There will also be reading from the manuscript of the forthcoming textbook Biological Kinetics by K. Dane Wittrup and Bruce Tidor.
Readings by Session
WHG = William H. Green
KDW = K. Dane Wittrup
|L1||Preliminaries and remembrance of things past. Reaction stoichiometry, lumped stoichiometries in complex systems such as bioconversions and cell growth (yields); extent of reaction, independence of reactions, measures of concentration. Single reactions and reaction networks, bioreaction pathways. (WHG)|
|L2||The reaction rate and reaction mechanisms: Definition in terms of reacting compounds and reaction extent; rate laws, Arrhenius equation, elementary, reversible, non-elementary, catalytic reactions. (WHG)||Fogler, sections 1.0-1.4.1 and 3.0-3.5.|
|L3||Kinetics of cell growth and enzymes. Cell growth kinetics; substrate uptake and product formation in microbial growth; enzyme kinetics, Michaelis-Menten rate form. (KDW)|| |
Fogler, sections 7.2 and 7.4.0-7.4.4.
"Enzyme Kinetics." Chapter 6 in Biological Kinetics.
|L4||Kinetics of cell growth and enzymes. Cell growth kinetics; substrate uptake and product formation in microbial growth; enzyme kinetics, Michaelis-Menten rate form. (KDW)||Fogler, section 7.1.|
|L5||Continuous stirred tank reactor (CSTR). Reactions in a perfectly stirred tank. Steady-state CSTR. (KDW)||Fogler, sections 1.4.1, 2.1, 2.3.1, 2.4, 2.5, 4.1, and 4.2.1.|
|L6||Concentration that optimizes desired rate. Selectivity vs. Conversion. Combining reactors with separations. (WHG)||Fogler, sections 6.0-6.4 and 6.6.|
|L7||Batch reactor: Equations, reactor sizing for constant volume and variable volume processes. (KDW)||Fogler, sections 1.2, 1.3, 1.5, 2.1, 2.2, 4.1, and 4.2.1.|
|L8||The plug flow reactor. (WHG)||Fogler, sections 1.4.2, 1.4.3, 2.1, 2.2.2, 2.3 (PFR), 2.4 (PFR), 3.3.3, 3.3.4, 3.4, 3.5, 4.3, and 4.4.|
|L9||Reactor size comparisons for PFR and CSTR. Reactors in series and in parallel. How choice of reactor affects selectivity vs. conversion. (KDW)||Fogler, sections 2.2, 2.3, 2.4, 2.5, and 4.7.|
|L10||Non-ideal reactor mixing patterns. Residence time distribution. Tanks in series model. Combinations of ideal reactors. (KDW)||Fogler, sections 13.1-13.4, 14.2, and 14.7.|
|L11||Non isothermal reactors. Equilibrium limitations, stability. Derivation of energy balances for ideal reactors; equilibrium conversion, adiabatic and nonadiabatic reactor operation. (WHG)||Fogler, sections 8.0-8.8.|
|L12||Data collection and analysis. Experimental methods for the determination of kinetic parameters of chemical and enzymatic reactions; determination of cell growth parameters; statistical analysis and model discrimination. (WHG)|| |
Fogler, chapter 5.
"Theory and Practice of Biomolecular Measurements." Chapter 4 in Biological Kinetics.
|L13||Biological reactors - chemostats. Theory of the chemostat. Fed batch or semi-continuous fermentor operation. (KDW)|| |
Fogler, section 7.4.
"Cell Growth and Death." Chapter 7 in Biological Kinetics.
|Midterm exam 1|
|R7||Recitation 7: Review of midterm exam 1 and WebLab experiment|
|L14||Kinetics of non-covalent bimolecular interactions. Significance; typical values and diffusion limit; approach to equilibrium; multivalency. (KDW)||"Noncovalent Binding Interactions." Chapter 2 in Biological Kinetics.|
|L15||Gene expression and trafficking dynamics. Approach to steady state; receptor trafficking. (KDW)||"Binding Equilibria and Kinetics." Chapter 3 in Biological Kinetics.|
|L16||Catalysis. Inorganic and enzyme catalysts and their properties; kinetics of heterogeneous catalytic reactions; adsorption isotherms, derivation of rate laws; Langmuir-Hinshelwood kinetics. (WHG)||Fogler, sections 10.1, 10.2, and 10.3.|
|L17||Mass transfer resistances. External diffusion effects. Non-porous packed beds and monoliths, immobilized cells. (WHG)||Fogler, sections 11.1, 11.2, and 11.3.|
|L18||External mass-transfer resistance: Gas-liquid reactions in multiphase systems. (KDW)||Fogler, section 11.3.|
|L19||Oxygen transfer in fermentors. Applications of gas-liquid transport with reaction. (KDW)|
|Midterm exam 2|
|L20||Reaction and diffusion in porous catalysts. Effective diffusivity, internal and overall effectiveness factor, Thiele modulus, apparent reaction rates. (KDW)||Fogler, sections 12.1, 12.2, 12.3, 12.4, and 12.5.|
|L21||Reaction and diffusion in porous catalysts (cont.). Packed Bed Reactors. (WHG)||Fogler, sections 12.5 and 12.6.|
|L22||Combined internal and external transport resistances. (WHG)||Fogler, sections 8.9 and 12.7.|
|L23||Pulling it all together; applications to energy/chemicals industry. Presentation of current research. (WHG)|
|L24||Pulling it all together; applications to bioengineering and medicine. Presentation of current research. (KDW)|
|L25||Course review. (WHG)|
Error in Fogler: Superficial Velocity or Actual Velocity (PDF)