Multiset of Agents in a Network for Simulation of Complex Systems

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.

[1]  E. Shapiro,et al.  Cellular abstractions: Cells as computation , 2002, Nature.

[2]  Thomas Duke,et al.  The logical repertoire of ligand-binding proteins , 2005, Physical biology.

[3]  David B. Fogel,et al.  SWARM-BOT: Design and Implementation of Colonies of Self-Assembling Robots , 2006 .

[4]  Marco Dorigo,et al.  Ant Colony Optimization and Stochastic Gradient Descent , 2002, Artificial Life.

[5]  Andrew J. Cowell,et al.  Evaluating Agent Architectures: Cougaar, Aglets and AAA , 2003, SELMAS.

[6]  Kevin M. Passino,et al.  Biomimicry of bacterial foraging for distributed optimization and control , 2002 .

[7]  Gergely Palla,et al.  Spectral transitions in networks , 2006 .

[8]  Zsolt Palotai,et al.  Emergence of scale-free properties in Hebbian networks , 2003, nlin/0308013.

[9]  John W. Keele,et al.  Software agents in molecular computational biology , 2005, Briefings Bioinform..

[10]  Jean-Louis Deneubourg,et al.  Optimality of communication in self-organized social behaviour , 2005 .

[11]  Thomas Stützle,et al.  Ant Colony Optimization , 2009, EMO.

[12]  K. Sneppen,et al.  Specificity and Stability in Topology of Protein Networks , 2002, Science.

[13]  Elhadi M. Shakshuki,et al.  Multi-agent development toolkits: an evaluation , 2004 .

[14]  Lada A. Adamic,et al.  Local Search in Unstructured Networks , 2002, ArXiv.

[15]  P. Maini,et al.  Mathematical Models for Biological Pattern Formation , 2001 .

[16]  Sasan Rahmatian Transaction Processing Systems , 2002, Encyclopedia of Information Systems.

[17]  James C. Spall,et al.  Introduction to stochastic search and optimization - estimation, simulation, and control , 2003, Wiley-Interscience series in discrete mathematics and optimization.

[18]  David E. Goldberg,et al.  Genetic Algorithms in Search Optimization and Machine Learning , 1988 .

[19]  Marco Dorigo,et al.  Swarm intelligence: from natural to artificial systems , 1999 .

[20]  S. N. Dorogovtsev,et al.  Evolution of networks , 2001, cond-mat/0106144.

[21]  Yaneer Bar-Yam,et al.  Dynamics Of Complex Systems , 2019 .

[22]  Robert C. Hilborn,et al.  Chaos and Nonlinear Dynamics , 2000 .

[23]  Stuart A. Kauffman,et al.  ORIGINS OF ORDER , 2019, Origins of Order.

[24]  Robin K. Milne,et al.  Point Processes and Some Related Processes , 2001 .

[25]  Luca Cardelli,et al.  Abstract Machines of Systems Biology , 2005, Trans. Comp. Sys. Biology.

[26]  Guy Theraulaz,et al.  Self-Organization in Biological Systems , 2001, Princeton studies in complexity.

[27]  D R Westhead,et al.  Petri Net representations in systems biology. , 2003, Biochemical Society transactions.

[28]  Andrew Ilachinski,et al.  Cellular automata , 1968 .

[29]  Hiroshi Tanaka,et al.  Artificial Life Applications of a Class of P Systems: Abstract Rewriting Systems on Multisets , 2000, WMP.

[30]  Kathleen Steinhöfel,et al.  Relating time complexity of protein folding simulation to approximations of folding time , 2007, Comput. Phys. Commun..

[31]  Gregory J. Chaitin Two Philosophical Applications of Algorithmic Information Theory , 2003, DMTCS.

[32]  Robert Shapiro,et al.  A simpler origin for life. , 2007, Scientific American.

[33]  Markus Stumptner,et al.  AI 2001: Advances in Artificial Intelligence , 2002, Lecture Notes in Computer Science.

[34]  Jonathan Timmis,et al.  Artificial Immune Systems: A New Computational Intelligence Approach , 2003 .

[35]  Vladimir G Ivancevic,et al.  Neuro-Fuzzy Associative Machinery for Comprehensive Brain and Cognition Modelling (Studies in Computational Intelligence) , 2007 .

[36]  M. Rees,et al.  The anthropic principle and the structure of the physical world , 1979, Nature.

[37]  Dima L. Shepelyansky,et al.  Kolmogorov Pathways from Integrability to Chaos and Beyond , 2003 .

[38]  Sergei Maslov,et al.  Correlation profiles and motifs in complex networks , 2005 .

[39]  S. Torquato Random Heterogeneous Materials , 2002 .

[40]  C. Cannings,et al.  Ch. 2. Models of random graphs and their applications , 2003 .

[41]  F. Chung,et al.  Complex Graphs and Networks , 2006 .

[42]  Daniel Kunkle,et al.  Emergence of constraint in self-organizing systems. , 2004, Nonlinear dynamics, psychology, and life sciences.

[43]  Frank Noé,et al.  Transition Networks: a unifying theme for molecular simulation and computer science , 2007 .

[44]  Albert,et al.  Emergence of scaling in random networks , 1999, Science.

[45]  Shyong Jian Shyu,et al.  Finding the longest common subsequence for multiple biological sequences by ant colony optimization , 2009, Comput. Oper. Res..

[46]  A. Bellouquid,et al.  Mathematical Modeling of Complex Biological Systems: A Kinetic Theory Approach , 2006 .

[47]  Arnaud Doucet,et al.  Particle filters for state estimation of jump Markov linear systems , 2001, IEEE Trans. Signal Process..

[48]  Salima Hassas,et al.  Self-Organisation: Paradigms and Applications , 2003, Engineering Self-Organising Systems.

[49]  E. Thompson Mind in Life , 2007 .

[50]  Shengxiang Yang,et al.  Evolutionary Computation in Dynamic and Uncertain Environments , 2007, Studies in Computational Intelligence.

[51]  David Harel,et al.  Reactive animation: realistic modeling of complex dynamic systems , 2005, Computer.

[52]  D J Evans,et al.  Parallel processing , 1986 .

[53]  Holger H. Hoos,et al.  An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem , 2005, BMC Bioinformatics.

[54]  Christian P. Robert,et al.  Monte Carlo Statistical Methods , 2005, Springer Texts in Statistics.

[55]  Anotida Madzvamuse Mathematical Modeling of Biological Systems , 2007 .

[56]  C. N Bouza,et al.  Spall, J.C. Introduction to stochastic search and optimization. Estimation, simulation and control. Wiley Interscience Series in Discrete Mathematics and Optimization, 2003 , 2004 .

[57]  Radhika Nagpal,et al.  Construction by robot swarms using extended stigmergy , 2005 .

[58]  Jürgen Branke,et al.  Multi-swarm Optimization in Dynamic Environments , 2004, EvoWorkshops.

[59]  Francis C. Moon,et al.  Chaotic and fractal dynamics , 1992 .

[60]  A. Pikovsky,et al.  Synchronization: Theory and Application , 2003 .

[61]  Shusaku Tsumoto,et al.  Foundations of Intelligent Systems, 15th International Symposium, ISMIS 2005, Saratoga Springs, NY, USA, May 25-28, 2005, Proceedings , 2005, ISMIS.

[62]  A. Vulpiani,et al.  Kolmogorov’s Legacy about Entropy, Chaos, and Complexity , 2003 .

[63]  K. S. Chan,et al.  Chaos: A Statistical Perspective , 2001 .

[64]  Gesine Reinert,et al.  Small worlds , 2001, Random Struct. Algorithms.

[65]  Victor A. Albert,et al.  Parsimony, phylogeny, and genomics , 2006 .

[66]  Stephanie Forrest,et al.  Parallelism and programming in classifier systems , 1990 .

[67]  Leon O. Chua,et al.  Practical Numerical Algorithms for Chaotic Systems , 1989 .

[68]  Susan Stepney,et al.  Artificial Immune Systems and the Grand Challenge for Non-classical Computation , 2003, ICARIS.

[69]  Yoseph Bar-Cohen,et al.  Biologically inspired intelligent robots , 2003, SPIE Smart Structures and Materials + Nondestructive Evaluation and Health Monitoring.

[70]  Gregor E. Morfill,et al.  A new diagnostic to characterize a plasma crystal , 2006 .

[71]  D.E. Goldberg,et al.  Classifier Systems and Genetic Algorithms , 1989, Artif. Intell..

[72]  Moonis Ali,et al.  Innovations in Applied Artificial Intelligence , 2005 .

[73]  Lakhmi C. Jain,et al.  Knowledge-Based Intelligent Information and Engineering Systems , 2004, Lecture Notes in Computer Science.

[74]  Andreas Deutsch,et al.  Bacterial Swarming Driven by Rod Shape , 2007 .

[75]  J. Sutherland The Quark and the Jaguar , 1994 .

[76]  Adam Szarowicz,et al.  The Application of AI to Automatically Generated Animation , 2001, Australian Joint Conference on Artificial Intelligence.

[77]  A. Turing The chemical basis of morphogenesis , 1952, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences.

[78]  Ziheng Yang,et al.  Computational Molecular Evolution , 2006 .

[79]  Stephanie Forrest,et al.  Learning and programming in classifier systems , 2004, Machine Learning.

[80]  Bruce A. MacDonald,et al.  Theoretical Considerations of Multiple Particle Filters for Simultaneous Localisation and Map-Building , 2004, KES.

[81]  Eshel Ben-Jacob,et al.  Smart Bacterial Colonies , 1997 .

[82]  Shlomo Havlin,et al.  Fractals in Science , 1995 .

[83]  Ahmed H. Zewail,et al.  Physical Biology: 4D Visualization of Complexity , 2008 .

[84]  Marie-Pierre Gleizes,et al.  Self-Organisation and Emergence in MAS: An Overview , 2006, Informatica.

[85]  Tamio Arai,et al.  Distributed Autonomous Robotic Systems 3 , 1998 .

[86]  Ilya Prigogine,et al.  From Being To Becoming , 1980 .

[87]  R. Twyman Principles of Proteomics , 2013 .

[88]  Steven H. Strogatz,et al.  Sync: The Emerging Science of Spontaneous Order , 2003 .

[89]  Bertrand Meyer,et al.  Applying 'design by contract' , 1992, Computer.

[90]  Bradley J Stith,et al.  Use of animation in teaching cell biology. , 2004, Cell biology education.

[91]  H. Arnstein The molecular biology of the cell : B. Alberts, D. Bray, J. Lewis, M. Raff, K. Roberts and J.D. Watson Garland Publishing; New York, London, 1983 xxxix + 1181 pages. $33.95 (hardback); $27.00, £14.95 (paperback, only in Europe) , 1986 .

[92]  Sean J. A. Edwards,et al.  Swarming on the Battlefield , 2006 .

[93]  Mark E. J. Newman,et al.  The Structure and Function of Complex Networks , 2003, SIAM Rev..

[94]  A. Wilkins The Evolution of Developmental Pathways , 2001 .

[95]  David Harel,et al.  A Grand Challenge: Full Reactive Modeling of a Multi-cellular Animal , 2003, HSCC.

[96]  A. Atilgan,et al.  Small-world communication of residues and significance for protein dynamics. , 2003, Biophysical journal.

[97]  Mark Alpert The triangular universe. , 2007, Scientific American.

[98]  Jeng-Shyang Pan,et al.  Parallel Ant Colony Systems , 2003, ISMIS.

[99]  Vincenzo Villani,et al.  Complexity of polypeptide dynamics: chaos, Brownian motion and elasticity in aqueous solution , 2003 .

[100]  Erik Mosekilde,et al.  Complexity, chaos, and biological evolution , 1992 .

[101]  Stephanie Forrest,et al.  Analogies with immunology represent an important step toward the vision of robust, distributed protection for computers. , 1991 .

[102]  William A. Dembski,et al.  Intelligent Design , 1999 .

[103]  Paulo S. C. Alencar,et al.  Software Engineering for Multi-Agent Systems II , 2004 .

[104]  Rolf Drechsler,et al.  Applications of Evolutionary Computing, EvoWorkshops 2008: EvoCOMNET, EvoFIN, EvoHOT, EvoIASP, EvoMUSART, EvoNUM, EvoSTOC, and EvoTransLog, Naples, Italy, March 26-28, 2008. Proceedings , 2008, EvoWorkshops.

[105]  John C Wooley,et al.  Catalyzing Inquiry at the Interface of Computing and Biology , 2005 .

[106]  Martin J Blaser,et al.  An endangered species in the stomach. , 2005, Scientific American.

[107]  Cristian S. Calude,et al.  Discrete Mathematics and Theoretical Computer Science , 2003, Lecture Notes in Computer Science.

[108]  J. Sprott Chaos and time-series analysis , 2001 .

[109]  Werner Ebeling,et al.  Self-Organization, Active Brownian Dynamics, and Biological Applications , 2002, cond-mat/0211606.

[110]  Eugene Shakhnovich,et al.  Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet. , 2006, Chemical reviews.