Project: 1.) Choose an application related to discrete mathematics. 2.) Write a description of your project (at least 1/2 page) in html format. 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

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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? 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.