Teaching at Washington University

Process Control ChE462 (2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016);

Bioprocess Engineering ChE453 (2013, 2014, 2015, 2017);

Fluid Mechanics Transport 1 ChE367 (2013);

Metabolic Engineering ChE596 (2010, 2011, 2012);

International Experience EECE401 (2012 in Brazil);

Advanced Energy Lab EECE439 (2011)

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**Bioprocess Engineering **

Bioprocess Engineering
ChE 506

Classroom:
Sever Hall 300;
Tuesday and Thursday: 5:30~7:00 pm

Yinjie Tang (Instructor) Email: yinjie.tang@wustl.edu

Ryan Lee (TA, Brauer Hall 1047); Email: vitamincwater@gmail.com

Office: Brauer Hall 1025 (Phone:314-935-3441)

Office Hours for Dr. Tang: 4:30–5:30 Tuesday and Thursday

TA office hours (You can email TA and make an appointment)

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HW1 (Due Jan 26): Text Book: 1.2, 1.3, 2.2, 2.5, 2.6, 2.8, 2.10, 2.11, 2.14, 2.16

HW2 (Due Feb 9): 4.2, 4.3, 4.4, 4.6, 4.8, 4.10, 5.1, 5.3, 5.6, 5.7, 5.9, 5.11

HW3 (Due Feb 23): 3.2, 3.3, 3.5, 3.7, 3.9, 3.13, 3.16, 3.17

**Midterm (March 7)**

HW4 (Due Mar 23): 6.1, 6.3, 6.5, 6.9, 6.17, 9.1, 9.2, 9.10, 9.12, 10.2; 10.15

HW5: 10.13; 11.2; 11.3; 12.3; 12.4; 12.5; 13.3; 14.3; 14.8; 16.1

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**Paper Reading: **
**File**

**
Step 1: Each student needs to read 5 papers
(assigned in the file above). Please extract quantitative information and fill
the excel Table (see above file) by March 30.**

**
Step 2: Three students form a team and perform
cross-validations for your readings. You are encouraged to discuss all 15 papers
within your team (March 30~April 13).**

**
Step 3: Each student needs to write a report (1~2
pages) to summarize the information gained from the five papers (e.g., a
mini-review on how to engineer cells and optimize fermentation to achieve
certain yield, rate and titer) by April 20. **

**
Step 4:
Each team prepares a 15-min presentation (April 25 and 27). The presentation includes Background,
Genetic strategies, Fermentation method, Products, and Future commercial
possibility. You can first summarize all 15 papers, then focus on 1~2 papers for
deep discussion.**

**
Step 5: Refine your report and excel sheet. Send
the report to TA and me (April 27). **

B*elow is the motivation
why we need to do this project:*

*Computational biology
models have been used to make predictions based on physical, biological and
chemical laws. Typically, these models need to simplify complex biological
systems and ignore bioprocess factors (such as reactor type/size, nutrient
conditions, and oxygen conditions) and genetic strategies employed. On the other
hand, rapid growth of synthetic biology in the past decade has generated a large
amount of literature and experimental databases. However, every case study uses
different conditions and the number of variables is huge. To overcome this problem we
need to standardize the datasets and build databases by extracting and
organizing published data. Such effort is called Knowledge Engineering. In the
past 15 years, over 30,000 papers have been published matching "metabolic
engineering or synthetic biology"ť, providing a rich dataset for Big Data
studies. In that sense, the amount and**
**modality of data have gone beyond the
capability of traditional modeling you have learned in Bioprocess classes.
Therefore, data driven approaches (i.e., machine learning) is needed to automate
biosystems design, to predict bioprocess performance, to offer guidelines for
commercialization, and to improve the
reproducibility of experimental work. *

**Pfizer Visit March 14 (12pm-5pm) **

**Class Presentations**

April 25 ---- Group 1 (Paul, Emily, Melanie); Group 2 (Chris, Austin, Miao); Group 3 (Anshuman, Anushree, Ermaike); Group 4 (Zhenwei, Deoukchen, Yaguang); Group 5 (Jeff, Nishit, Amy).

April 27 ---- Group 6 (Thomas, Daozhou, Chengyuan); Group 7 (Liyu, Dan and Nai-hua)

Presentation description: Each team will have ~15 minutes. You will briefly summarize 15 papers then pick 1 or 2 papers (as most interesting research) for detailed discussion. You can be critical to these papers. Your presentation can focus on influential factors, production titer/yield/rate or merit of new technology. You may tell the class what authors have done, why they do it, how they do it, how you know if they have succeeded, what would be the future plan, and what benefits could accrue from the research outcome.

**
Q-exam guidelines. **

**
Part 1: Short Answer Questions will cover basic knowledge about biochemistry,
microbiology, waste water treatment, and biofuel fundamentals. All contents can
be found in your text book and class notes (Biofuel fundamentals).
**

**
Part 2: Model calculations will cover membrane separations, fermentation yields,
genetic instability, and bioreactor/enzyme kinetics. You need to use proper
equations to solve bioprocess questions. All equations can be found in your text
book.**

**
Part 3: Problems to test your research skills. In those problems, you need to
use your knowledge from this class as well as other classes (such as Dr. Moon
and Zhang's classes) to develop new concept or modeling approaches. Those
questions include: 1) how to develop kinetic models from fermentation data; 2)
****
how to develop and simply enzyme kinetic model to describe cell pathway
functions; 3) how to use s****tructured
or/and segregated model to describe cellular process; 4)**
**how to use model to provide new insights
into metabolic regulations.**

**
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**Process Control 401**

Class Time : 9–10 MWF ; Classroom : Lopata Hall 101 (Computer Lab in Ubuer 218); Help session : Whitaker 216 (7 – 8 pm, Tuesdays)

TA: Dishant Khatri; Email: dishant@wustl.edu; Brauer Hall 3039; Tolutola Oyetunde; Email: toyetunde@wustl.edu ; Brauer Hall 1042

**
Coverage: **
Model development and simplifications; Dynamics of first order and second order process
(including time delays); Determine the process features based on the roots of
characteristic equation; Draw and analyze systems using block diagram ; Develop transfer functions based on block diagram; Stability analysis and process safety ; P-I-D control features and design
; Feedforward ; Cascade control ; Simulink and MATLAB questions; Frequency responses

**Final Exam (Lopata Hall 101, 8-10am, Dec 16)**

**Coverage **

**1. Dynamics of first order and second
order process (including time delays) **

**2. Determine the process features based on
the roots of characteristic equation **

**3. Draw and analyze systems using block
diagram **

**4. Develop transfer functions based on
block diagram **

**5. Stability analysis, process safety and
Ruth array **

**6. P-I-D control features and design
**

**7. Feed forward and cascade control
**

**8. Simulink and MATLAB questions **

**9. Frequency responses **

**10. Class presentation questions **

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**Class in 2015: Bioprocess Engineering ChE 453 Classroom: Whitaker
216; Tuesday and Thursday: 10~11:30 am **

Tang Office: Brauer Hall 1025 (Phone:314-935-3441) Office Hours: 11:30–1:30 Tuesday and Thursday

TA: Wen Jiang (Brauer Hall 1044). TA office hour: 2~5pm, Monday

HW1: Text book, 1.2, 1.3, 2.2, 2.5, 2.6, 2.8, 2.10, 2.11, 2.14, 2.16, 3.1

HW2: 3.2, 3.3, 3.5, 3.7, 3.9, 3.13, 3.16, 3.17

HW3: 4.2, 4.3, 4.4, 4.6, 5.1, 5.3, 5.6, 5.7, 5.9, 5.11, 6.1, 6.3, 6.5, 6.9, 6.17(note: biomass yield Y = 0.4 g X/g S)

HW4: 7.2, 7.4, 7.5, 8.3, 8.7, 8.10, and Midterm Long Question 4 (using MATLAB to solve Fungal fermentation, you need to develop a model then use parameter fitting to find the model parameters).

HW5: 9.1, 9.2, 9.10, 9.12, 10.2; 10.15; 11.2 (Due April 7)

HW6: 12.3; 12.4; 12.5; 13.3; 14.3; 14.8; 16.1 (Due April 14)

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Fluid Mechanics (Transport 1, ChE367)

Tuesday and Thursday from 1pm-2:30pm (Classroom: Lopata 101); Office Hour (Brauer Hall 1025, 4~5pm, Monday)

Help Session: Brauer Hall 3015, 5:30pm-6:30pm Tuesday; Brauer Hall 3014, 5:30pm-6:30pm Wednesday

TA: Chris Oxford: Ph(314-935-7970), Email: coxford@wustl.edu; Mike Kuan-Yu Shen: Ph(314-935-7563), Email: kys9466@gmail.com

Class notes: Part 1; Part 2; Part 3

**Course Coverage**

9-3-2013 and before: Laminar vs turbulent flow; Reynolds number: Flow transition criteria; Friction factor: Darcy and Fanning definitions; Pipe roughness parameter; Friction factor charts: Some mathematical representations of the same; Pipe flow pressure drop calculations for a given flow; Pipe flow rate calculations given a pressure drop; Concept of fully developed flow; Relation between wall shear stress and pressure drop for a fully developed flow

9-5-2013: Newtonain vs non-Newtonain fluids; Bulk modulus; Speed of sound Mach number; Incompressibilty criteria; Surface tension; Contact angle; Level rise in a capillary; Laplace-Young equation; Pressure inside a bubble; Normal vs shear stress; Pressure as a scalar: Pascal’s law Equation of hydrostatics

9-10-13: Archimedus principle; Pressure variation in a column of gas; Pressure variation in a column of liquid; Pressure force on a plane surface; Center or pressure concept; Pressure force on a curved surface

9-12-13: Linear acceleration; Rigid body rotation; Compressible gas pressure with depth; Resultant force on a plane surface

9-17(19)-13: Newton second law; Streamlines in steady flow; Streamwise acceleration Normal acceleration; ;Newton’s law along a streamline; Bernoulli equation; Newton’s law normal to a streamline; Stagnation point and pressure

9-24-13 : Pressure profile in a tornado; Continuity equation; Pitot tube analysis; Free jet and draining of a tank; Flow meter equation; Sluice gate equation; Use of head balance; Head due to turbine or pump; Head due to friction

9-26-13 : Modified Bernoulli equation; Sudden expansion; Cavitation; Bernoulli for unsteady flow; Acceleration of a fluid particle: General derivation; Streamline calculation for 2-D steady state flows

10-1-13 : Oscillating manometer; Bernoulli for compressible fluids; Example: Working rate needed for a compressor; Macroscopic momentum balances; Sudden expansion revisited

10-3-13 : Jet flowing along a vane; Rocket acceleration analysis; Sluice gate momentum balance; Momentum correction factor; Angular momentum balance

10-8-13: Macroscopic balances examples

10-10-13 : Angular momentum: Examples; Energy equation; Converging-diverging nozzle

10-17-13 (Midterm in class, Open notes)

10-22-13: Velocity field, Eulerian and Lagrangian flow description, streakline/pathline/streamline, Steady flow

10-24-13: Acceleration field and unsteady effects, Concept of streamline coordinates

10-29-13: Reynolds Transport Theorem, Fluid element motion and deformation, Volumetric dilatation, Angular motion and fluid rotation/irrotation, Conservation of mass and continuity equation

10-31-13: Continuity equations for incompressible fluid, Cylindrical coordinate, Stream function/Streamlines, Conservation of linear Momentum (Euler's Equation of motion), The concept of the Navier-Stokes equation, Bernoulli Equation, Simplification of Navier-Stokes equation.

11-5-13: Velocity potential, Laplace equation, Source-sink pair, Simple solutions for fluids, Assumption of Bernoulli equation

11-12-13 : Model simplification via dimensionless variables, Re number, Froude number

11-14-13: Pipe flow, Laminar and Turbulent flow (By Chris)

11-19-13: Poiseuille's Law, Fully developed flow, Laminar flow pressure drop, Turbulent flow shear stress, Viscous sublayer, Dimensional Analysis of pipe flow

11-21-13: Turbulent velocity profiles (three regions), Turbulent pressure drop, Roughness, Major and minor head loss, Modified Bernoulli equation, Moody chart, Flow rate Measurement (orifice or nozzle meter)

11-26-13/Dec-3-13: Laminar and turbulent flow over immersed bodies; Life and Drag coefficients; Boundary layer definitions, Boundary layer separation, Effect of Re on Drag,

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**WUSTL and MSU are working together to improve
teaching in systems biology. **

Dolan KD, Tang YJ, Liao W “Improvement of Bioengineering Courses through Systems Biology and Bioprocess Modeling”. 121 Annual conference of American Society for Engineering Education. Indiana. 2014.

http://www.asee.org/public/conferences/32/registration/view_session?session_id=3412

**We shared Class Materials with
Dr. Wei Liao and Dr. Kirk Dolan from Michigan State**** University. More MATLAB
lectures can be found at the website below:**
**http://tang.eece.wustl.edu/MATLAB_WUSTL.htm**