|
||
Subject Information
Lectures: MWF 10, room 34-101
Recitations: TR 10 or 11, room 36-112
Units: 5-2-5
Objectives
- develop engineering approaches to understanding cell physiology.
- develop mathematical models for how molecules get into and out of cells: diffusion (Fick's Law), osmosis (van't Hoff's Law), chemical transport, and ionic transport (Nernst-Planck Equation).
- develop mathematical models for how cells generate electrical signals: core-conductor model for large cells, cable model, Hodgkin-Huxley model for electrically excitable cells, saltatory conduction in myelinated fibers.
- relate mathematical models to underlying measurements.
Desired Outcomes
- recognize and apply conservation laws that govern transport.
- understand and calculate the space-time evolution of one-dimensional diffusion processes, osmosis, first and second-order reversible reactions, and ionic currents.
- understand and calculate cellular resting potentials.
- understand and calculate the distinctive properties of neural signals, including all-or-none responses, thresholds, refractoriness, and decrement-free propagation.
- formulate and solve modern models of transport through integral membrane proteins.
Teaching/Learning Activities Changes?
- Three lectures each week to introduce new material.
- Two recitations each week to solve problems and answer questions.
- Two projects -- one experimental and one theoretical -- to help students learn to pose testable hypotheses, to conduct research, and to communicate results.
- Weekly homework assignments to encourage students to actively assimilate the course material.
- Two evening examinations and one final examination to provide occasions to integrate the subject material and to obtain an objective evaluation of the student's understanding of the material.
Staff
|
Name |
Role |
Office |
Phone |
email at mit.edu |
|
Dennis M. Freeman |
Lecturer |
36-889 |
x3-8795 |
freeman |
|
Jay Han |
Recitation Instructor |
36-841 |
x3-2290 |
jyhan |
|
Joel Voldman |
Recitation Instructor |
36-824 |
x3-2094 |
voldman |
|
Mya Poe |
Writing Instructor |
14N-229B |
x3-7893 |
myapoe |
|
Susan Ruff |
Writing Instructor |
32-083 |
x3-3039 |
ruff |
|
Soumyajit Mandal |
T.A. |
|
|
soumya |
|
Austin Che |
T.A. |
|
|
ausche |
|
Tri Ngo |
T.A. |
|
|
ngotm |
|
Jianping Fu |
T.A. |
|
|
jpfu |
|
Janice Balzer |
secretary |
36-825 |
3-7349 |
balzer |
Homework
Weekly homework assignments provide an opportunity to develop intuition for new concepts by actively applying the new concepts to solve problems and answer questions. The process of actively struggling with the use of new ideas until you understand them is an effective and rewarding form of education.
Weekly homework assignments will typically be posted on our web site on Thursday and will be due the following Thursday, in recitation. Late homework will not be accepted. Homework assignments will be corrected, graded, and returned the week after they are due. The solution to each homework assignment will generally be made available on our web site a few days after the homework due date. Paper copies of homework assignments and solutions will not be distributed.
Homework problems will be chosen for their educational value. Some of our best problems were assigned in previous years, and it is a relatively easy matter to acquire solutions. Reading someone's solution to a problem is not educationally equivalent to generating your own solution. If you skip the process of personally struggling with the use of new concepts, you will have destroyed your most important educational experience.
Collaboration Policy
We encourage students to discuss the homework with other students and with the teaching staff to better understand the concepts. However, we expect that you wrote the solutions that you submit under your name. Students should not use solutions of other students (from this year or from previous years) in preparing their own solutions. Students should not take credit for computer code or electronic plots generated by other students. Students should not share their solutions with other students.
Any student caught plagiarizing will
receive a grade of zero on the assignment. All incidents of plagiarism will be
reported to the Committee on Discipline (COD). More information about what
constitutes plagiarism can be found at
http://web.mit.edu/academicintegrity/
Examinations
Two evening examinations will be given: one on Thursday, October 12, 2006 and one on Thursday, November 16, 2006. Both exams run from 7:30-9:30 PM. Students will have two hours to complete the exam, which will be designed as a one-hour exam. These exams are closed-book: notes on both sides of one 8.5x11 inch sheet of paper may be used for reference in the first examination, and notes on both sides of two 8.5x11 inch sheets of paper may be used for reference in the second examination. Cell phones, music players, and other electronic communications devices are not allowed in any of the examinations.
All students are expected to take the evening examinations at the scheduled times and locations. If you have a legitimate reason for not being able to make the scheduled time (such as a conflict with another subject), please see the lecturer as soon as possible. No accommodations will be made unless the lecturer is contacted more than one week before the scheduled times.
Regrade Policy
If you find a grading error in an examination, please submit your exam along with a cover sheet that describes the error that you found to your TA. We will review your concern and then regrade the entire exam to try to eliminate the error that you identified as well as any other grading errors. Requests for regrades must be made within one week of the date when the graded exams were returned.
Final Examination
A three-hour final examination, given during the Final Examination Period, will cover all the material in the subject, but will be weighted more heavily on material not covered in the examinations given during the term. The final examination is closed-book; notes on both sides of three 8.5x11 inch sheets of paper may be used for reference. Cell phones, music players, and other electronic communications devices are not allowed in any of the examinations. The final examination is scheduled by MIT's Registrar's Office. Conflicts with the scheduled time must be resolved by scheduling a conflict examination with MIT's Registrar's Office.
Computer-Aided Exercises
Six
software packages will be used: (1) the random-walk model of diffusion, (2) macroscopic
diffusion processes, (3) chemically-mediated transport across membranes, (4)
the Hodgkin-Huxley space-clamped model for neural membranes, (5) the
Hodgkin-Huxley propagated action potential model, and (6) voltage-gated ion
channels in membranes. These software packages will be used in lectures,
recitations, and homework. No knowledge of computers is required to use this
software. Documentation is available online, and can be accessed from the
subject home page. The software packages are written in MATLAB and run with the
student version of MATLAB, which is available to MIT students at
https://msca.mit.edu/cgi-bin/matlab
Projects
This subject includes two projects. In the first, microfluidics platforms (in 38-600) are used to study diffusion and osmosis in cells (two or more 3-hour laboratory sessions scheduled at your convenience). In the second project, computer simulation is used to understand neural behaviors (done on Athena). The projects provide an opportunity to learn about (1) planning experiments, (2) acquiring, processing, and interpreting data, and (3) communicating the results to others. Both projects require a written proposal, which includes a well-defined hypothesis and procedures to test the hypothesis.
Students are encouraged to work in pairs for both projects. Partners are encouraged to submit a joint proposal and to cooperate in processing data, in discussing interpretations, and in preparing their reports. Partners are also encouraged to submit a joint report. We strongly believe that students learn more by working with other students than by working in isolation.
The report for the first project is written. It should be approximately 10 pages long and structured as a scientific paper. The report for the second project is oral. It should be 12 minutes in length and should be delivered during the next to last week of the semester. The reports for both projects have firm due dates, which are listed on the subject calendar. There are severe lateness penalties for missing the due dates.
Communications Intensive
This subject is communications intensive. We feel that communications skills are essential for professional engineers and scientists. We also feel that the process of creating written manuscripts and oral presentations can help clarify thinking and can be an effective way to learn technical material.
Homework assignments and examinations will often ask you to explain something or to define something that you have been taught. In addition, each of the projects is communications intensive. For each project, you and your partner must submit a written proposal and revise the proposal until it is approved by the staff. For each project you and your partner must prepare a formal report that is structured as a scientific paper or oral presentation. First drafts of each report are due approximately one week before the final drafts, and will be reviewed by the technical staff, staff from the Writing Program, and by student peers. You and your partner will be assigned to prepare a written critique of a first draft from a different team. The critiques will be discussed during a special recitation session held between the first draft and final draft deadlines. EECS students can satisfy their junior year communications requirement in their major (CI-M) by taking this subject.
Grade
Because of the variety of work in this subject, grades do not depend heavily on performance on any single assignment or examination. The letter grade for the subject will be determined from a weighted sum of letter grades for the homework assignments, projects, and examinations. The weighting factors are
|
Homework |
5% |
|
Exam I |
15% |
|
Exam II |
20% |
|
Lab Project |
15% |
|
HH Project |
15% |
|
Final Exam |
30% |
For students near grade boundaries, other factors may be taken into account, including participation in class, laboratory performance not evidenced in the laboratory grade, etc. The grades are determined by the staff. Students registered for undergraduate and graduate versions of this subject will be graded separately.
Text
The course text has two volumes, both available at Quantum Books:
- Weiss, T. F. (1995). Cellular Biophysics. Volume 1: Transport, MIT Press. errata
- Weiss, T. F. (1995). Cellular Biophysics. Volume 2: Electrical Properties, MIT Press. errata
Supplementary reading is available in the following texts:
- Vander, A. J., Sherman, J. H., and Luciano, D. S. (1997). Human Physiology, The Mechanisms of Body Function, McGraw-Hill.
- Aidley, D. J. (1998). The Physiology of Excitable Cells, Cambridge University Press.
- Kandel, E. R., Schwartz, J. H., and Jessell, T. M. (1992). Principles of Neural Science, Elsevier.