01/24/2012 Introduction

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:

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:

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:

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:

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

05/10/2012