Syllabus

 

 

 

Biophysics, Spring 2014

 

PHY642 CRN 29216

PHY490 CRN 25775

 

 

 

Instructor: Dr. Jaan Mannik (Physics and Astronomy)

Office: 210 Nielsen Physics Bldg.

Class Hours: Tue.,Thur. 9:40 - 10:55 AM

Office Hours: Tue., Thur. 11:00 - noon

Phone: 974-6018

Email: jmannik@utk.edu

 


Overview:

 

Biology has become one of the most exciting frontiers of physics research. Over the past century biologists have gathered massive amount of phenomenological data. Physics offers tools to address these data from common underlying principles. The aim of the course is to describe the main principles that form a foundation for contemporary biophysics. After initial overview on cellular organization and statistical mechanics, the course will cover aspects of polymer physics, membrane mechanics, electrical phenomena in cells, osmosis and crowding, molecular motors, self-assembly processes and pattern formation in nature.

 

In addition to theoretical understanding, the course also describes new experimental techniques including single molecule imaging, magnetic and optical tweezers, AFM and lab-on-a-chip devices.

 

 

Learning Objectives of the Course

 

The main objective is to learn the theoretical principles and experimental techniques that form a foundation for contemporary biophysics.

 

The aim of the course is also to bring the students to the level where they will be able critically read and analyze biophysics related scientific papers.

 


Course textbook:

 

Rob Phillips, Jane Kondev, Julie Theriot and Hernan G. Garcia, Physical Biology of the Cell, 2nd Edition, Garland Science.

 

ISBN:  9780815344506

 

Other relevant books:

 

1.  Philip Nelson, Biological Physics, 1st Edition, W. H. Freeman and Company

2.  M. Rubinstein, R. H. Colby, Polymer Physics, Oxford University Press

3.  B. Alberts, A. Johnson, J. Lewis et al, Molecular Biology of the Cell, 5th Edition, Garland Science

 

 

Grading policy:

 

40% homework, 30% attendance/participation in discussions, 30% final project.

 

 

Homework

 

The homework will be typically due on a weekly bases every Thursday at 9:40 am (before class begins). Please hand in the homework on paper. Handwriting is OK as far as it is readable for the graders (me and Matthew Bailey, mbaile25@utk.edu).

 

The two lowest scoring homework will not count on your final score. For those of you, who have a limited background in biology, the deadline for the first homework can be extended to allow you to catch up.

 

 

Final Presentation

 

Final project is a seminar-style presentation of a paper. The presentation will be 15 min + 5 min for discussions. Presentations will be discussed by everybody in the class; participation in this discussion contributes to the grade.  

 

Many of you are involved in biophysics related research. In this case you are welcome to present a broader review of your research topic rather than a research paper as your final presentation. If you choose this option then you should prepare a 30 min presentation. There will be 5-10 min for questions after your presentation. Please contact me if you decide to choose this option. These presentations will be arranged at the times when we cover the related material rather than in the end of the semester.

 

I will help to identify research presentations for those of you who are not yet involved in research or prefer to do the presentation on a new topic.

 


Preliminary Schedule

 

Lecture

Date

Topic

1

Jan. 9

Cell, the basic phenomenology

2

Jan. 14

Cell, the basic phenomenology

3

Jan. 15

Recap on statistical mechanics

4

Jan. 21

Recap on statistical mechanics

5

Jan. 23

Physical environment of cell

6

Jan. 28

Physical environment of cell

7

Jan. 30

Polymer physics, optical tweezers

8

Feb. 4

Polymer physics, magnetic tweezers

9

Feb. 6

Polymer physics

10

Feb. 11

Membrane mechanics

11

Feb. 13

Membrane mechanics

12

Feb. 18

Membrane potentials

13

Feb. 20

Membrane potentials

14

Feb. 25

Molecular motors, single molecule tracking

15

Feb. 27

Molecular motors

16

Mar. 11

Self assembly

17

Mar. 13

Self assembly

18

Mar. 25

Pattern formation in biology

19

Mar. 27

Pattern formation in biology

20

Apr. 1

Experimental methods:

Single molecule microscopy

21

Apr. 3

Experimental methods:

Single molecule microscopy

22

Apr. 8

Experimental methods:

AFM and TEM based methods

23

Apr. 10

Lab-on-a-chip technology

24

Apr. 15

Presentations

25

Apr. 17

Presentations

26

Apr. 22

Presentations

27

Apr. 24

Presentations