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),
malber@nd.edu
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.
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)
Classes 5 and 7 (January
25 and February 1) Biocomplexity at the Nanometer Scale.
Prof. Holly
Goodson
Dept. of Chemistry &
Biochemistry
439 Stepan
631-7744
goodson.1@nd.edu
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
alb@nd.edu
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
631-7454
izaguirr@cse.nd.edu
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
631-7521
hellmann.3@nd.edu
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
631-4665
mlieberm@nd.edu
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
Michael.T.Ferdig.1@nd.edu
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
Jeffrey.L.Feder.2@nd.edu
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:
Bioethics
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
BOOKS:
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. |
