APM 530 – Mathematical Models of Nucleic Acids
Fall 2010

Instructor: Dr. Jay Taylor, office: PSA 447; phone: 965-2641; e-mail: jtaylor@math.asu.edu
Time: Tuesdays and Thursdays 3:00-4:15
Location: PSH 331
Office Hours: Tuesdays 4:15-5:00 and by appointment.

Course Description: This course will examine some of the ways in which mathematics has been used to investigate the structure and function of DNA and RNA. Topics to be covered may include:

Text: In lieu of a textbook, there will be regular reading assignments taken mainly from the primary literature. Links to PDFs will be posted below on the syllabus. Each reading should be the subject of a short (1-2 page) report, written in the style of a peer review, i.e., it should describe the main aims of the paper and comment critically on how well these aims were met.

Assignments: Each student will be expected to complete a small research project, which will be the subject of a short (25 minute) presentation at the end of the semester and a written report. A project proposal (about 2-3 pages) is due on Oct. 19. This should describe the background to the project as well as the main question that will be investigated and how it will be investigated. A short bibliography (with at least 5 references to primary literature) should be included.

Grading: Grades will be based on class participation (30%), the peer review reports (30%), and the oral and written presentations of the research project (40%).

Syllabus:


Date

Topic

Readings

19 Aug

Overview and introduction to nucleic acids.


24 Aug

Overview: molecular genetics

Watson & Crick (1953);

26 Aug

Structural biology of nucleic acids

Zimmerman (1982)

31 Aug

Quantum chemistry: Theory

Sponer et al. (2004)

2 Sept

QC: Application to thymine dimer formation

Schreier et al. (2007); Boggio-Pasqua et al. (2007)

7 Sept

Molecular mechanics: force fields

Mackerell (2004)

9 Sept

Molecular mechanics: optimization

Nash & Nocedal (1991); Xie & Schlick (1999)

14 Sept

Molecular mechanics: Ewald summation


16 Sept

Molecular mechanics: Ewald summation

Toukmaji & Board (1996); Smith & Pettitt (1996)

21 Sept

Molecular mechanics: implicit solvation models

Makarov & Pettitt (2002); Baker et al. (2001)

23 Sept

Molecular dynamics: introduction

Amaro et al. (2007); Amaro et al. (2008)

28 Sept

Symplectic integrators and MD: geometry


30 Sept

Symplectic integrators and MD: geometry

Skeel et al. (1997)

5 Oct

Symplectic integrators and MD: numerics


7 Oct

Symplectic integrators and MD: numerics


12 Oct

Stochastic dynamics: mathematical foundations


14 Oct

Stochastic dynamics: Langevin/Brownian models

Alexandrov et al. (2009)

19 Oct

Monte Carlo methods


21 Oct

Rare event simulation

Bolhuis et al. (2002)

26 Oct

Rare event simulation

Hu et al. (2008)

28 Oct

No class (JET away)


2 Nov

Coarse-grained models of DNA: ideal polymers


4 Nov

Coarse-grained models of DNA: dynamics

Rosa & Everaers (2008)

9 Nov

Coarse-grained models of DNA: loops

Bohn et al. (2007)

11 Nov

Veterans Day


16 Nov

3-d Geometry of the Human Genome

Lieberman-Aiden et al. (2009)

18 Nov

Multiscale models: the Lac operon

Villa et al. (2005)

23 Nov

Targeting of DNA-binding proteins

Halford & Marko (2004); Bancaud et al. (2009)

25 Nov

Thanksgiving


30 Nov

Evolution of gene regulation

Tsankov et al. (2010)

2 Dec

Selection and gene expression noise

Zhang et al. (2009)

7 Dec

Student presentations.