| 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 |