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BIOENG 304 Engineering Physiology

Course Schedule for BIOEN 304 (2008) - updated Sept. 08

This course is a mixture of basic physiology and engineering aspects related to physiology.





304 Lab

Book Chapters




Transport – Diffusion, Membranes, Osmosis, Electropotentials, Nernst

Expand 302 circuit to build working photometer given few details about the LED, emission/detection spectra

Chap. 2,3,5


Sept. 29

Oct. 1

Oct. 3


Capstone: N130 - mandatory

Capstone: N130 - mandatory

Continue Week 1  



Oct. 6

Oct. 8

Oct. 10

Membrane Transport

Prof. Dan Ratner

Open, Closed Systems, Kinetics

Data handling, acquisition, fitting, and Beer-Lambert law

Chap. 4


Oct. 13

Oct. 15

Oct. 17


Control of Pathways

Control of Pathways

“Enzyme Kinetics” – by hand test of Trypsin/Chymotrysin and whether there is moving data 



Oct. 20

Oct. 22

Oct. 24

Digestion, Food stuffs, vitamins

Physiology of Digestion

Physiology of Digestion

Automation of Week 4 through digital interface. True enzyme kinetics  

Chap 21


Oct. 27

Oct. 29

Oct. 31

Metabolism – Energy

Organ systems in nutrition

Hormonal Control

Examine two glucose assays, Benedict’s and Glucose oxidase/peroxidase. Qualitative detection. 



Chap 22


Nov. 3

Nov. 5

Nov. 7

Integrated nutrition during

starvation and fed states

MidTerm Quiz

No Lab this week 

Chap 25,




Nov. 10

Nov. 12

Nov. 14

Hormonal Control Systems

Simulating Control Systems

Insulin Control System

Two enzyme system, decoupling of signals. Direct reference to previous 304 HW 

Chap 7,22




Nov. 17

Nov. 19

Nov. 21


Special Dynamics

Kidney Function

Simulation of blood or urine samples. Instrumentation at the interface of biological samples. Satisfies an ABET criterion K 



Chap 19


Nov. 24

Nov. 26

Nov. 28

Sensory Systems

Eye Function

Engineered Synthetic Retina

Dissection and acquisition of pancreatic tissue sample from dead rats

Chap 10


Dec. 1

Dec. 2

Dec. 5

Ear, structure and function

Pain, heat and other sensors

Artificial Neural Nets

Analysis of tissue samples in terms of Trypsin and Chymotrypsin

Handouts and

Chap 10


Dec. 10

GLD 322

Final Exam in GLD 322

at 8.30 to 10.20

No Lab this week 




Grading will be based on Mastery-Based Grading which is based solely on a students' master of the material. In terms for breakdown, the final grade is based on the following partitioning:

  • 20% Homework problems (almost weekly)
  • 35% Labs
  • 20% Midterm quizes
  • 25% Final exam

Grades will be made available on the new Catalyst online grading system.

Class Information

Textbook: Silverthorn, Human Physiology an Integrated Approach (3rd or 4th Edition or above)

In addition there is a very useful but optional pocket sized text book:

Color Atlas of Physiology (Thieme Flexibook) (Paperback)

Agamemnon Despopoulos and Stefan Silbernagl

Amazon Link


 Class Meeting Times and Location:
 M,W,F 9:30-10.20am in GLD (Gould) 322
Teaching Assistants:
  Kassandra Thomson
  Fan Lee

Familiarity with Matlab or some suitable programming language will be expected.


Week 0
Week 2
Week 3
Week 4
Week 5

Organ Integration with Nutrition

Organ Integration

Starvation Notes

Term Assignment

Week 6
Week 7/8

Class Project (graded as an assignment): Split into roughly 11 groups of 4 per team. Pick one of the following 6 papers and spend 10 mins discussing the paper in front of the class. Present next week on 17th and 19th of Nov (with spill over on to the 21st if necessary).

1. Calcium Control

Calcium Homeostasis and Parturient Hypocalcemia: An Integral Feedback Perspective

Review paper on Calcium Homeostasis

2. Chemotaxis Control

Control Analysis of Bacterial Chemotaxis Signaling Tau-Mu Yi, Burton W. Andrews and Pablo A. Iglesias Methods in Enzymology Volume 422, 2007, Pages 123-140 Two-Component Signaling Systems, Part A Health Series or Natural Sciences Stacks

3. Thyroid Control

AN IMPROVED MATHEMATICAL MODEL OF HUMAN THYROID HORMONE REGULATION SARATCHANDRAN and CARSON and REEVE Clinical Endocrinology Volume 5 Issue 5, Pages 473 - 483 Health Science Library

4. Integral Rein Control in Insulin/Glucagon

Integral Rein Control in Physiology Saunders P.T; Koeslag J.H; Wessels J.A2 Journal of Theoretical Biology, Volume 194, Number 2, September 1998, pp. 163-173(11), available online.

5. Integral Rein Control: Generalization

Integral Rein Control in Physiology II: a General Model PETER T. SAUNDERS, JOHAN H. KOESLAG and JABUS A. WESSELSb

Journal of Theoretical Biology Volume 206, Issue 2, 21 September 2000, Pages 211-220 Available online

Week 9/10

Reading assignments for the last two weeks of term:

Chapter 10: Sections on Ear, Eye, Pain, Heat, Taste and Smell

Chapter 19: Kidney.

The remainder of term will be on these topics.

The Eye

The Ear

Other Senses and the Kidney

End of Term Exam Topics

Two hour exam in room MEB 246
Wednesday, December 10, 2008,830-1020


Diffusion, Fick's law, diffusion coefficients (units)
Stokes-Einstein Equation
Root mean square distance and time

Membrane bilipid layer
Diffusion through membranes
Transport by passive and facilitated diffusion, active transport
Channels (aquaporins etc)
Carriers - uniport, symport, antiport
Examples: Na/K ATPase etc.
Origin of resting potential
Nernst Equation
Osmosis - how to measure molecular weight using osmosis

Definitions for control coefficients, elasticities, and response coefficients.
Understanding the importance of the flux summation theorem.
State the connectivity theorems.
Understand the importance of the Response Coefficient relationship (R = C e).
Being able to derive a control equation when given summation and connectivity theorems.
Understanding the basic properties conferred by negative feedback.
Understanding why negative feedback can use useful in a physiological situation.
Difference between proportional and integral control


Challenges aced by digestion
Function of digestion
Basic Anatomy of digestive system
Anatomy of stomach and intestinal wall
Function of each part of the digestive system
Enzymes involved in digestion
Digestion of different food types
Hormonal control in the stomach and intestine
Difference in metabolism between different organs
Brain, Muscle, Adipose, Liver, RBC
Fasting and Starvation
Basic Circulatory System


Different kinds of control strategies
Advantages and disadvantages of strategies
Insulin/Glucagon Control


Taste and Smell
TED Video on in silico biologically inspired sensors


Basic Function
Basic Hormonal Control

sysbio/labmembers/304_engineering_physiology.txt · Last modified: 2008/12/05 10:33 (external edit)

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