Simulation of Biological Systems

CS 8803 SBS
Instructor: Greg Turk
Semester: Spring 2013

Time: 11:05 - 11:55pm, MWF
Location: Environmental Science and Technology L1125


Homework

Homework 1 (Life Cellular Automata) - This first homework is due at the end of the second week of class.

Homework 2 (Flocking)

Homework 3 (Reaction-Diffusion)


Reading

Week 1
Chapter 1 in Origins of Life.
Christopher Langton's Self-Reproducing Loops.
Stephen Wolfram's Cellular Automata Classes. Optional: Christopher Langton's Edge of Chaos.

Week 2
Chapter 2 in Origins of Life.
Craig Reynolds' flocking of virtual creatures.

Week 3
Chapter 3 in Origins of Life.
Metabolic pathways chart1 and chart2.
Wolfgang Banzhaf's self-organization in binary strings.

Week 4
Chapter 4 in Origins of Life.
Tim Hutton's self-reproducing simulated molecules.
2D version of protein folding. Optional: Cyrus Levinthal on protein folding complexity.
Classic DNA paper by Watson and Crick. Optional: Stanley Miller's bubbling flask to produce amino acids.
Seeing if genetic code is optimal.

Week 5
Chapter 5 in Origins of Life.
Pattern formation by reaction-diffusion.

Week 6
Simulation of lipid micelles.

Week 7
Chapter 6 in Origins of Life.
The
Genetic Algorithm.

Week 8
Chapter 7 and 8 in Origins of Life.
Simulation of
Sympatric Speciation.
Plant growth simulation with voxel space automata.

Week 9
Plant growth using L-systems.
Creating branching patterns using Laplacian growth.
Simulation of leaf venation.

Week 10
Chapter 9 in Origins of Life.
Development papers:
Fleischer/Barr, Eggenberger, Furusawa/Kaneko.

Week 11
Chapter 10 in Origins of Life.
Evolving
virtual creatures from Karl Sims.
Evolving autonomous agents from Frank Dellaert and Randall Beer.

Week 12
Evolution and manufacturing of crawling robots.
Swimming creatures from Tu and Terzopoulos. 
Evolved flying creatures.

Week 13
Chapter 11 in Origins of Life.
Thomas Ray's
Tierra system of evolving programs.
Robert Axelrod and the Iterated Prisoner's Dilemma.

Week 14
Chapter 12 in Origins of Life.
Craig Reynolds on
Co-Evolution for game of tag. 
Ant foraging behavior.


Related Web Links

Flocking resources, compiled by Craig Reynolds.

Mass-spring locomotion at sodaplay.  (Be sure your browser can run Java!)

Evolved virtual creatures from Karl Sims (locomotion and competition).

Dr. Prusinkiewicz's research on plant development.

Tierra (digital creatures that execute code) from Thomas Ray.

Langton-style self-reproducing loops from Hiroki Sayama.

Artificial life links.


Course Description

This course covers a broad array of techniques for computer simulation of biological systems. The course material will draw from biology, artificial life, robotics, computer graphics and other research areas. Some of the course topics include self-replication, artificial chemistry, multi-cellular development, simulation of evolution, cellular automata, mass-spring simulators, L-systems for plant development, animal locomotion (walking, swimming, jumping), flocking and herding behavior in groups, predator/prey systems, parasites, and foraging behavior.

Students will carry out several programming projects during the course. Basic programming skills are recommended for students entering the course, but no previous background in biology is necessary. There will be three or four small programming projects during the first part of the course. During the second half, students will propose and work on a large project of their choice. Projects can be done individually or in teams of two students.


Course Topics

Self-Organization

self-replication (von Neumann, Christopher Langdon, others)
complexity at edge of chaos

Molecules

artificial chemistry
metabolism
molecular hypercycles
RNA folding
DNA codon optimality

Membranes and Cells

membrane formation
cell models
cell cytoskeletons
immune systems


Cell aggregation (courtesy of Kurt Fleischer)

Development

multicellular development
slime mold aggregation
pattern formation
gene cascades/networks
cell simulation of development (Fleischer and Barr)
L-systems for plant development


Plant growth (courtesy of Przemyslaw Prusinkiewicz)

Evolution

evolution
speciation
Dawkins on major events in evolution
genetic algorithms
blind watchmaker
co-evolution (Karl Sims, Craig Reynolds, Danny Hillis)
sexual selection

Locomotion

modes of locomotion
Braitenberg vehicles
evolution of walking and hopping motion (Karl Sims)
swimming (Terzopoulos)


Walking simulation (courtesy of Karl Sims)

Physics Simulation Techniques

partial differential equations (PDE's)
reaction-diffusion
cellular automata (life, spiral waves, etc.)
mass-spring systems


Tentacle motion (courtesy of Andrew Cantino)

Multi-Organism Interaction

communication
Prisoner's dilemma, tit-for-tat
predator/prey
flocks, schools, swarms
ant foraging
parasites
digital creatures (Thomas Ray)


Flocking with collision avoidance (courtesy of Craig Reynolds)


Go to Greg Turk's Home Page.