Biological and Environmental Systems Engineering Laboratory Educational Resources

Resources for Educators

1. Inverted-classroom teaching modules to educate MATLAB in chemical process control

USA students are falling behind their peers in other countries as shown in . The aim of our study is to develop innovative teaching modules to facilitate students' learning in the field of process modeling and control. In particular, we implemented the core techniques of process modeling and control in MATLAB/Simulink, which offers user-friendly interface and which makes solving math problems like kids playing Lego. Three teaching modules are developed, including 11 examples and 13 videos that deal with solving ODE models, performing Laplace transform, and designing PID controllers. Our teaching modules have been published in Paper "X. Li, Z. Huang. An Inverted Classroom Approach to Educate MATLAB in Chemical Process Control, Education for Chemical Engineers, 19, 1-12, 2017. " These materials are only allowed for academic purpose, NOT for commercial usage. Questions are welcomed to send to Dr. Huang (zuyi.huang@villanova.edu), but they are not guaranteed for prompt response due to Dr.Huang鈥檚 work commitment.

1) Paper "X. Li, Z. Huang. An Inverted Classroom Approach to Educate MATLAB in Chemical Process Control, Education for Chemical Engineers, 19, 1-12, 2017"
2) Videos for Example 1 include , , and .
3) Videos can be downloaded for , , , , , , , and .
4) Videos can be downloaded for and .
5) The handout of all MATLAB modules can be found in this .

2. MATLAB training videos for Engineering students

Dr. Sergey Nersesov and Dr. Huang developed 17 videos that covered basic MATLAB skills for solving typical problems in engineering (mainly mechanical engineering and chemical engineering). The handouts maybe available upon request. YouTube videos for these 17 MATLAB modules can be found in the following links:

2. A MATLAB based teaching module for solving and analyzing biological ODE models (Systems Biology)

Dr. Huang is enthusiastic in educating students with practical modeling skills that can be implemented in MATLAB. He is developing innovative teaching strategies (such as flipped-classroom) to enhance students鈥� enthusiasm in learning process simulation and control techniques.

The MATLAB based teaching module for solving and analyzing ODE models was presented in the paper: K. Lee, N. Comolli, W.J. Kelly, Z. Huang. MATLAB Based Teaching Modules in Biochemical Engineering. Chemical Engineering Education, in press, 2015.The ODE model as well as the MATLAB programs can be found in .

3. A video to introduce Cell Metabolism recorded by Dr. Huang

4. MATLAB Programs for Signaling Pathway

4.1 The IL-6 ~ IL-10 signaling model

The MATLAB model was presented in the paper " C. Moya*, Z. Huang*, P. Cheng, A. Jayaraman, and J. Hahn. Investigation of IL-6 and IL-10 Signaling in Steatosis via Mathematical Modeling. IET Systems Biology, 5, No. 1, pp. 15-26, 2011 (*equal contribution)". Please read the appendix of this paper for the detail of the ODE model and parameters. The inputs of the model are the concentrations of IL-6 and IL-10, while the outputs the model include the concentrations of transcription factors nuclear STAT3 dimer and C/EBP尾.

The MATLAB program can be downloaded . Please run the Main function to run the simulation. Please cite our paper if you use our model/program.

4.2 The TNF-伪 ~ NF魏B signaling model

This is the model that was presented in our paper Z. Huang, F. Senocak, A. Jayaraman, and J. Hahn. Integrated Modeling and Experimental Approach for Determining Transcription Factor Profiles from Fluorescent Reporter Data. BMC Systems Biology 2:64 (2008).The input of the model is the concentrations of TNF-伪, while the output the model include the concentrations of transcription factor NF魏B.