Morphogenesis Applet
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Morphogenesis Applet
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Morphogenesis Applet
The applet was written with Java 2 graphical libraries and necessitates the
Java 2 run-time environment. However, this environment is not supported at
present by default by Internet Explorer and Netscape browsers. A Java plug-in
which enables Internet Explorer and Netscape browsers to run this program is
available free of charge for download from : http://java.sun.com/products/plugin/index.html
The simulation of pattern formation in this applet is based on an equation formulated by Hans Westerhoff. A biochemical compound is produced in the cell and stimulates its own production there, which is termed autocatalysis. The compound, termed a morphogen, also leaks out of the cell. Once outside the cell, the morphogen inhibits further morphogen production in its cell of origin, but also in the neighbor cell. Hans Westerhoff calculated this for a one dimensional organism consisting of seven cells. Here you can build an organism consisting of as many cells as your computer allows. My Pentium II with 192 MB RAM supports model organisms with more than a million cells. If you try large numbers of cells (rows x columns x height) computation may become very slow and there is no guarantee that the program or even the operating system may crash. However, with a modest number of cells in the simulation you will probably be alright. The computer model is similar to a biological model designed by Alan Turing. Turing was one of the founding fathers of computer science, but he also designed this "simple" model which nicely illustrates complex behavior in biology. Besides the variety of the process modelled in this applet according to an equation of Hans Westerhoff, I also programmed an animation of Turing's original model. This is a Java application at present, and is not yet available as an applet to run from your browser. The point of the model is that cells which start out with exactly the same properties and content become very different over time due to their position with respect to other cells and the surface of the organism. You will note that the brighter cells inhibit their neighbors giving rise to alternating (1D) and checkerboard (2D, 3D) patterns.
Meaning of the parameters you can change: Rows, columns, and height: The number of cells in the x, y and z direction. Vmax: the maximal rate of intracellular morphogen production Km: The Km of the morphogen production, that is the intracellular concentration of morphogen at which stimulation of morphogen production by the morphogen itself is 50% of maximum Color intensity: you have to tweak this one to get optimal color rendition for your particular simulation. If too high, the color intensity overflows. In this particular version of the applet, this means that the color value is reset to zero (black). This is reported in the title bar of the window. You can make use of high color intensity factors: setting the color intensity factor in the model too high often yields very pretty animated pictures, which may look like dynamically changing stained glass windows or Tiffany lamps. Sleep : this pauses the Java thread for the indicated number of milliseconds. Increasing this number leads to slower running of the program, but the advantage is that you may be able to obtain a smoother and easier to follow animation. |
You can contact me by e-mail at jhgm.van.beek@mdw.vu.nl.
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