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教學大綱


本頁翻譯進度

燈號說明

審定:無
翻譯:韓銀花(簡介並寄信)
編輯:方珮維(簡介並寄信)

這個大綱包括課程內容、教學方法、作業和參加本課程學習的學生規則和指南。


麻省理工學院
電子工程與電腦科學系
機械工程系
生物工程與環境健康部
哈佛大學-麻省理工大學 健康科技部

計量生理學:細胞與組織
2.791J/2.794J/6.021J/6.521J/BEH370J/BEH470J/HST541J

2002年秋季

「在科學的思想中,我們採用最簡單的理論來解釋所有要考慮的現象,預測相同條件下的新情況。而這個標準的關鍵在於『最簡單』。這實際上是一種美學教條,就好象我們批評詩和畫的含蓄。外行人會覺得像 x/∂t= κ(∂2x/∂y2) 這樣的定理要比它所要表達的數學描述簡單(『滲漏了』)得多。而物理學家們則持相反的觀點,就預言來說,他的描述一定是兩個中比較有成效的。」 Haldane, 1985年

課程內容

在這門課程中,我們要討論細胞生物物理學中的兩個基本的主題,這堨H問題的形式給出:
  • 什麼分子可以傳輸通過細胞膜,以及傳輸的機制是什麼?細胞如何保持自身的分子組成、體積和膜電勢?
  • 細胞膜上的電勢是如何產生的,這些電勢有什麼作用?

雖然這些問題是非常基本的生物學問題,但是解決這些問題的方法卻是需要多學科的知識。例如,為了理解分子跨細胞膜傳輸的機制,需要瞭解細胞膜的結構和跨膜物質傳輸的原理。因為傳輸物質可能會與跨膜大分子發生化學反應或帶有電荷,所以需要瞭解電場中的帶電荷分子的動力學和傳輸原理。目前跨膜傳輸的知識主要是基於測試方法,根據測試的結果,得出以物理、化學為基礎的數學模型,用以驗證基於這些測試的理論。數學模型的作用是為了更精確地表達概念,得到更精確的結論(引用Haldane的話,見上)。凡是涉及到的題目,本課程都會從理論和實踐兩方面加以考慮。對於學生來講,驗證理論與實驗的相互關係要比從課程本身獲得的專業知識更有意義。


教學方法

下列活動用以幫助學習本課程。

  • 每週三次課介紹新內容。
  • 每週二次復習已經學過的材料、解決疑問、回答問題。
  • 一次實驗專案設計和一次理論專案設計,幫助學生學習如何提出可測試的假設,如何進行研究以及如何說明結果。
  • 每週一次家庭作業,鼓勵學生積極地吸收課程內容。
  • 兩次晚間考試,一次期終考試,給學生提供一個整合課程的機會,以及使老師正確瞭解學生理解課程的程度。

課後作業

每週一次的課後作業,給學生提供了一個機會,可以通過積極地應用新概念解決問題來培養對新概念的理解 。積極努力地使用新概念直到你完全理解它們,這是一個非常有效和有益的教育過程。每週的課後作業會在週四佈置,然後下一周的同一天交。晚交作業是不被接受的

作業會被批改、評分,並在上交後的下一個星期返還學生。作業的答案會與批改過的作業一起發下去。我們會根據學習的情況來決定作業的題目,一些好的題目已經在前幾年佈置過了,想要獲得答案是相對容易的事情。如果你跳過自己努力學習新概念的過程,你將錯過獲得最重要的學習經歷的過程。看懂別人的答案不等於你自己會寫答案。我們鼓勵學生一起工作,一起研究作業堛熒妝嚏A但是,每個學生都應該有他/她自己的答案。上交的作業應該反映出個人的知識。如果你與其他學生一起工作(住在一起的學生或者是以前學生留下來的底稿),請把他們的名字寫在作業上。把作業推到截止日期的前一天晚上完成看起來是個不錯的主意,但卻是個不佳的計畫。因為,這樣就限制了你與其他同學和老師之間的協調能力的發展。

考試

共有兩次晚間考試,一次是在第24天,一次是在第42天。每次考試時間為一個小時,考試為閉卷考試。在第一次考試中,可以使用一頁雙面的筆記作為參考,第二次考試中可以使用二頁雙面筆記作為參考。期末考試在學期末進行,考試時間為三個小時。考試內容將包括本課程的所有內容,但是會偏重於前兩次考試中沒有涉及的內容。期末考試為閉卷考試,可以使用三頁雙面的筆記作為參考。


電腦輔助練習

我們將使用六個套裝軟體:(1)擴散的隨機漫步模型,(2)宏觀擴散過程,(3)化學調節的跨膜傳輸,(4)神經細胞膜的Hodgkin-Huxley的空間夾模型,(5)動作電勢傳播的Hodgkin-Huxley模型,(6)細胞膜上的膜電位敏感型離子管道 。這些套裝軟體在課堂中、復習和作業中都會用到。使用這些練習包並不要求有電腦知識。在開始練習之前需要註冊Athen計畫,並獲取一個用戶名

這學期,我們將使用基於MATLAB®的不同版本的套裝軟體。套裝軟體的文檔可以在網上下載,也可以從課程主頁上獲得。還有一些其他版本的套裝軟體可以從Athena的“dash”中獲得。在完成作業時你可以隨意使用各種版本的軟體,但是,如果你沒有使用最新的版本,請注明你使用的版本。的不同版本的套裝軟體。套裝軟體的文檔可以在網上下載,也可以從課程主頁上獲得。還有一些其他版本的套裝軟體可以從Athena的“dash”中獲得。在完成作業時你可以隨意使用各種版本的軟體,但是,如果你沒有使用最新的版本,請注明你使用的版本。

項目

本課程包括兩個項目。第一個是關於青蛙坐骨神經的混合動作電勢的實驗項目。這個項目要向學生們介紹生理學研究的實驗方法,並且為理解實驗基本概念提供第一手實踐經驗。第二個專案是使用軟體來建立神經細胞膜Hodgkin-Huxley模型,向學生們介紹如何使用電腦類比來理解複雜的系統。通過這些項目使同學們有機會學習(1)如何進行實驗計畫,(2)如何獲取、處理和解釋資料,(3)如何與其他人交流實驗結果。這兩個專案都需要提交書面大綱,包括明確描述的假設和驗證假設的過程。實驗專案需要4個小時的實驗室工作來完成;如果認為有必要,你可以安排更多的實驗。理論項目主要是在Athena上實現。每個專案需要提交大概10頁學術文章樣式的終期報告。我們鼓勵學生在這兩個項目中以兩個人為一組進行工作,並鼓勵他們提交一個共同的大綱,合作處理資料,討論解釋資料,準備報告,也鼓勵合作者提交一份報告。我們相信與其他學生一起工作會比單獨工作要學得更多。學習生理學過程中,理論和實驗項目對於理解理論與實驗之間的相互關係是非常重要的一個環節。但是,如果由於道德上或是信念上的原因,不能參加實驗項目的同學請與指導老師聯繫。兩個專案報告的上交截止日期是必須嚴格遵守的,詳細日期列在附件的教學日程堙C如果報告晚於截止日期上交,那麼在分數上就有嚴厲的懲罰,分數將乘以晚交的係數
L=.3e-t/4 + .7e-t/72
其中t是晚交超過的小時數。

交流強化:寫作、評論、階段2學分

本課程非常強調交流,我們認為寫作(寫作也是一種交流)的過程有助於清晰思路,也是一種學習專業知識的有效方法。

在作業和考試過程中,常常會要求你解釋或定義一些你已經學過的事物。另外,每個專案是要求很強的表達交流能力的。每個項目,你和你的拍擋必須提交一份書面的大綱,並且進行修改直到老師同意為止。每個專案,你和你的拍擋必須準備一份正式的以學術論文格式書寫的報告。每個專案的報告初稿要在終稿期限前一個星期提交。你和你的拍擋會要求提交一份對其他小組的報告初稿的書面評論。評論將會在初稿和終稿截止時間之間的一個專門的時間進行討論 。

第二階段評分由寫作專案部來給予。主要是給那些在課堂寫作練習中獲得B和B以上以及在本課程中表現出好的交流技巧的同學。

學生和老師的職責

作為學生,你有權利要求老師們精心備課,積極反應,嚴格守時。在我們不能每時每刻提供引人入勝和深刻的講演的同時,你當然有權利要求我們更加專業些。在雙方合適的時間內,學生可以向老師請教。我們希望在提交後一周時間內返還所有評過分的問題、考試以及在三個星期時間內返還實驗項目報告。理論專案報告將在學期末返還

當然我們也對你們也有所期望。我們希望學生能夠完成作業,並按時提交。此外,我們希望你所提交上來的署著你的簽名的作業真正是你自己做出來的。我們鼓勵學生們對作業中所涉及的概念進行交流,這對於學習是非常有幫助的。但是每個學生都應該拿出自己的答案。提交的作業應該反映出個人的知識程度。如果你和其他同學一起工作,請把他們的名字也列在你的作業上。提交抄襲前人的結果的答案是一種不成熟、不誠實的行為,浪費所有人時間,也是一種損害自己名譽的行為。總之,如果你提交的不是你自己的工作,包括作業、實驗報告、大綱或是報告,這將構成剽竊,是和在考試中作弊一樣嚴重的過錯。

評分

因為本課程中的工作非常多,所以分數不側重於單個作業或考試的完成情況。課程的最終字母評分由作業、專案和考試所得的字母分數所決定。各部分的比重分別為:

作業 實驗I 實驗II 實驗專案 HH專案 期末考試
5% 15% 20% 15% 15% 30%
對於那些成績落在邊界分數的學生,我們還要考慮其他的影響因素,包括上課的情況,實驗室得分中沒有體現的實驗室表現等。最終由老師來決定分數。

大學生和研究生將分別評分。

教材

本課程教材包括兩本:

Weiss, T. F. (1995). 《細胞生物物理學,第一卷:傳輸》(Cellular Biophysics. Volume 1: Transport), MIT Press.

Weiss, T. F. (1995). 《細胞生物物理學,第二卷:電子屬性》(Cellular Biophysics. Volume 2: Electrical Properties), MIT Press.

對於細胞的電子特性部分,請參考以下補充讀物:

Vander, A. J., Sherman, J. H., 與 Luciano, D. S. (1997). 《人類生理學,人體功能機制》(Human Physiology, The Mechanisms of Body Function), McGraw-Hill.

Aidley, D. J. (1998). 《可興奮細胞生理學》(The Physiology of Excitable Cells), Cambridge University Press.

Kandel, E. R., Schwartz, J. H., and Jessell, T. M. (1992). 《神經科學原理》(Principles of Neural Science), Elsevier.

MATLAB®為The MathWorks公司的商標。




This syllabus describes the course's contents, teaching methods, assignments, and general policies and guidelines for students enrolled in the course.


MASSACHUSETTS INSTITUTE OF TECHNOLOGY
Department of Electrical Engineering and Computer Science,
Department of Mechanical Engineering,
Division of Bioengineering and Environmental Health,
Harvard-MIT Division of Health Sciences and Technology

Quantitative Physiology: Cells and Tissues
2.791J/2.794J/6.021J/6.521J/BEH370J/BEH470J/HST541J

FALL 2002

"In scientific thought we adopt the simplest theory which will explain all the facts under consideration
and enable us to predict new facts of the same kind. The catch in this criterion lies
in the word 'simplest'. It is really an aesthetic canon such as we find implicit in our criticisms
of poetry or painting. The layman finds such a law as
x/∂t= κ(∂2x/∂y2) less simple than
'it oozes', of which it is the mathematical statement. The physicist reverses this judgment, and
his statement is certainly the more fruitful of the two, so far as prediction is concerned."
-Haldane, 1985

Subject Contents

In this subject, we consider two basic topics in cellular biophysics, posed here as questions:
  • Which molecules are transported across cellular membranes, and what are the mechanisms of transport? How do cells maintain their compositions, volume, and membrane potential?
  • How are potentials generated across the membranes of cells? What do these potentials do?

Although the questions posed are fundamentally biological questions, the methods for answering these questions are inherently multidisciplinary. For example, to understand the mechanism of transport of molecules across cellular membranes, it is essential to understand both the structure of membranes and the principles of mass transport through membranes. Since the transported matter may combine chemically with membranespanning macromolecules and/or carry an electrical charge, it is essential to understand the principles of chemical kinetics and of transport of charged molecules in an electric field.Knowledge of transport through membranes is based on measurements. These measurements lead to physically and chemically based mathematical models that are used to test concepts based on measurements.The role of mathematical models is to express concepts precisely enough that precise conclusions can be drawn (see quote by Haldane, above). In connection with all the topics covered, we will consider both theory and experiment. For the student, the educational value of examining the interplay between theory and experiment transcends the value of the specific knowledge gained in the subject matter.


Teaching Methods

Several kinds of activities are provided to help the learning process.

  • Three lectures each week to introduce new material.
  • Two recitations each week to review material, solve problems, and answer questions.
  • Two projects — one experimental and the other 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 an occasion to integrate the subject material and to obtain an objective evaluation of the student’s understanding of the material.

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 issued on fourth weekday and will be due the following week same day, in recitation. LATE HOMEWORK WILL NOT BE ACCEPTED.

Homework assignments will be corrected, graded, and returned the week after they are due. Solutions to the homework will be distributed with the corrected homework. 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. IF YOU SKIP THE PROCESS OF PERSONALLY STRUGGLING WITH THE USE OF NEW CONCEPTS, YOU WILL HAVE DESTROYED YOUR MOST IMPORTANT EDUCATIONAL EXPERIENCE. Reading someone’s solution to a problem is not educationally equivalent to generating your own solution. We encourage students to work together to understand the concepts in the homework. However, each student should work out his/her own solutions. Submitted homework should reflect the knowledge of the individual. If you work with other students (living students or the written testaments of previous students), please include their names on your homework sets. It is generally tempting to postpone working on homework until the night before it is due. This is a poor plan because it limits your ability to interact with fellow students and the teaching staff.

Examinations

Two evening examinations will be given: one on Day 24, and one on Day 42. 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 sheet of paper may be used for reference in the first examination, and notes on both sides of two sheets of paper may be used for reference in the second 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 sheets of paper may be used for reference.


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 perform these exercises. Students will be required to register with Project Athena and acquire an Athena username before they start on the exercises.

This term we will use versions of each software package based on MATLAB®. Documentation is available online, and can be accessed from the subject home page. There are several other versions of these software packages available from Athena’s “dash.” You may use any version you like for any assignment. However,if you don’t use the latest version, please make a note of the version that you used.

Projects

This subject includes two projects. The first is an experimental project on compound action potentials from a frog sciatic nerve. This project introduces students to experimental methods of physiological research and provides first-hand experience with the experimental basis for concepts in the subject. In the second project,a software representation of the Hodgkin-Huxley model for a neural membrane will be used to introduce students to the use of computer simulation to understand the behavior of complex systems.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. The experimental project typically requires one 4 hour session in the laboratory ; you are welcome to arrange for additional laboratory time if necessary. The theoretical project is done on Athena. Each project requires a roughly 10-page final report that is organized as a scientific paper.Students are encouraged to work in pairs in both projects. Partners are encouraged to submit a joint proposal, 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 theoretical and experimental projects are key parts of learning about interplay between theory and experiment in developing knowledge about cell physiology. However, if for a moral or philosophical reason you feel that you cannot participate in the experimental exercise, please see the instructors. The final reports for both projects have FIRM DUE DATES, which are listed on the attached calendar. THERE IS A SEVERE LATENESS PENALTY: the grade for a late report will be multiplied by a lateness factor
L=.3e-t/4 + .7e-t/72
where t is the number of hours late.

Communications Intensive: Drafts, Critiques, and Phase 2 Credit

This subject is communications intensive. We feel that the process of writing 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.First drafts of each report are due approximately one week before the final drafts. 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.

Phase 2 credit will be awarded by the Writing Program to all students who receive a B or higher grade for their participation in the writing clinic and for communication skills demonstrated in this subject.

Student-Staff Responsibilities

You, the student, have a right to expect the staff to be prepared and responsive and punctual. While we cannot always deliver entertaining and incisive lectures and recitations, you have a right to expect us to act professionally. The staff will be available for consultation at mutually agreeable times. We expect to return all graded problem sets and exams within one week of submission and all experimental project reports within three weeks of submission. The theoretical project report will be returned at the end of the semester.

We also have expectations for you. We expect you to do the work and to submit your work on time!Furthermore, we expect that the work you submit to us under your name is your work. Interaction of students on the concepts involved in the homework assignments is often helpful and is encouraged, but each student should work out his/her own solutions. Submitted homework should reflect the knowledge of the individual. If you do work with other students, please include their names on your problem sets. Submission of problem sets that are copies of solutions previously distributed in this subject is immature, dishonest, a waste of everyone’s time, and a discredit to the perpetrator. In general, submission of work that is not your own — in the form of solutions to homework assignments, laboratory reports, proposals, or reports — constitutes plagiarism and is as serious an offense as is cheating on examinations.

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 Exam I Exam II Exp. project HH project Final exam
5% 15% 20% 15% 15% 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.

Texts

The course text has two volumes:

Weiss, T. F. (1995). Cellular Biophysics. Volume 1: Transport, MIT Press.

Weiss, T. F. (1995). Cellular Biophysics. Volume 2: Electrical Properties, MIT Press.

For the portion of the subject that deals with electrical properties of cells, 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.

MATLAB® is a trademark of The MathWorks, Inc.




 
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