Bi381
Introduction
to Complex Systems
An
interdisciplinary Synthesis and Applications Course in the Sciences
Instructor: Dr. David Oline E-mail: olined@sou.edu
Southern
Spring
2007
Week
1
Waldrop,
Chapter 1
Lab on
Thursday April 5: Starlogo Program Download
The NetLogo Models Library
Page
Our list of
the Characteristics
of Complex Adaptive Systems
Week
2
Waldrop,
Chapter 2
Handout on Green
Cars
Chaos
The Lorenz
Attractor Applet – 3 simple equations that produce complex unpredictable
behavior
What is Chaos? An
excellent introductory presentation (warning – a 1.6 MB PDF file)
An Introduction to Chaos
Theory and Fractal Geometry A good intro that provides some links
between chaos and fractals
The
Logistic Equation and the Bifurcation Diagram
The Chaos Lab Page (for lab on
4/12)
Week
3
Handout on fractals
in Jackson Pollack paintings
The
Logistic Equation and the Bifurcation Diagram
What is Chaos? An
excellent introductory presentation (warning – a 1.6 MB PDF file)
Fractals Everywhere
(another large PDF file)
More Fractals
Everywhere - Frame and Mandelbrot’s Fractal Panorama
Worksheets: Geometric
scaling of simple cubes
What is the BOX-COUNTING method of measuring a fractal? Here’s an illustrated example: a galaxy
Zooming in on
the Koch Snowflake – there’s always more detail to see! Animation created
by Jim Loy
Week
4
Links for Lab
on Thursday April 26
The Sugarscape StarLogo file
The RedBlueSugarscape StarLogo
file
The NetLogo Models Library
Page
Starlogo Program Download (only if you need it – you
may have this installed already)
Week
5
The virtual sandpile A fun applet which simulates the
dynamics of a sandpile (as seen in class)
Links for the Week 5 Lab –
Fractal Structures II
A
copy of the
assignment (handed out in class on Wednesday)
A good example of the box counting
method on a fractal structure – a galaxy
The box-counting applet
with which to gather your data
Week
6
The NetLogo Giant
Component model (as seen in class)
The
NetLogo Preferential
Attachment model (how scale-free networks are created)
Links for
Lab on Thursday, May 10
A java applet of
Kauffman’s NK Boolean networks
Another introduction to Kauffman’s NK
Boolean networks
Another java applet of
Kauffman’s NK Boolean networks, with network topology
The Discrete
Dynamics Laboratory – visualizations of attractor basins from complex
networks
Week
8
Tutorial
on emergence in cellular automata
The Game of Life – Java
applet implementing John Conway’s original Game of Life
Another online implementation of
Conway’s Game of Life, with more options for initial patterns
Download “Life in the Fast Lane” – the ultimate Game of Life program
Cellebration! – a
versatile online cellular automata program
Download
CELLAB – an even more versatile cellular automata program, as seen
in class
Week
9
Scientific
Paper Format – for writing up your independent projects
The
two-dimensional Drunkard’s walk
QUIZ
ANSWERS
Modeling Links
The NetLogo
Models Library Page
For
Lab on Tuesday, April 4:
The RabbitsAndGrass Model
Chaos
The Lorenz
Attractor Applet – 3 simple equations that produce complex unpredictable
behavior
What is Chaos? An
excellent introductory presentation (warning – a 1.6 MB PDF file)
An Introduction to Chaos
Theory and Fractal Geometry A good intro that provides some links
between chaos and fractals
The
Logistic Equation and the Bifurcation Diagram
Fractals
Zooming in on
the Koch Snowflake – there’s always more detail to see! Animation created
by Jim Loy.
Fractals Everywhere
- Frame and Mandelbrot’s Fractal Panorama
A good example
of the box counting method on another large-scale fractal structure – a galaxy
A supplement to
the coastline lab –
practice the box-counting method online
Self-Organized Criticality
Sandpiles and self-organized criticality
Self-organized criticality in drainage
landscape formation
The virtual sandpile A fun applet which simulates the
dynamics of a sandpile
Cellular Automata
Tutorial
on emergence in cellular automata
The Game of Life – Java applet
implementing John Conway’s original Game of Life
Another online implementation of
Conway’s Game of Life, with more options for initial patterns
Download “Life in the Fast Lane” – the ultimate Game of Life program
Cellebration! – a versatile online cellular
automata program
Download
CELLAB – an even more versatile cellular automata program, as seen
in class
Complex Systems, Chaos, Fractals –
General Links Pages
Open, Dissipative Systems, and Entropy
Networks
A java applet of
Kauffman’s NK Boolean networks
Stuart Kauffman’s Scientific
American article from 1991. “Anti-chaos” is an early (poorly
chosen, perhaps) term he used
for what we now call
“Complex” behavior.
Another introduction to Kauffman’s NK
Boolean networks
Another java applet of
Kauffman’s NK Boolean networks, with network topology
The Discrete
Dynamics Laboratory – visualizations of attractor basins from complex
networks
Correlated Fitness Landscapes
An
introduction to fitness landscapes and diversification from Klaus Saul
A wide ranging covering genetic
and technological diversification on rugged fitness landscapes from Thomas Berngruber
(warning – a huge Power Point file!)
Journals: