SYLLABUS:
PHYS 157
Special
Topics in Biological Physics:
Macromolecular
Machinery
SPRING
2004
¬ General Webpage: http://www.physics.ucsb.edu/~deborah/phys157
¬ Homework: http://www.physics.ucsb.edu/~phys157/s2004
¬ Lectures: MWF 9:00 - 9:50, Arts 1247
¬ Instructor: Deborah Fygenson, Broida 2419, 893-2449
¬ TA: Joseph Chan, cjc54@physics.ucsb.edu
Machines are what sets biology apart among the natural sciences. Living things make machines, and are themselves machines, but the level of an organism phenomena are so complicated that an explanation for why they are the way they are or work the way they do is currently beyond physical reasoning. The exciting development of the last half century in biology is the discovery that living things are also made of machines naturally occurring, inanimate machines. These machines are made of macromolecules (sometimes single macromolecules) and there is therefore reason to expect their physics to explain why they look and work the way they do.
This course is an introductory survey of statistical mechanics, thermodynamics and physical chemistry as applied to understanding macromolecular machinery. It will expose you to key physical insights relevant to how these machines work. It will change the way you look at life forever more.
There will be homework, a midterm and a final. The midterm is expected (but not guaranteed) to fall on Wednesday, April 28, 2004. The final is scheduled for Wednesday, June 9, 2003 from 8:00 am to 11:00 am in Arts 1247. Check the website for any changes.
Note that there is an extra 50% in the total below:
Homework: 45% of the grade
Midterm: 45% of the grade
Final: 45% of the grade
One part of your grade (45%) will be minimized (to 10%) in order to maximize your score. If your worst grade is on the final exam, the final will only count for 10% of your grade. If you miss an exam, you final grade will be based on the other exam and the homework, but will not exceed 90% of the maximum possible. Since exams and homeworks end up having different numbers of points possible, all scores will be recalibrated to the same mean score to determine which grade is dropped.
Exams will consist primarily of problems from the text, at least one of which will have been assigned as homework (with slight modification). I will not provide an equation sheet, but you will be allowed to use your own sheet of notes throughout the exam. Your notes should fit on one 8.5 x 11² sheet of paper. There will be no make-up exams.
Biological Physics: Energy, Information, Life, by Philip Nelson
I like the style and organization of this text, but it is a brand new book (©2004) and since I have never taught this course before, your opinion of it as a learning aid will be very valuable feedback. We will follow the book rather closely, and I strongly recommend you read the associated chapters before their corresponding lecture so that you can get the most out of the class period. The text is very good about pointing out other resources and I will try to make the ones I find most valuable available to you either on the course web page or on reserve at the library.
Homework assignments will be posted on the course webpage the Friday before they are due. Homework is due in a box in the PSC on Thursdays at Noon. Graded homework will be available for collection from the TA the following week.
I encourage you to work together on homework, but you must show your own work in your submission. Even if you find the material straightforward, you will deepen and improve your understanding by explaining/discussing concepts with other students.
I welcome your questions during lecture and am interested in your comments or feedback about how the course is going for you. Drop by during my office hours, set up an appointment or send me an e-mail with PHYS 157 in the subject line. I encourage you to contact me directly, but if you feel uncomfortable doing so, contact the TA and ask him to relay the message without your name attached.
At this point in your undergraduate career you are (or should be) contemplating future jobs or graduate school. (By the way, if you attend graduate school in physics, you get paid >$20,000/yr to study and learn how to do research!) The Physics Department Main Office maintains files on graduate schools. It also generates a weekly bulletin and web page listing seminars. I strongly encourage you to attend seminars and especially colloquia, which are more general talks. I have no idea how students can make decisions about what field of physics to go into without seeing what current science is being done. Going to seminars is the easiest way I know of to learn about current research. Almost all talks begin with a 5-minute introduction to the field. It is perfectly acceptable to sit in the back near the door and then quietly slip out after the speaker¹s introduction if you become bored.
How do you find out what seminars are going on? There is unfortunately no central website that will tell you every single talk and seminar on our campus. Try surfing the websites of your favorite departments, most have a link to events or seminars on their home page, or look for notices posted in the elevators or main traffic areas of Broida or other science buildings. I will advertise some of the more general (and probably more accessible) talks in class and on the course web site.
As an extra encouragement to go to seminars and broaden your exposure to biological physics, one of your homework assignments will be to attend and answer questions about one seminar. You can use any bio-related seminar on campus for this assignment, not merely one that I recommend.
SCHEDULE OF
ASSIGNMENTS (in progress...)
Thursday, April 1: Homework 1
Chapter 1: Problems 1.1, 1.3, 1.5, 1.7
Chapter 2: Printout two of your choice from 2.2 through 2.5
Thursday, April 8: Homework 2
Chapter 3: Problems 3.2, 3.3, 3.4
Chapter 4: Problems 4.1, 4.3, 4.5
Thursday, April 15: Homework 3
Chapter 4: Problems 4.7, 4.9, 4.10
Chapter 5: Problems 5.1, 5.4, 5.5
Thursday, April 22: Homework 4
Chapter 5: Problems 5.6, 5.7, 5.10
Cumulative:
Your problem will be graded based on:
2. Appropriateness to concepts discussed so far
3. Clarity of presentation
Thursday, April 29: Homework 5 (half size)
Chapter 6:
Thursday, May 6: Homework 6
Chapter 7:
Thursday, May 13: Homework 7
Chapter 8:
Thursday, May 20: Homework 8
Chapter 9:
Thursday, May 27: Homework 9
Chapter 10:
Thursday, June 3: Last day for Homework 1B (seminar report)