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wiki:chapter_3:emergent_properties_of_small_networks [2013/03/24 17:04] emj created |
wiki:chapter_3:emergent_properties_of_small_networks [2013/04/03 15:45] (current) emj |
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| - | ====== Chapter 3: Emergent Properties ====== | + | ====== Chapter 3: Emergent Properties of Small Networks ====== |
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| - | * Mass action kinetics | + | * {{:wiki:chapter_3:goldbeter-koshland-1981-v3.nb|Goldbeter-Koshland ultrasensitivity}} |
| - | * | + | * {{:wiki:chapter_3:hillfeedbackanalysis.nb|Hill feedback analysis}} |
| - | * Analytic solution of trivalent reaction A+B <–> C | + | * {{:wiki:chapter_2:huang_ferrell_1996_mapkv2.nb|Huang and Ferrell 1996 MAPK}} |
| + | * {{:ch_4:nadji_2006_asp_thr_biosynthesis.nb|Najdi 2006 Asp Thr biosynthesis}} | ||
| + | * MAPK cascade in solution with feedback, according to models of {{:wiki:chapter_3:bardwell_mapk_4.nb|Bardwell}} and {{:wiki:chapter_3:mapk-kholodenko.nb|Kholodenko}} | ||
| + | * MAPK cascade stochastic | ||
| + | * MAPK cascade on scaffold (old Cellerator {{:wiki:chapter_3:mapk-on-scaffold.nb|model}}) | ||
| + | * more | ||
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| - | * Hill functions | + | * Emergent dynamics |
| - | * Master equation | + | * MAPK exercises |
| - | * Trivalent mass action | + | |
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| - | * Hill functions, n=1 and n=2 | + | * MAPK cascade and transfer function |
| - | * S-E-P stochastic simulation | + | * Asp Thr biosynthesis |
| + | * elementary behaviors | ||
| + | * Brusselator (Figure 3.13c) {{:wiki:chapter_3:brusselator.nb|model file}} and {{:wiki:chapter_3:brusselator-phase-limit-cycle.pdf|pdf}}. | ||
| + | * feedback loop nullclines | ||
| + | * repressilator oscillations | ||
| + | * MAPK with feedback transfer functions | ||
| + | * stochastic MAPK | ||
| + | * scaffolded MAPK | ||
| - | ==== Bibliography - electronic access - chapter 2 ==== | + | ==== Bibliography - electronic access - chapter 3 ==== |
| - | * [[:wiki:chapter_2:chapter_2_electronic_bibliography|Here]] | + | * [[:wiki:chapter_3:chapter_3_electronic_bibliography|Here]] |
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| - | * 2.1 Example: Growth factor response | + | * 3.1 Network behavior |
| - | * | + | * 3.2 Elementary network analysis |
| - | * 2.5 Summary | + | * 3.3 Small network examples: S-E-P, MAPK, and threonine metabolism |
| + | * 3.4 Dynamical consequences of feedback | ||
| + | * 3.5 Building larger networks: MAPK in depth | ||
| + | * 3.6 Summary | ||
| ===== Missing Topics ===== | ===== Missing Topics ===== | ||
