CHAPTER I: Introduction to DNA structure
01/26/2012 Prof. Shimokawa's lecture
01/31/2012 Basic concepts on DNA structure
02/02/2012 Basic concepts on DNA structure II
02/12/2012 Homework 1 assigned.
CHAPTER II: Biological problems in DNA topology
02/07/2012 Basic concepts on DNA topology
02/09/2012 Background for papers: Liu et al and
Ryvenkov et al.
02/09/2012 Homework 1 due.
02/14/2012 Background for papers: Ryvenkov et al
and Chen et al.
02/16/2012 Lecture by Mr. J. Long. Using the UCSC genome browser
02/16/2012 Homework II assigned. UCSC genome browser.
02/21/2012 Paper by Lieberman-Eiden et al.
02/23/2012 Paper by Lieberman-Eiden et al.
CHAPTER III: Knot theory
02/28/2012 Basic definitions in knot theory. Homework 3 assigned
03/01/2012 Introduction to knot invariants: Reidemester moves
03/06/2012 Crossing Number, unknotting number of a knot and Linkign number of a link
03/08/2012 Seifert surfaces: introduction to 2D manifolds
03/13/2012 Computing the Seifert Surface of a knot diagram, genus of a knot
03/15/2012 The Alexander polynomial and its computation
03/20/2012 Spring Break
03/22/2012 Spring Break
CHAPTER IV: Computational models
03/27/2012 Basic Computational models of DNA. Intro to matlab
03/29/2012 Implementation of DNA models in matlab
04/03/2012 The Monte Carlo method: examples
04/05/2012 The Monte Carlo method: Markov Chains
04/10/2012 The Monte Calro method: Markov Chains
04/12/2012 Asymptotic results
04/17/2012 Asymptotic results: Sumners and Whittington's Theorem
CHAPTER V: DNA Supercoiling
04/18/2012 Visit Dr. Pasion's lab starting at 12:15pm
04/19/2012 The biology of supercoiling
04/24/2012 Background on papers
04/26/2012 Definition of Lk, Tw and Wr.
05/01/2012 White's theorem
05/03/2012 Computer calculations of Lk, Tw and Wr.
05/08/2012 Asymptotic results