Tutorial


Liquid and Reaction Theory for Artificial Chemistry


Organizer: Hideaki Suzuki (NICT, Japan)


AIMS AND SCOPE:

Chemical reactions are the most fundamental processes that are proved to cause self-organization and emergence of life. Their basic reaction rules are simple (or at least, clarified by the modern physico-chemistry), and yet they have enough power to bring about self-assembly of molecules to create such highly functional molecules as ribosome.

Self-assembly or self-organization are driving force to create higher structures or functions in the bio-chemical system, and to make such life-like phenomena happen in an computational medium, Artificial Chemistry (AChem) takes a bottom-up (adding) approach that prepares environmental factors in a computer one by one. Unlike numerical/analytic methods auch as Monte Carlo or MD (molecular dynamics), AChem requires a model to be as simple/abstract as it can be computationally tractable, and as complex as it causes self-organization. A key issue here is the balance between the neglected and actualized bio-chemical factors, and to choose an appropriate design for AChem, we have to be familiar with theories on molecular collisions and reactions from the perspective of what lower-level factors are responsible/critical for the higher-level phenomena.

This tutorial is intended to give the audience the knowledge on these AChem's background theories. The first half of the lecture is primarily focused on the chemical reaction velocity theory. After prerequisite conditions for an AChem design are presented, the collision frequency between molecules with various sizes is evaluated. Then, after the merits and demerits of several AChem models are discussed in light of this theory, a promising model, a method to describe molecular interactions with a mathematical graph, is presented. In the final part of the lecture, we discuss possible future directions for designing self-organizing computational systems under the framework of AChem.


INTENDED AUDIENCE:

* ALife researchers interested in chemical reaction approaches,
* AChem researchers trying to find more substantial theoretical background for their models,
* young students interested in self-organization in chemistry, self-organized computation, etc.


TENTATIVE CONTENTS (Definitive program to be announced soon):

1. Solution Space and Self-organization
2. Some Requirements for Biological Evolution
2-1. Early Stages of Biological Evolution
2-2. Qualitative Conditions
3. Statistical Theory of Chemical Reaction Velocity
3-1. Molecular/Atomic Force
3-2. Analysis on a Gas Phase
3-3. Analysis on a Liquid Phase
4. Topological Analysis on Molecular Movements in Solution
4-1. Topological Properties of Encounter Network
4-2. Hard-sphere Random-walk Simulation
5. Various Spatial Models
6. Network Solution Model
7. Conclusions and Future Directions

More information upcoming


Contact
Hideaki Suzuki

Hideaki Suzuki, Ph.D
Kobe Advanced ICT Research Center (KARC)
National Institute of Information and Communications Technology (NICT)
588-2, Iwaoka, Iwaokaka-cho, Nishi-ku, Kobe, 651-2492 Japan