bio-physics-wiki

1. Genetic Engineering
   1. Restriction Enzymes
   2. Ligase
   3. Plasmids
   4. How to prepare electrocompetent E. coli
   5. Transformation with E. coli
   6. Polymerase Chain Reaction (PCR)
   7. Primer Design
2. Cell Physiology
   1. Bacterial Growth
   2. Metabolism
      1. Glycolysis and Gluconeogenisis
      2. Tricarboxylic Acid Cycle (also Krebs or Citric Acid Cycle)
      3. Cellular Respiration (also Oxidative Phosphorylation, mediated by the Electron Transport Chain)
      4. ATP Synthase
      5. Pentose Phosphate Pathway
   3. Immune System
3. Cell Signaling
   1. lac operon
   2. Gene Regulation and Protein Levels
   3. Simple Gene Regulation
   4. Statistical Mechanics of Binding
   5. Stochastic Gene Expression
   6. Optimality and Evolution
   7. Genetic Toggle Switch
   8. The Repressilator
   9. Transcription Networks
   10. Network Motifs
       1. Lever
       2. Buzzer (Goldbeter-Koshland switch)
       3. Fuse
       4. Autoregulation
          1. Negative Autoregulation (NAR)
          2. Positive Autoregulation
       5. Feed Forward Loop (FFL)
       6. Single Input Module (SIM)
   11. Hill Function
   12. Robustness
4. Biochemical Kinetics and Theromdynamics
   1. Isolated, Closed and Open Systems
   2. Chemical Potential
   3. Fluctuations about the mean energy
   4. Law of Mass Action (Reaction Rate Law)
   5. Michaelis Menten Kinetics
   6. Reversible Michaelis Menten Kinetics
   7. Brusselator
   8. Glycolytic Oscillations
   9. Stoichiometric Matrix
   10. Separation of Timescales
   11. General Enzyme Kinetics
   12. Open Systems - Mass Balance Equations
   13. Open Systems - Entropy Balance Equation
   14. Open Systems - Flux Balance Equations
   15. Flux Balance Analysis (FBA)
   16. Osmosis and the Cell Membrane
   17. Cells and Membrane Potentials - Equivalent Circuits
   18. Succinic Acid Efflux Energy Coupling
   19. Fick's Law: From Concentration Gradients to Fluxes
   20. Diffusion
   21. Bayes Theorem
   22. Markov Processes
   23. Stochastic Simulations with StochKit2
   24. Isotopomer
   25. Elementary Metabolic Unit (EMU)
5. Control Systems
   1. Dynamical Systems
   2. Regulating vs. Steering
   3. Convolution
   4. Transfer Function
   5. State and Output Equation
6. Molecular Biology
   1. Saccharides
   2. DNA Structure
   3. Central Dogma
   4. Promoter Strength
   5. Chromatin
   6. Cell Cycle
   7. Antibiotics
   8. Protein Modification
   9. Protein Translocation
   10. mRNA Processing
   11. Splicing
   12. Apoptosis
   13. Protein Trafficking
   14. G-Protein Signaling
   15. Insulin Signaling
   16. cAMP Signaling
   17. PI3K/AKT Signaling
   18. MAPK Signaling
   19. Wnt Signaling
   20. Protein Kinase C