chapter  18
24 Pages

Modeling the Dynamics of Cellular Signaling for Communication Networks

WithJIAN-QIN LIU AND KENJI LEIBNITZ

Contents 18.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 458 18.2 The Dynamics of Cellular Signaling. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 460

18.2.1 Spatial Dynamics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 460 18.2.2 Temporal Dynamics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 462 18.2.3 Concluding Remarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 465

18.3 Dynamical Graph Representation of Cellular Signaling . . . . . . . . . . . . . . . . 465 18.3.1 Formulating the Structural Variations of Pathway Networks

by Graph Rewriting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 466 18.3.2 Representation of Cellular Signaling by Graph Automata . . . . . 466 18.3.3 Methodologies of Pathway Networking . . . . . . . . . . . . . . . . . . . . . . . . 469

18.4 Graph Rewiring Operations for Self-Configuration of Dynamical Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 470 18.4.1 Self-Configuration in Communication Networks . . . . . . . . . . . . . . 470

18.4.2 Graph Rewiring Algorithm for Self-Configuring Dynamical Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 471

18.4.3 Information Theoretic Measures for Cellular Signaling Coding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 472

18.4.4 Concluding Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 474 18.5 Robustness of Pathway Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 474

18.5.1 The Heat Shock Response Pathway . . . . . . . . . . . . . . . . . . . . . . . . . . . . 475 18.5.2 The MAPK Pathway for Ultrasensitivity . . . . . . . . . . . . . . . . . . . . . . . 476

18.6 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 477 Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 478 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 478

In this chapter, we discuss models of the dynamics of cellular signaling by characterizing their essential features in terms of dynamical network graphs. It is shown that the classical models in molecular information processing correspond to graph rewriting and graph rewiring. Inspired by the cellular signaling pathway networks, we investigate the dynamical features and illustrate how this understanding can be a step toward building more robust and resilient information networks in dynamical environments.