Project:
1.) Choose an application related to discrete mathematics.
2.) Write a description of your project (at least 1/2 page). Due March 12.
3.) Turn in an outline by March 26.
3.) Write a first draft in html format. E-mail the URL to
me by April 5.
4.) Written report should be in html format with a length of
about 2 pages/person. Hence a group of 2-3 people should write at
least 5 pages (not including figures). E-mail the URL to me
by April 26.
5.) Present your work in class during the last week of
class. Presentation should be about 10 minutes/person.
Hence a group of 2-3 people should give a 20-25 minute presentation.
The following information should be included in your written report
Title:
5 key words:
Mathematics used:
Mathematical Difficulty:
Area of Application:
Application Area Difficutly:
The report should be organized into sections logically. For example, an
introduction should tell what the purpose is and how your paper is
organized. Following the introduction, one or more sections should
present your main points, the mathematical ideas, applications,
history, reasoning, etc. Finally, a last section should summarize what
you have done, emphasizing the significant points. There should be a
bibliography of at least 3 sources used. When you use quotes or
other material directly or indirectly from a source, you must cite the
source with the page number at that point. Your written report
can also include writing a worksheet which can be used in a future M151
class.
You may choose one of the following projects or you may find your
own. Extra credit will be given
for finding a good project.
References are given to introduce the topics below. These
references are a good place to start, but
you need to find additional, preferably more current references.
The following are potential topics OR may be covered in class.
Some require more biology background
than others.
1.) Sequence Comparison
Chapter 3 in Setubal, Meidanis, Introduction to Computational Molecular
Biology.
2.) Fragment Assembly
Chapter 4 in Setubal, Meidanis, Introduction to Computational Molecular
Biology.
3.) Physical Mapping of DNA
Chapter 5 in Setubal, Meidanis, Introduction to Computational Molecular
Biology.
4.) Phylogentic trees
Chapter 6 in Setubal, Meidanis, Introduction to Computational Molecular
Biology.
5.) Genome rearrangements
Chapter 7 in Setubal, Meidanis, Introduction to Computational Molecular
Biology.
6.) RNA/Protein Folding
Chapter 8 in Setubal, Meidanis, Introduction to Computational Molecular
Biology.
7.) DNA computing
DNA
Computation, Leonard Adleman
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
Jonoska
N, Karl SA, Saito M.Three dimensional DNA structures in computing, Biosystems.
1999 Oct;52(1-3):143-53.
8.) Pairwise alignment using hidden markov models
Biological sequence analysis by Durbin, Eddy, Korgh, Mitchenson.
9.) Genetics Inbreeding
Section 2.9 in An introduction to stochastic processes with
applications to biology by Allen
I am not familiar with this book, but will look more at this section
when we get to Markov chains.
10.) Chemical chirality
When Topology Meets Chemistry : A Topological Look at Molecular
Chirality
by Erica Flapan
11.) Chen J. Rauch CA. White JH. Englund PT. Cozzarelli NR. The
topology of the kinetoplast DNA
network. Cell. 80(1):61-9, 1995 Jan 13.
12.) Voting?
13.) Eulerian closed chain algorithm and applications
Other methods of finding project material.
1.) Search the web.
1a.) Use MathSciNet (05 and ...)
1b.) Search the Dimacs, Rutgers website.
1c.) Search the web for Research Experiences
for Undergraduates (REU) and Discrete Mathematics.
1d.) Search for any area of interest.
2.) Look at Humanities Math books such as For all Practical
Purposes, COMAP.
3.) Check other discrete math books such as Applied Combinatorics
by Roberts.