Biophysics 101 Genomics and Computational Biology
Pro3: Last week's take home lessons
Networks Why model?
Net1: Today's story & goals Bio101 21-Nov-2000
Cell Division Cycle G2 arrest to M arrest switch
Hill coefficients
“The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes.”
Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected E. coli cells.
Efficient exact stochastic simulation of chemical systems with many species& many channels
Utilizing Noise
Engineering stability in gene networks by autoregulation
Feedback simulation with linear stability analysis
Copy Number Control Models
ColE1 CNC
Replication Transcription read-through
Assumptions?
Dynamic Mass Balance: ColE1 RNAI [concentration]
PPT Slide
Restate dynamic mass balance, solve for N(t)
Mathematica ODE program
Stochastic models for CNC
Approach to studying behavior of defined genotypes …
Factors Constraining Metabolic Function
Description of metabolism
Dynamic Description
Flux-Balance Analysis
Stoichiometric Matrix
Additional Constraints
Flux Balance Example
FBA Example
FBA
Incomplete Set of Metabolic Constraints
Under-Determined System
FBA - Linear Program
Very simple LP solution
Applicability of LP & FBA
Precursors to cell growth
in silico cells
H. pylori
E. coli in silico mutant growth
E. coli knockout mutants
Types of interaction models
ATP & Redox loads
Phase plane diagrams: concentration of metabolite A vs B over a specific time course
Phase plane diagrams: relating concentrations (ODE) or fluxes (FBA)
Acetate-Oxygen Phenotype Phase Plane
Acetate Experimental Data
Acetate 3-D Phase Plane
E. coli predicted mutant growth
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