Abstract
A Complex System (CS) exhibits the four salient properties: (i) Collective, coordinated and efficient interaction among its components (ii) Self-organization and emergence (iii) Power law scaling under emergence (iv) Adaptation, fault tolerance and resilience against damage of its components. We describe briefly, three interrelated mathematical models that enable us to understand these properties: Fractal and percolation model, Stochastic / Chaotic (nonlinear) dynamical model and Topological (network) or graph model. These models have been very well studied in recent years and are closely related to the properties such as: self-similarity, scale-free, resilience, self-organization and emergence. We explain how these properties of CS can be simulated using the multi-set of agents-based paradigm (MAP) through random enabling, inhibiting, preferential attachment and growth of the multiagent network. We discuss these aspects from the point of view of geometric parameters-Lyapunov exponents, strange attractors, metric entropy, and topological indices-Cluster coefficient, Average degree distribution and the correlation length of the interacting network.
We also describe the advantages of agent-based modelling, simulation and animation. These are illustrated by a few examples in swarm dynamics- ant colony, bacterial colonies, human-animal trails, and graph-growth. We briefly consider the engineering of CS, the role of scales, and the limitations arising from quantum mechanics. A brief summary of currently available agent-tool kits is provided. Further developments of agent technology will be of great value to model, simulate and animate, many phenomena in Systems biology-cellular dynamics, cell motility, growth and development biology (Morphogenesis), and can provide for improved capability in complex systems modelling.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Adamic, L.A., et al.: Local search in Unstructured Networks. In: Born holdt, S., Schuster, H.G. (eds.) Handbook of Graphs and Networks, pp. 295–317. Wiley-VCH, New York (2003)
Albert, V.A.: Parsimony, Phylogeny and Genomics. Oxford University Press, Oxford (2005)
Alberts, B., et al.: The Molecular Biology of the Cell. Garland Science, New York (2002)
Atilgan, A.R., et al.: A Small -world Communication of Residues and Significance in Protein Dynamics. Biophysical Journal 86(1), 85–91 (2004)
Aviv, R., Shapiro, E.: Cellular Abstractors: Cellular computation. Nature 419, 343 (2002)
Baker, G.L., Blackburn, J.A.: The Pendulum. Oxford University Press, Oxford (2005)
Barabasi, A., et al.: Emergence of Scaling in Random Networks. Science 286, 509–512 (1999)
Bar-Cohen, Y., Breazeal, C.: Biologically-Inspired Intelligent Robotics. S.P.I.E.Press, Bellingham (2003)
Bar-Yam, Y.: Dynamics of Complex Systems. Addison Wesley, Reading (1997)
Belew, R.K., Forrest, S.: Learning and Programming in classifier Systems. Machine Learning 3, 193–223 (1988)
Belloquid, A., Delitala, M.: Mathematical Modelling of Complex Biological Systems. Birkhauser, Boston (2006)
Ben-Jacob, E., et al.: Smart bacterial colonies in Physics of Biological systems: From Molecules to Species. Lecture Notes in Physics, vol. 480, pp. 307–340. Springer, New York (1997)
Ben-Naim, E., et al. (eds.): Complex Networks. Lecture Notes in Physics, vol. 650. Springer, New York (2004)
Bininda-Emonds, O.R.P.: Phyogenetic Super trees: Combining Information to reveal the tree of life. Kluwer Academic Press, Dordrecht (2004)
Blackwell, T., Branke, J.: Multi-swarm Optimization in Dynamic Environments. In: Raidl, G.R., Cagnoni, S., Branke, J., Corne, D.W., Drechsler, R., Jin, Y., Johnson, C.G., Machado, P., Marchiori, E., Rothlauf, F., Smith, G.D., Squillero, G. (eds.) EvoWorkshops 2004. LNCS, vol. 3005, pp. 489–500. Springer, Heidelberg (2004)
Boahen, K.: Neuromorphic microchips. Scientific American 292, 38–41 (2005)
Booker, L.K., et al.: Classifier systems and Genetic Algorithms. Artificial Intelligence 40, 235–282 (1989)
Bonabeau, E., et al.: Swarm Intelligence: From Natural to Artificial Systems. Oxford University Press, London (1999)
Born holdt, S., Schuster, G.H.: Handbook of Graphs and Networks. Wiley-VCH, New York (2003)
Bunde, A., Havlin, S.: Fractals in Science. Springer, New York (1994)
Camazine, S.: Self-Organization in Biological Systems. Princeton University Press, Princeton (2002)
Cannings, C., Penman, D.D.: Models of random Graphs and their Applications. In: Rao, C.R. (ed.) Handbook of Statistics, vol. 21, pp. 51–91. North Holland, Amsterdam (2003)
Cardelli, L.: Abstract Machines in Systems Biology. Springer Transactions on Biological Systems (2005)
Carr, B., Rees, M.: The anthropic principle and the structure of the physical world. Nature 278, 605–612 (1979)
Chaitin, G.: Two Philosophical Applications of Algorithmic Information Theory. In: Calude, C.S., Dinneen, M.J., Vajnovszki, V. (eds.) DMTCS 2003. LNCS, vol. 2731, pp. 1–10. Springer, Heidelberg (2003)
Chan, K.S., Tong, H.: Chaos: A statistical Perspective. Springer, New York (2002)
Chu, S., et al.: Parallel Ant colony Systems. In: Zhong, N., Raś, Z.W., Tsumoto, S., Suzuki, E. (eds.) ISMIS 2003. LNCS (LNAI), vol. 2871, pp. 279–284. Springer, Heidelberg (2003)
Chung, F., Lu, L.: Complex Graphs and Networks, American Mathematical Society. In: CBMS, Providence, Rhode Island, vol. 107 (2006)
Coello, C.A.C., et al.: Evolutionary algorithm for Solving Multi-objective Problem. Kluwer, New York (2002)
Crutchfield, J.P., Schuster, P.: Evolutionary Dynamics. Oxford University Press, Oxford (2003)
de Castro, L.N., Timmis, J.I.: Artificial Immune Systems: A New computational Intelligence Approach. Springer, New York (2002)
Dembski, W.A.: Intelligent Design. InterVarsity Press, Downers Grove, Ill (1999)
Deneubourg, J.L., et al.: Optimality of communication in self-organized behaviour. In: Hemelrijk, C.K. (ed.) Self -Organization and Evolution of Social Systems, ch.2, pp. 25–35. Cambridge University Press, Cambridge (2005)
Deutsch, A., et al.: Mathematical Modeling of Biological Systems, vol. 1 and 2. Birkhauser, Boston (2007)
Dorigo, M., et al.: Ant Algorithms 2002. LNCS, vol. 2463. Springer, Heidelberg (2002)
Dorigo, M., Stutzle, T.: Ant Colony optimization. M.I.T. Press, Cambridge (2004)
Dorigo, M., et al.: Swarm-Bot: design and implementation of colonies of self-assembling robots. In: Yen, G., Fogel, D.B. (eds.) Computational Intelligence, pp. 103–136. IEEE Press, New York (2006)
Dorogovtsev, S.N., Mendes, J.F.F.: Evolution of Networks. Oxford University Press, Oxford (2003)
Doucet, A., Gordon, N., Krishnamurthy, V.: Particle Filters for State Estimation of Jump Markov Linear Systems. IEEE Trans. Signal Processing 49, 613–624 (2001)
Ebeling, W., Schweitzer, F.: Self-organization, Active Brownian dynamics and biological Applications. Nova Acta Leopoldina 88(332), 169–188 (2003)
Edwards, S.J.: Swarming on the Battlefield, National Defence Research Institute, RAND,U.S.A (2000)
Effroni, S., et al.: Reactive animation: Realistic Modeling of Complex Dynamic Systems. IEEE Computer, 33–46 (January 2005)
Eigen, M.: StepTowards Life. Oxford University Press, Oxford (1992)
Falcioni, M., et al.: Kolmogorov’s legacy about entropy, Chaos and Complexity. Lecture Notes in Physics, vol. 636, pp. 85–108. Springer, New York (2003)
Felenstein, J.: Inferring Phylogenesis. Sinauer associates, Sunderland (2007)
Finkelstein, A.V., Ptitsyn, O.B.: Protein Physics. Academic Press, New York (2002)
Forrest, S.: Parallelism and Programming in classifier systems. Morgan Kauffman, San Mateo (1991a)
Forrest, S.: Emergent Computation. M.I.T Press, Cambridge (1991b)
Gell-Mann, M.: The Quark and the Jaguar. W.H.Freeman, New York (1994)
Goldberg, D.E.: Genetic algorithms in search, optimisation and machine learning. Addison Wesley, Reading (1989)
Goncharova, L.B., Melnikov, Y., Tarakanov, A.O.: Biomolecular Immunocomputing. In: Timmis, J., Bentley, P.J., Hart, E. (eds.) ICARIS 2003. LNCS, vol. 2787, pp. 102–110. Springer, Heidelberg (2003)
Gorton, I., Haack, J., McGee, D.R., Cowell, A.J., Kuchar, O., Thomson, J.: Evaluating Agent Architectures: Cougaar, Aglets and AAA. In: Lucena, C., Garcia, A., Romanovsky, A., Castro, J., Alencar, P.S.C. (eds.) SELMAS 2003. LNCS, vol. 2940, pp. 264–278. Springer, Heidelberg (2004)
Graham, I., Duke, T.: The logical repertoire of ligand-binding proteins. Physical Biology 2, 159–165 (2005)
Grimmett, G.: Percolation. Springer, New York (2004)
Guerin, S., Kunkle, D.: Emergence of Constraint in Self-organizing Systems, Nonlinear dynamics. Psychology and Life Sciences 8(2), 131–146 (2004)
Harel, D.: A grand challenge for computing: towards full reactive modeling of a multicellular animal, EATCS Bulletin (2003), http://www.wisdom.weizmann.ac.il/~dharel/papers/grandchallenge.doc
Hilborn, R.C.: Chaos and Nonlinear Dynamics. Oxford University Press, Oxford (2003)
Hofstadter, D.: Fluid concepts and creative analysis. Basic Books inc., New York (1995)
Holland, J.H., et al.: Induction. M.I.T.Press, Cambridge (1987)
Ilachinski, A.: Cellular Automata. World Scientific, Singapore (2001)
Ishida, Y.: Immmunity Based Systems. Springer, New York (2004)
Ivancevic, V.G., Ivancevic, T.T.: Neuro-Fuzzy Associative Machinery for Comprehensive Brain and Cognition Modelling. Springer, New York (2006)
Jain, S., Krishna, S.: Graph theory and Autocatalytic networks. In: Born holdt, S., Schuster, H.G. (eds.) Handbook of Graphs and Networks, pp. 355–394. Wiley-VCH, New York (2003)
Kauffman, S.A.: The origins of Order. Oxford University Press, Oxford (1993)
Keele, J.W., Wray, J.E.: Software Agents in molecular computational Biology. Briefings in Bioinformatics 6(5), 370–379 (2005)
Kennedy, J., Eberhart, R.C.: Swarm Intelligence. Morgan Kauffman, London (2001)
Kennedy, J.: Swarm Intelligence. In: Zomaya, A. (ed.) Handbook of Nature-Inspired & Innovative Computing, pp. 187–221. Springer, New York (2006)
Koza, J.R.: Genetic programmingIII. Morgan Kaufmann, San Francisco (1999)
Krishnamurthy, E.V.: Parallel Processing. Addison Wesley, Reading (1989)
Krishnamurthy, E.V., Murthy, V.K.: Transaction Processing Systems. Prentice Hall, Sydney (1992)
Lam, L.: Nonlinear Physics for Beginners. World Scientific, Singapore (1998)
Livi, R., et al.: Kolmogorov Pathways from integrability to chaos and beyond. Lecture Notes in Physics, vol. 636, pp. 3–32. Springer, New York (2003)
Maini, P.K., Othmar, H.G. (eds.): Mathematical models for biological pattern formation. Springer, New York (2001)
Manrubia, S.C., et al.: Emergence of dynamical order. World Scientific, Singapore (2004)
Maslov, S., et al.: Specificity and stability in topology of protein networks. Science 296, 910–913 (2002)
Maslov, S., et al.: Correlation profiles and motifs in complex networks. In: Bornholdt, S., Schuster, H.G. (eds.) Handbook of Graphs and Networks, pp. 168–198. Wiley-VCH, New York (2003)
McCullogh, A.D., Huber, G.: Integrative Biological modelling in silico biological processes. In: Bock, G., Goode, A. (eds.) Novatis Foundation symposium, pp. 4–19. John Wliey and Sons, Chichester (2002)
Meuleau, N., Dorigo, M.: Ant colony optimization and Stochastic Gradient Descent. Artificial Life 8, 103–121 (2002)
Meyer, B.: Applying design by contracts. IEEE Computer 25(10), 40–52 (1992)
Milne, R.K.: Point processes and some related Processes. In: Rao, C.R. (ed.) Handbook of Statistics, vol. 19, pp. 599–641. North Holland, Amsterdam (2001)
Moon, F.C.: Chaotic and Fractal Dynamics. John Wiley, New York (1999)
Mosekilde, E., Mosekilde, L. (eds.): Complexity, Chaos and Biological Evolution. Plenum Press, New York (1991)
Nagel, K.: Traffic Networks. In: Bornholdt, S., Schuster, H.G. (eds.) Handbook of Graphs and Networks, pp. 248–272. Wiley-VCH, New York (2003)
Newman, M.E.J.: The Structure and Function of complex Networks, Santa Fe Institute (2004)
Noe, F., Smith, C.: Transition Networks: A unifying theme for Molecular Simulation and Computer Science. In: Deutsch, A., et al. (eds.) Mathematical Modeling of Biological Systems, ch. 11, vol. 1, pp. 121–135. Birkhauser, Boston (2007)
Orengo, C.A., et al.: Bioinformatics. BIOS Scientific Publishers, New York (2003)
Pacino, K.M.: Biomimicry of bacterial foraging for distributed optimisation and control. IEEE Control System Magazine 22(3), 52–68 (2002)
Palla, G., Vattay, G.: Spectral Transitions in Networks. New Journal of Physics 8, 306–314 (2006)
Parker, L.E., et al. (eds.): Distributed Autonomous Robotic Systems. Springer, New York (2000)
Parker, T.S., Chua, L.O.: Practical Numerical algorithms for chaotic systems. Springer, New York (1989)
Petrucci, R.H., et al.: General Chemistry. Prentice-Hall, NJ (2002)
Pikovsky, A., et al.: Synchronization. Cambridge University Press, Cambridge (2003)
Pinney, J.W., et al.: Petri net representations in systems biology. Biochemical Society Transactions 31, Part 6 (2003)
Prigogine, I.: From being to becoming. W.H.Freeman and Co., San Francisco (1980)
Robert, C.P., Casella, G.: Monte Carlo Statistical Methods. Springer, Heidelberg (1999)
Scargle, J.D., Babu, G.J.: Point Processes in Astronomy. In: Rao, C.R. (ed.) Handbook of Statistics, vol. 21, pp. 795–825. North Holland, Amsterdam (2003)
Schweitzer, F.: Brownian Agents and Particles. Springer, Berlin (2002)
Serugendo, G.D.M., et al.: Self Organization: Paradigms and Applications. In: Di Marzo Serugendo, G., Karageorgos, A., Rana, O.F., Zambonelli, F. (eds.) ESOA 2003. LNCS (LNAI), vol. 2977, pp. 1–19. Springer, Heidelberg (2004)
Serugendo, G.D.M., et al.: Self-organization and Emergence in MAS: A overview. Informatica 30, 45–54 (2006)
Shakhnovich, E.: Protein folding Thermodynamics and dynamics: Where Physics, Chemistry and Biology meet. Chemical Reviews 106, 1559–1588 (2006)
Shakshuki, E., Jun, Y.: Multi-agent development toolkits: An Evaluation. In: Orchard, B., Yang, C., Ali, M. (eds.) IEA/AIE 2004. LNCS (LNAI), vol. 3029, pp. 209–218. Springer, Heidelberg (2004)
Shapiro, R.: A simpler origin for life. Scientific American 296, 24–31 (2007)
Shmygelska, A., et al.: An ant colony optimization algorithm for the 2D and 3D hydrophobic polar protein folding problem. BMC Bioinformatics 6, 30–47 (2005)
Shyu, S.J., Tsai, C.-Y.: Finding the longest common subsequences for multiple biological sequences by ant colony optimization. Computers and Operations Research 36, 73–91 (2009)
Spall, J.C.: Introduction to Stochastic Search and Optimization. Wiley Interscience, New York (2003)
Sprott, J.C.: Chaos and Time Series Analysis. Oxford University Press, Oxford (2003)
Starrus, J., et al.: Bacterial Swarming Driven by Rod shape. In: Deutsch, A., et al. (eds.) Mathematical Modeling of Biological Systems, ch. 14, vol. 1, pp. 163–174. Birkhauser, Boston (2007)
Steinhofel, K., et al.: Relating time complexity of protein folding simulation to approximations of folding time. Computer Physics Communications 176, 465–470 (2007)
Stepney, S., et al.: Artificial Immune System and the grand challenges for non- classical computation. In: Timmis, J., Bentley, P.J., Hart, E. (eds.) ICARIS 2003. LNCS, vol. 2787, pp. 204–216. Springer, Heidelberg (2003)
Stith, B.J.: Use of animation in teaching cell biology. Cell. Biology Education 3(3), 181–188 (Fall 2004)
Strogatz, S.H.: Sync:The emerging science of spontaneous Order. Hyperion Press, New York (2003)
Suzuki, Y., et al.: Artificial Life applications of a class of P systems: Abstract rewriting systems on Multisets. In: Calude, C.S., Pun, G., Rozenberg, G., Salomaa, A. (eds.) Multiset Processing. LNCS, vol. 2235, pp. 299–346. Springer, Heidelberg (2001)
Szarowicz, A., et al.: The application of AI to automatically generated animation. In: Stumptner, M., Corbett, D.R., Brooks, M. (eds.) Canadian AI 2001. LNCS (LNAI), vol. 2256, pp. 487–494. Springer, Heidelberg (2001)
Szirtes, G., et al.: Emergence of Scale-free Properties in Hebbian Networks. International Journal of Neural Systems (2001)
Thompson, E.: Mind in Life. Harvard University Press, Cambridge (2007)
Torquato, S.: Random Heterogeneous Materials. Springer, New York (2002)
Turing, A.M.: The Chemical Basis for Morphogenesis. Phil.Trans. Roy. Soc. London 237, 37–79 (1952)
Twyman, R.M.: Principles of Proteomics. BIOS Scientific Publishers, New York (2003)
Vaughan, R.T., et al.: Blazing a trail: Insect - inspired reource transportation by a robot team. In: Parker, L.E., et al. (eds.) Distributed Autonomous Robotic Systems, pp. 112–120. Springer, New York (2000)
Villani, V.: Complexity of polypeptide dynamics:Chaos, Brownian motion and elastcity in aqueous solution. Journal of Molecular Structure:THEOCHEM 621, 127–139 (2003)
Watts, D.: Small Worlds. Princeton University Press, Princeton (1999)
Weiss, T.F.: Cellular Biophysics, vol. 1and 2. MIT Press, Cambridge (1996)
Werfel, J., et al.: Construction by robot swarms using extende stigmergy,Technical Report, AI Memo AIM -2005-011, MIT,C S and AI Lab (2005)
Wilkins, A.S.: The Evolution of Developmental Pathways. Sinauer Associates, Inc., Sunderland (2002)
Wolfram, S.: A New Kind of Science. Wolfram Media Inc., Champaign, Ill (2002)
Wooley, J.C., Lin, H.C. (eds.): Catalyzing inquiry at the interface of computing and biology. National Research council of the National Academies, National Academies Press, Washington, DC (2005)
Woolridge, M.: Introduction to Multi-Agent Systems. John Wiley, New York (2002)
Yang, S., et al.: Evolutionary computation in Dynamic and Uncertain Environments. Springer, New York (2007)
Yang, Z.: Computational Molecular Evolution. Oxford University Press, Oxford (2007)
Yuen, D.C.K., MacDonald, B.: Theoretical considerations of Multiple particle Filters for simultaneous Localization and Map-Building. In: Negoita, M.G., Howlett, R.J., Jain, L.C. (eds.) KES 2004. LNCS (LNAI), vol. 3213, pp. 203–209. Springer, Heidelberg (2004)
Zewail, A.H.: Physical Biology-From Atoms to Medicine. Imperial College, London (2008)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Murthy, V.K., Krishnamurthy, E.V. (2009). Multiset of Agents in a Network for Simulation of Complex Systems . In: Kyamakya, K., Halang, W.A., Unger, H., Chedjou, J.C., Rulkov, N.F., Li, Z. (eds) Recent Advances in Nonlinear Dynamics and Synchronization. Studies in Computational Intelligence, vol 254. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04227-0_6
Download citation
DOI: https://doi.org/10.1007/978-3-642-04227-0_6
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-04226-3
Online ISBN: 978-3-642-04227-0
eBook Packages: EngineeringEngineering (R0)