Courses:

Statistical Physics in Biology >> Content Detail



Calendar / Schedule



Calendar

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

Outline of the Course, Procedures and Requirements

Cell Types; Contents of a Cell; Central Dogma

Probability and Information
2Molecular Evolution

Mutations, Gene Duplications

Divergent/Convergent

Polymorphism

Phylogenetic Trees
3Mutations

Drift, Selection, Fixation
4Gene Annotation and Similarity Detection

Origin and Importance of Problem

Scoring Similarities

Alignment Types: Local, Global, Gapped, etc.

BLAST and Database Searches
Assignment 1 due
5Substitution Matrices

Markov Texts

PAM Matrices
6Dynamic Programming and Transfer Matrices

Dynamic Programming Algorithms for Optimal Alignments

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

Extreme Value (Gumbel Distribution)

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

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

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

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

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
12The Random Energy Model

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

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

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

DNA Melting, the Poland-Scheraga Model

Unzipping, Translocation
16RNA

Roles of RNA: mRNA, tRNA, Ribosomal RNA

Secondary and Tertiary Structure

Secondary Structures without Pseudo-knots
Assignment 5 due
17Protein-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
18Hemoglobin

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
19Microtubules and Filaments

Microtubule Growth and Dynamic Instability
20Molecular Motors

Ratchets, Asymmetric Hopping Models

Motor-Microtubule Assemblies and Patterns
21Membranes

Lipid Bilayers: Bending Energy, Fluctuations, Shapes

Channels, Pumps
Assignment 7 due
22Cell Motility

Life at Low Reynolds Number, Brownian Motion

Chemotaxis, Biased Random Walks
23Networks

Random Networks, Scale Free Networks, Percolation

Dynamics on Networks

Fixed points, Hopfield Model of Neural Networks

Cycles, Clocks, Synchronization
24Introduction to Networks

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

Prevalence of Power-Laws
Assignment 8 due
25Dynamics

Chemical Interactions and Flux Balance Equations

Deterministic and Stochastic Analysis in Networks
26Biological Patterns

Morphogenesis

Turing Model

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

 








© 2010-2021 OpenCollege.com, All Rights Reserved.
Open College is a service mark of AmeriCareers LLC.