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Calendar

SES # TOPICS KEY DATES
1 Introduction to Course (Material and Organization)

Outline of the Course, Procedures and Requirements

Cell Types; Contents of a Cell; Central Dogma

Probability and Information		  
2 Molecular Evolution

Mutations, Gene Duplications

Divergent/Convergent

Polymorphism

Phylogenetic Trees		  
3 Mutations

Drift, Selection, Fixation		  
4 Gene Annotation and Similarity Detection

Origin and Importance of Problem

Scoring Similarities

Alignment Types: Local, Global, Gapped, etc.

BLAST and Database Searches		 Assignment 1 due
5 Substitution Matrices

Markov Texts

PAM Matrices		  
6 Dynamic Programming and Transfer Matrices

Dynamic Programming Algorithms for Optimal Alignments

Correspondence to Transfer Matrix Methods for Summing Over Directed Paths		  
7 Sequence Alignment and Statistical Physics

Extreme Value (Gumbel Distribution)

Relations to Surface Growth and Asymmetric Exclusion Processes		  
8 Biomolecular Forces and Energies

Covalent Bonds, Hydrogen Bonds, Van Der Waals Interactions, Hydrophobicity, etc.		 Assignment 2 due
9 Electrostatics

Macro-ions, Counter-ions, pH, Poisson-Boltzmann Equation, Debye Equation		  
10 Polymer Theory

Softening of Rigidity by Fluctuations, Entropy and Markov Chains, Attractions, Repulsions, Flory Theory, Loop Entropies		 Assignment 3 due
11 Proteins

Interactions: Hydrophobicity, Van Der Waals, Coulomb, Covalent Bonds

Secondary Structure Elements

Classification of Structures, and the Difficulty of Structural Determination

Folding in the Cell: Chaperones, Co-translational, Aggregation and Fibrils		  
12 The Random Energy Model

General Description, Application to Protein Folding and Design		  
13 Protein Folding

Experiments, Theories, and Numerics		 Assignment 4 due
14 Nucleic Acids

Introduction to DNA and RNA, the Double Helix		  
15 Fluctuating DNA

DNA Melting, the Poland-Scheraga Model

Unzipping, Translocation		  
16 RNA

Roles of RNA: mRNA, tRNA, Ribosomal RNA

Secondary and Tertiary Structure

Secondary Structures without Pseudo-knots		 Assignment 5 due
17 Protein-DNA Complexes

Specific and Non-specific Binding of Factors to DNA Regulatory Elements

Borg-von Hippel, Weight Matrices (Profiles), Information Content

Large Scale Packaging of DNA, Histones, Heterochromatin		  
18 Hemoglobin

Molecular Evolution, Polymorphism, Selection etc.

Folding and Fibrillation (of Normal and Abnormal Hemoglobin)

Protein Function from Molecular Level to Physiology

Physics of Allosteric Regulation		 Assignment 6 due
19 Microtubules and Filaments

Microtubule Growth and Dynamic Instability		  
20 Molecular Motors

Ratchets, Asymmetric Hopping Models

Motor-Microtubule Assemblies and Patterns		  
21 Membranes

Lipid Bilayers: Bending Energy, Fluctuations, Shapes

Channels, Pumps		 Assignment 7 due
22 Cell Motility

Life at Low Reynolds Number, Brownian Motion

Chemotaxis, Biased Random Walks		  
23 Networks

Random Networks, Scale Free Networks, Percolation

Dynamics on Networks

Fixed points, Hopfield Model of Neural Networks

Cycles, Clocks, Synchronization		  
24 Introduction to Networks

Examples in Biological Context (Metabolic, Regulatory, etc.)

Prevalence of Power-Laws		 Assignment 8 due
25 Dynamics

Chemical Interactions and Flux Balance Equations

Deterministic and Stochastic Analysis in Networks		  
26 Biological Patterns

Morphogenesis

Turing Model

Patterns of Orientation Selectivity		 Final project due one day after Ses #26