| 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 |
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| 2 |
Molecular Evolution
Mutations, Gene Duplications
Divergent/Convergent
Polymorphism
Phylogenetic Trees |
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| 3 |
Mutations
Drift, Selection, Fixation |
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| 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 |
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| 6 |
Dynamic Programming and Transfer Matrices
Dynamic Programming Algorithms for Optimal Alignments
Correspondence to Transfer Matrix Methods for Summing Over Directed Paths |
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| 7 |
Sequence Alignment and Statistical Physics
Extreme Value (Gumbel Distribution)
Relations to Surface Growth and Asymmetric Exclusion Processes |
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| 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 |
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| 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 |
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| 12 |
The Random Energy Model
General Description, Application to Protein Folding and Design |
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| 13 |
Protein Folding
Experiments, Theories, and Numerics |
Assignment 4 due |
| 14 |
Nucleic Acids
Introduction to DNA and RNA, the Double Helix |
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| 15 |
Fluctuating DNA
DNA Melting, the Poland-Scheraga Model
Unzipping, Translocation |
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| 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 |
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| 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 |
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| 20 |
Molecular Motors
Ratchets, Asymmetric Hopping Models
Motor-Microtubule Assemblies and Patterns |
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| 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 |
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| 23 |
Networks
Random Networks, Scale Free Networks, Percolation
Dynamics on Networks
Fixed points, Hopfield Model of Neural Networks
Cycles, Clocks, Synchronization |
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| 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 |
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| 26 |
Biological Patterns
Morphogenesis
Turing Model
Patterns of Orientation Selectivity |
Final project due one day after Ses #26 |