturmfels,et al.  Monomial Dynamical Systems over Finite Fields , 2006, Complex Syst..

[23]  Damien Regnault,et al.  About non-monotony in Boolean automata networks , 2011, Theor. Comput. Sci..

[24]  D. A. Baxter,et al.  Mathematical Modeling of Gene Networks , 2000, Neuron.

[25]  R. Thomas,et al.  Boolean formalization of genetic control circuits. , 1973, Journal of theoretical biology.

[26]  M. Gossen,et al.  Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[27]  F. Fages,et al.  Long-term model predictive control of gene expression at the population and single-cell levels , 2012, Proceedings of the National Academy of Sciences.

[28]  J J Hopfield,et al.  Neurons with graded response have collective computational properties like those of two-state neurons. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[29]  John Maloney,et al.  Scalar equations for synchronous Boolean networks with biological applications , 2004, IEEE Transactions on Neural Networks.

[30]  Igor Razgon,et al.  Computing Minimum Directed Feedback Vertex Set in O(1.9977n) , 2007, ICTCS.

[31]  D. Pincus,et al.  In silico feedback for in vivo regulation of a gene expression circuit , 2011, Nature Biotechnology.

[32]  S. Kauffman Metabolic stability and epigenesis in randomly constructed genetic nets. , 1969, Journal of theoretical biology.

[33]  R. Laubenbacher,et al.  Boolean Monomial Dynamical Systems , 2004, math/0403166.

[34]  Mario di Bernardo,et al.  In-Vivo Real-Time Control of Protein Expression from Endogenous and Synthetic Gene Networks , 2014, PLoS Comput. Biol..

[35]  P. Brown,et al.  Exploring the metabolic and genetic control of gene expression on a genomic scale. , 1997, Science.

[36]  L. Raeymaekers,et al.  Dynamics of Boolean networks controlled by biologically meaningful functions. , 2002, Journal of theoretical biology.

[37]  Qianchuan Zhao,et al.  A remark on "Scalar equations for synchronous Boolean networks with biological Applications" by C. Farrow, J. Heidel, J. Maloney, and J. Rogers , 2005, IEEE Transactions on Neural Networks.

[38]  Eric Goles Ch.,et al.  Disjunctive networks and update schedules , 2012, Adv. Appl. Math..

[39]  Lequn Zhang,et al.  Controllability and observability of switched Boolean control networks , 2012 .

[40]  C Hélène,et al.  The anti-gene strategy: control of gene expression by triplex-forming-oligonucleotides. , 1991, Anti-cancer drug design.

[41]  Satoru Miyano,et al.  Identification of Genetic Networks from a Small Number of Gene Expression Patterns Under the Boolean Network Model , 1998, Pacific Symposium on Biocomputing.

[42]  Abdul Salam Jarrah,et al.  The Dynamics of Conjunctive and Disjunctive Boolean Network Models , 2010, Bulletin of mathematical biology.

[43]  Adrien Richard,et al.  Number of Fixed Points and Disjoint Cycles in Monotone Boolean Networks , 2016, SIAM J. Discret. Math..

[44]  Eric Goles Ch.,et al.  On limit cycles of monotone functions with symmetric connection graph , 2004, Theor. Comput. Sci..

[45]  Tamer Basar,et al.  Stability structures of conjunctive Boolean networks , 2016, Autom..

[46]  Daizhan Cheng,et al.  Controllability and observability of Boolean control networks , 2009, Autom..

[47]  YuanJie Zheng,et al.  Controllability of Boolean networks via input controls under Harvey's update scheme. , 2016, Chaos.

[48]  Shuhong Gao,et al.  Monomial Dynamical Systems in # P-complete , 2012 .

[49]  Edward R. Dougherty,et al.  From Boolean to probabilistic Boolean networks as models of genetic regulatory networks , 2002, Proc. IEEE.

[50]  T. Başar,et al.  On the Stability of Conjunctive Boolean Networks , 2016 .

[51]  Tamer Başar,et al.  Asymptotic Behavior of Conjunctive Boolean Networks Over Weakly Connected Digraphs , 2017, IEEE Transactions on Automatic Control.

[52]  Adrien Richard,et al.  Asynchronous Simulation of Boolean Networks by Monotone Boolean Networks , 2016, ACRI.

[53]  Tianping Chen,et al.  Cluster Consensus in Discrete-Time Networks of Multiagents With Inter-Cluster Nonidentical Inputs , 2012, IEEE Transactions on Neural Networks and Learning Systems.

[54]  W S McCulloch,et al.  A logical calculus of the ideas immanent in nervous activity , 1990, The Philosophy of Artificial Intelligence.

[55]  T. Chu,et al.  Controllability and observability of Boolean networks arising from biology. , 2015, Chaos.