Xholon - Cell Model with Aupopoiesis

This is a model of a simple biological cell, demonstrating autopoiesis.

Run it:

1. Run the Java application through the XhnCellontro GUI (org.primordion.cellontro.app.XhnCell.java), and select File --> Open --> cellontro --> CellAutop --> Autop_xhn.xml.
2. Expand the Controller node in the tree.
3. Press the Start node.
4. You should see some text in the console window, a line chart showing how the quantities of small molecules change over time, a graph showing the biochemical pathways, and a tree that shows the entire composite structure of the model.

The composite structure hierarchy can be viewed in the Xhn GUI.

The composite structure hierarchy can also be viewed graphically if JUNG is installed.

Connections between xholons can be viewed graphically if you have JUNG installed. In this network graph, bilayer active objects are yellow rectangles, other active objects (enzymes, the hydrophobic force of water, and lipid disintegration) are red rectangles with a circular area missing, and passive objects (small molecules) are green circles.

This model is based on a conference paper.

Webb, K., & White, T. (2004). Combining Analysis and Synthesis in a Model of a Biological Cell. SAC '04, March 14-17, 2004, Nicosia, Cyprus.

This paper, and the model, is based partly on the published work of Francisco Varela and Barry McMullin.