Course Meeting Times
Lectures: 2 sessions / week, 1 hour / session
Recitations: 1 session / week, 1 hour / session
A list of topics by session is available in the calendar below.
This course applies the concepts of reaction rate, stoichiometry and equilibrium to the analysis of chemical and biological reacting systems. Derivation of rate expressions from reaction mechanisms and equilibrium or steady state assumptions. Design of chemical and biochemical reactors via synthesis of chemical kinetics, transport phenomena, and mass and energy balances. Topics in this course include: chemical/biochemical pathways; enzymatic, pathway, and cell growth kinetics; batch, plug flow and well-stirred reactors for chemical reactions and cultivations of microorganisms and mammalian cells; heterogeneous and enzymatic catalysis; heat and mass transport in reactors, including diffusion to and within catalyst particles and cells or immobilized enzymes.
There will also be reading from the manuscript of the forthcoming textbook Biological Kinetics by K. Dane Wittrup and Bruce Tidor.
The purpose of the recitation section is to give you practice working difficult problems in a supportive environment, with a focus on moving from the problem statement to solvable systems of equations. We will also review homework solutions, discuss problem solving strategies, answer questions concerning lecture material, and discuss exam solutions. You must have read and thought about the homework problems before you come to recitation. Be prepared to be asked to do problems on the chalkboard.
|Midterm exam 1||15%|
|Midterm exam 2||20%|
Weekly problem sets will be assigned approximately 6-7 days in advance of their due date. They will be graded and returned the following week. Homework policy and honor code: While students are encouraged to discuss problem solutions and strategies, they are expected to work individually in arriving at solutions. Electronically copying or cutting and pasting any section of another student's homework will be considered cheating and will lead to disciplinary action against both the copier and any student who made the electronic version available before the due date. Please do each problem on separate and stapled sheets with your name on it. Homework is normally due at the end of class on Wednesdays. Late homework will be accepted until 10 pm of the date it is due in a box outside one of the TAs' offices. 50% of the grade will be deducted from late homework unless there are extenuating circumstances that justify the late submission. Solutions to problem sets will be provided at 10 pm on the due date.
Unannounced quizzes on the material presented in class or assigned for reading during the previous class. One quiz can be missed or dropped from grading. Most quizzes will be given during recitations.
The first two exams will be 1 hour long and will be given during class time. The third exam will be given during the final exam period and will be three hours long.
WHG = William H. Green
KDW = K. Dane Wittrup
The calendar below provides information on the course's lecture (L) and recitation (R) sessions.
|SES #||TOPICS||KEY DATES|
|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)||Problem set 1 out|
|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)|
|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)|
|L4||Reaction mechanisms and rate laws: Reactive intermediates and steady state approximation in reaction mechanisms. Rate-limiting step. Chain reactions. Pyrolysis reactions. (WHG)|| |
Problem set 1 due
Problem set 2 out
|L5||Continuous stirred tank reactor (CSTR). Reactions in a perfectly stirred tank. Steady-state CSTR. (KDW)|| |
Problem set 2 due
Problem set 3 out
|L6||Concentration that optimizes desired rate. Selectivity vs. Conversion. Combining reactors with separations. (WHG)|
|L7||Batch reactor: Equations, reactor sizing for constant volume and variable volume processes. (KDW)|| |
Problem set 3 due
Problem set 4 out
|L8||The plug flow reactor. (WHG)|
|L9||Reactor size comparisons for PFR and CSTR. Reactors in series and in parallel. How choice of reactor affects selectivity vs. conversion. (KDW)|| |
Problem set 4 due
Problem set 5 out
|L10||Non-ideal reactor mixing patterns. Residence time distribution. Tanks in series model. Combinations of ideal reactors. (KDW)|
|L11||Non isothermal reactors. Equilibrium limitations, stability. Derivation of energy balances for ideal reactors; equilibrium conversion, adiabatic and nonadiabatic reactor operation. (WHG)|| |
Problem set 5 due
Problem set 6 out
|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)||WebLab experiment out|
|L13||Biological reactors - chemostats. Theory of the chemostat. Fed batch or semi-continuous fermentor operation. (KDW)||Problem set 6 due|
|Midterm exam 1||WebLab follow-up assignment out|
|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)||Problem set 7 out|
|L15||Gene expression and trafficking dynamics. Approach to steady state; receptor trafficking. (KDW)||WebLab follow-up assignment due|
|L16||Catalysis. Inorganic and enzyme catalysts and their properties; kinetics of heterogeneous catalytic reactions; adsorption isotherms, derivation of rate laws; Langmuir-Hinshelwood kinetics. (WHG)|| |
Problem set 7 due
Problem set 8 out
|L17||Mass transfer resistances. External diffusion effects. Non-porous packed beds and monoliths, immobilized cells. (WHG)|
|L18||External mass-transfer resistance: Gas-liquid reactions in multiphase systems. (KDW)|
|L19||Oxygen transfer in fermentors. Applications of gas-liquid transport with reaction. (KDW)|
|R9||Recitation 9||Problem set 8 due|
|Midterm exam 2|
|L20||Reaction and diffusion in porous catalysts. Effective diffusivity, internal and overall effectiveness factor, Thiele modulus, apparent reaction rates. (KDW)||Problem set 9 out|
|L21||Reaction and diffusion in porous catalysts (cont.). Packed bed reactors. (WHG)|| |
Problem set 9 due
Problem set 10 out
|L22||Combined internal and external transport resistances. (WHG)|
|L23||Pulling it all together; applications to energy/chemicals industry. Presentation of current research. (WHG)||Problem set 10 due|
|L24||Pulling it all together; applications to bioengineering and medicine. Presentation of current research. (KDW)|
|L25||Course review. (WHG)|