Activation energy-based simulation for self-assembly of multi-shape tiles

ABSTRACT

Building artificial systems using self-assembly is one of the main issues of artificial life [17]. Scientists are trying to understand this process either using experimental approaches or computer simulation approaches. This paper aims at supporting research using computer simulation approaches mimicking self-assembly as it occurs in the real world using basic principles in physics such as Brownian motion and basic concepts in Chemistry such as activation energy required to build molecules at molecular level. In this paper, a simulator has been implemented to mimic the process of self-assembly. In this simulator, objects are modeled by shapes such as cubes, tetrahedrons, wedges and pyramids with colors in their faces. The objects move randomly in Brownian motion, and the faces' colors determine how the objects interact with each other. Each object has its own probability to move which depends on the energy that the object gains through its interaction with other objects. The higher energy an object has the less probability that the object has to move and vise verse.

REFERENCES

• 1: Ellabaan, M. "3D Simulation Of Self-assembly", M.Sc, Dissertation, the University of Nottingham, Nottingham, UK (2006).
• 2: Tiequan Zhang , Rori Rohlfs , Russell Schwartz, Implementation of a discrete event simulator for biological self-assembly systems, Proceedings of the 37th conference on Winter simulation, December 04-07, 2005, Orlando, Florida
• 3: Katayoun Sohrabi , William Merrill , Jeremy Elson , Lewis Girod , Fredric Newberg , William Kaiser, Methods for Scalable Self-Assembly of Ad Hoc Wireless Sensor Networks, IEEE Transactions on Mobile Computing, v.3 n.4, p.317-331, October 2004 [doi>10.1109/TMC.2004.43]
• 4: Patwardhan, J.; Dwyer, C.; Lebeck, A.; and Sorin, D. (2004): Circuit and System Architecture for DNA-Guided Self-assembly of Nanoelectronics, Proceedings of the 1st Conference on the Foundations of Nanoscience, April, 2004.
• 5: Vadim Gerasimov , Ying Guo , Geoff James , Geoff Poulton , Philip Valencia, Multiagent Self-Assembly Simulation Environment, Proceedings of the Third International Joint Conference on Autonomous Agents and Multiagent Systems, p.1382-1383, July 19-23, 2004, New York, New York [doi>10.1109/AAMAS.2004.189]
• 6: Terrazas, G.; Krasnogor, N.; Georghe, M. and Kendall, G. (2005), Automated Tile Design for Self-assembly Conformations; Proceedings of the 2005 IEEE Congress on Evolutionary Computation, September 2--5, 2005, Edinburgh, Scotland.
• 7: Winfree, E.; Liu, F., Wenzler, L. A., and Seeman N. C. (1998) Design and Self-assembly of Two-Dimensional DNA Crystals, Nature 394, p. 539--544.
• 8: Lin Li , Natalio Krasnogor , Jon Garibaldi, Automated Self-Assembly Programming Paradigm: Initial Investigations, Proceedings of the Third IEEE International Workshop on Engineering of Autonomic & Autonomous Systems (EASE'06), p.25-36, March 27-30, 2006 [doi>10.1109/EASE.2006.3]
• 9: Shwartz, R. Shor, P. Prevelige, P., and Berger, B. 1998, local rules simulation of kinetics of virus capsid Self-assembly, Biophysics 75: p.2626--2636.
• 10: Maillet, J. B. Lachet, V. and Coveney, P. V. (1999): Large scale molecular dynamics simulation of Self-assembly processes in short and long chain cationic surfactants, Phys Chem Chem Phys, 1, 5277--5290 (1999).
• 11: Winfree E. Schulman R. Lee, S. and Papadakis, N., (2003 B), One Dimensional boundaries for DNA tile Self-assembly. DNA 2003, p. 108--126.
• 12: Cook, M. Rothemund P. and Winfree, E (2003): Self-assembled Circuit Patterns. DNA 2003: P. 91--107.
• 13: Wikipedia, "Self-assembly definition", June 2006 URL: "http://en.wikipedia.org/wiki/Self-assembly"
• 14: Wikipedia, "Energy Definition", Chemistry Section, June 2006 URL: "http://en.wikipedia.org/wiki/Energy#Chemistry"
• 15: Deamer, D. (1999), the origin of life, Evolutionary theory conference November 14-19, 1999, URL: http://www.esalenctr.org/display/confpage.cfm?confid=5&pageid=50&pgtype=1all
• 16: Ellabaan, M. and Brailsford T, "Wang Cube Simulator for Self-assembly", the 4th International conference for information and communication technology, ICICT 2006, Cairo, Egypt.
• 17: Brooks, R. "The relationship between matter and life by Rodney Brooks. Nature 409, 409--411 (2001) "Nature 409, 409--411 (2001).
• 18: Whitesides, G. "Self-assembly and Nanotechnology", abstract for the fourth foresight conference on molecular nanotechnology, May 2006, URL: "http://www.zyvex.com/nanotech/nano4/whitesidesAbstract.html

INDEX TERMS

Primary Classification:
  J. Computer Applications
  J.2 PHYSICAL SCIENCES AND ENGINEERING
      Subjects: Chemistry

Additional Classification:
  J. Computer Applications
  J.2 PHYSICAL SCIENCES AND ENGINEERING
      Subjects: Physics
  J.3 LIFE AND MEDICAL SCIENCES
      Subjects: Biology and genetics

General Terms:
Algorithms, Design, Performance, Theory

Keywords:
artificial life, self-assembly, self-organization, simulation