Multi Scale 06
Math Bio Seminar
Math Modeling 05
Math Modeling 06
Dynamical Systems

Seminar on Interdisciplinary Biological Research:  
Mathematical and Computational Modeling in Biology


SC 190, Spring 2005, 2:00-3:15pm, Hayes-Healy 117

Instructor: Mark Alber (631-8371),



Sponsored by the Center for the Study of Biocomplexity


What is "Biocomplexity"? Biocomplexity is the science that looks at a butterfly's wings and asks: "How does the pattern arise?  Is the origin similar to that of a zebra's stripes?"  It looks at a fruit fly or a frog  and asks: "What are the fundamental physical principles that allow the head to become different from the tail?"  It develops models of epidemics and suggests new ways of treating HIV. It looks at the electrical signals that flow through the heart, driving its unfailing pulse, and asks: "Can we understand the form and propagation of these signals, and if so, can this help us fix hearts that don't work properly?" Finally, it explains formation of bacteria colonies and fish schools.    

                                  Fish School

Goals: The first goal of this class will be to introduce students to classic examples of biological modeling, to let them think about these problems and try to come up with their own hypotheses and approaches. The second goal will be to discuss some of the modeling approaches that have been successful thus far. The overarching goal is to make students sensitive to biological and medical issues in the world around them, familiar with the interdisciplinary  approaches necessary to study them, and open to the idea of incorporating similar questions and approaches in their own work 


Projects: Students will be divided into small groups. Each group will be given a project. Each group will present their results in the end of the semester. Lectures and discussions will be complemented by visits to biological and computational laboratories and meetings with professors from different departments at Notre Dame as well as with researchers visiting Notre Dame.


List of Projects


Textbook: Reading assignments will be distributed in class.

Supplemental Texts:

  • Self-Organization in Biological Systems, Scott Camazine, Jean-Louis Deneubourg, Nigel R. Franks, James Sneyd, Guy Theraulaz, and Eric Bonabeau, Princeton Studies in Complexity, Princeton University Press, 2003.         

  • Nonlinear Dynamical Systems and Chaos with Applications to Physics, Biology, Chemistry, and Engineering, Steven H. Strogatz, Studies in Nonlinearity, Addison-Wesley Publishing Company, 1994.

Class Topics:

Class 1 (January 11) FIRST DAY OF CLASS Introduction and Overview.

Class 2 (January 13)  Pattern Formation in Biology.

Paper on Pattern Formation in Bacterial Colonies.


Class 3 (January 18)  Self-Organization in Biology. 

How Leopard Gets Its Spots; How the Zebra Gets Its Stripes.




Class 4 (January 20)

Game of Life

Classes 5 and 7 (January 25 and February 1)  Biocomplexity at the Nanometer Scale.


Prof. Holly Goodson

Dept. of Chemistry & Biochemistry

439 Stepan



Classes 6 and 8, 9 (January 27 and February 3, 8) Fractals and Chaos in Biology, Physics and Other Fields.            



Classes 10 , 11  (February 10, 15)  


Prof. Albert-Laszlo Barabasi

Department of Physics

Nieuwland Science Hall 203   



Map of protein-protein interactions. The colour of a node signifies the phenotypic effect of removing the corresponding protein (red, lethal; green, non-lethal; orange, slow growth; yellow, unknown).

Classes 12 and 13  (February 17, 22)  



Class  14  (February 24) 

Molecular Dynamics.

Paper on Molecular Dynamics Simulations.


                                           Prof. Jesus Izaguirre
                                           Dept. of Computer Science and Engineering
                                           326C Cushing Hall


Classes 15 and 16 (February 28 and March 2)  Projects and Discussion.

Classes  17 and 18 (March 15 and 17)  Mark Alber. Stochastic Model of Cell Aggregation.



                                 Simulation of  myxobacteria aggregation

Class 19  (March 24) Dr. Ray Sepeta.

The control of complexity in the human genome.


Class  20 (March 29)  How many species are there? 

Paper: Counting the uncoutable.



                                            Prof. Jessica Hellmann
                                            Department of Biological Sciences
                                            107 Galvin Life Sciences

Class 21 (March 31) Mark Alber. Statistical methods for model matching.


Classes  22, 23  (April 5 and 7)  Biofilms.

Class  24  (April  12)   DNA tiling  and self-assembly.

Paper on nanotechnology and the double helix.  


                                             Prof. Marya Lieberman
                                             Dept. of Chemistry & Biochemistry
                                             271 Stepan Chemistry
Class 25  (April 14) Genetic complexity and the regulation of biological phenotypes. Visit to a biological  laboratory.


                                            Prof. Michael Ferdig
                                            Department of Biological Sciences
                                            107 Galvin Life Sciences
                                            631 9973
Class 26  (April 19) Understanding Species and Speciation.

Paper: Theory and speciation.

Paper on Speciation by Nicholas Barton.


                                            Prof. Jeffrey Feder
                                            Department of Biological Sciences
                                            107 Galvin Life Sciences
                                            631 4159


                   Final Projects:

                   Kathy Lee: Bacterial Populations as Multicellular Organisms
                   Jim Goebl:  Biofilms
                   Ryan Emptage and Cole Davis: The Future of Molecular Biology
                   Lara Canham and Danny Nolan:
                   Will Brennan:  How Leopards get their Spots
                   Cassie Kuchta and Tim Rohman: Tissue Engineering
                   Hebroon Obaid and Maggie Schramm:  SIR Epidemics
                   Lindsay Meyer:  The New Science of Networks
                   Brett Janecek and Kate Kenehan: 
Scale-free Networks






Nonlinear Dynamical Systems and Chaos with Applications to Physics, Biology, Chemistry, and Engineering, Steven H. Strogatz, Studies in Nonlinearity, Addison-Wesley Publishing Company, 1994.


An Introduction to Stochastic Processes with Applications to Biology, Linda J.S. Allen, Pearson Education,  Inc., 2003.


Modeling Biological Populations in Space and Time, Eric Renshaw,  Cambridge Studies in Mathematical Biology, Cambridge University Press, 1995.