This is a sketchy, tentative list of some readings we might use in CS851.

Concepts from Biology

• Morphogenesis
• DNA, genes and cell actions
• Mechanisms
  • Chemical Diffusion
  • Differentiation

Fault Tolerance in Biology's Programs

• Healing and Regeneration
• Re-organisation
• Evolution

Models

• Chemical Abstract Machine
• Santa Fe Cell Simulator

Cellular Automata

• Marianne Delorme, An introduction to Cellular Automata, 1998.
  • Von Neuman, Theory of Self Reproducing Automata, 1956.

Amorphous Computing

• H. Abelson, D. Allen, D. Coore, C. Hanson, G. Homsy, T. Knight, R. Nagpal, E. Rauch, G. Sussman and R. Weiss, Amorphous Computing, AI Memo 1665, Aug 1999.
• Radhika Nagpal, Organizing a Global Coordinate System from Local Information on an Amorphous Computer, AI Memo 1666, August 1999
• Jacob Beal, An Algorithm for Bootstrapping Communications, International Conference on Complex Systems (ICCS), June 2002

Genetic Algorithms

Stigmergic Systems

Neural Networks

Arificial Life

• Jens Breyer, Jorg Ackermann, John McCaskill, Evolving Reaction-Diffusion Systems with Self-Assembling Structures in Thin Films, Artificial Life VI, 1998
• Jeffrey O. Kephart, James E. Hanson, Jakka Sairamesh, Price-War Dynamics in a Free Market Economy of Software Agents, Artificial Life VI, 1998
• Thomas S. Ray, Joseph Hart, Evolution of Differentiated Multi-threaded Digital Organisms, Artificial Life VI, 1998
• Jason Noble, Evolved Signals: Extensive Hype vs. Conspiratorial Whispers Artificial Life VI, 1998

Applications

• R. Weiss, G. H. Homsy, and T. F. Knight, Jr., "Toward in vivo Digital Circuits." Proceedings of DIMACS Workshop on Evolution as Computation (1999).
• self-reconfiguring robots

University of Virginia Department of Computer Science CS 851: Biologically-Inspired Computing

evans@cs.virginia.edu