BIOEN 6002 Molecular Biophysics

University of Utah

Spring Semester 2008

 

Instructor:

Prof. Vladimir Hlady

Office Hours:  Immediately after class or by apoint. in Rm. 108A BPRB

e-mail: vladimir.hlady@utah.edu                     ph: 801-581-5042

 

COURSE OBJECTIVE

This intermediate-level 3 credit-hour course is focused on the application of physical principles to:

1)    develop quantitative understanding of biophysical processes in natural and engineered macromolecules, membranes, and tissues,

2)    learn about modern biophysical methods capturing single molecule properties, and

3)    apply biophysical principles to the solution of biomedical engineering problems.

 

 

TA/Grader: None

 

Lecture: Tues. & Thurs. 12:25-1:45 pm. Room 501 BPRB

Web Site: http://afm1.pharm.utah.edu/MBiophysics/index.html

 

Textbooks and Resources:

The readings come from several excellent books listed below. You should own at least one of these books, that is close to your own research topic.The first one is recommended as a textbook as it covers the majority of the topics and more. Additional readings come from the recent reviews and papers from the literature.

 

M. B. Jackson: "Molecular and Cellular Biophysics" Cambridge U. Press, 2006

(abbr: MJB) (ISBN 0-521-62470-3) (recommended textbook, comprehensive coverage of topics)

K.A. Dill et al: "Molecular Driving Forces" Garland Science, 2003

(abbr: KAD) (ISBN 0-8153-2051-5)

T.F. Weiss: "Cellular Biophysics: Vol I and II" MIT Press, 1996 

(abbr: TFW1 and TFW2) (ISBN 0-262-23183-2; ISBN 0-262-23184-0)

J. Howard: "Mechanics of Motor Proteins and the Cytoskeleton" Sinauer Assoc., 2004

(abbr. JH) (ISBN: 0-8789-3333-6)

P. Nelson:"Biological Physics" WH Freeman, 2004

(abbr. PN) (ISBN 0-7167-4372-8)

              

Selected readings from these books are available on the course website (see the reading links below):

 

 

Tentative Lecture Schedule, Homework Distribution and Quiz Schedule:

 

Week 1                       Probability, Statistical thermodynamics;

1/8, 1/10                      (reading: ch. 6KAD available from publisher; ch. 7KAD available from publisher, Solved Problems)

Week 2                       Free Energies, Diffusion

1/15, 1/17                    (readings: ch. 8KAD; ch. 3TFW1_1 (3.1 - 3.4), Solved Problems)

Week 3 (HW1)            Brownian motion, Membrane diffusion

1/22, 1/24                    (readings: ch. 7MD, ch. 3TFW1_2 (3.5.1, 3.6 and 3.8), Solved Problems)

Week 4 (HW1_Sol)     Measuring molecule diffusion in 2D and 3D; QUIZ #1 (QUIZ1_solutions)

1/29, 1/31                    (readings: single molecule imaging, FCS_PNAS, FCS_BioEss)

Week 5                       Osmotic pressure; Mechanical forces acting on molecules

2/5, 2/7                        (readings: lecture notes, Solved Problems)

Week 6                       Molecular basis of viscoelasticity; Chemical forces

2/12, 2/14                    (readings: ch. 5JH, lecture notes, Solved Problems)

Week 7 (HW2)            Ligand binding; Carrier-mediated transport

2/19, 2/21                    (readings: lecture notes, background reading, Solved ProblemsA and Solved ProblemsB

Week 8 (HW2_Sol)   Measuring molecular binding forces; QUIZ #2 (QUIZ2_solutions)

2/26, 2/28                    (readings: Evans, Gaub, Guntheroth papers)

Week 9                       Ligand-receptor equilibria;

3/4,3/6                         (lecture notes, parts of ch. 28 KAD, Solved Problems)

Week 10                     Polymer conformation and mechanics;

3/11, 3/13                    (readings: lecture notes)

Week 11                     Spring Break

3/18, 3/20                    (readings: all of the above)

Week 12 (HW3)         Cytoskeleton and filaments; Force generation by filaments;

3/25, 3/27                    (readings: lecture notes, paper by Matsudaira; )

Week 13 (HW3_Sol)  Measuring motor protein forces; QUIZ #3 (QUIZ3_solutions)

4/1, 4/3                        (papers on motor proteins: Vale, Stewart papers, Optical tweezers review )

Week 14                     Electrical Properties of Molecules; Polyelectrolytes, gels;

4/8, 4/10                    (readings: lecture notes; Solved Problems)

Week 15 (HW4)         Ion transport and cell membranes; Active Ion Transport;

4/15, 4/17                    (readings: lecture notes; Solved Problems1; Solved Problems2)

Week 16 (HW4_Sol)  Measuring ion transport through single voltage-gated ion channel;

4/22                             (readings: lecture notes)

 

Homework Due Dates

 (Here is an example of what is expected in homework presentations and format).

Assignment  1:            Tuesday, Jan 29th

Assignment  2:            Tuesday, Feb 26th

Assignment  3:            Tuesday, April 1rd

Assignment  4:            Tuesday, April 22th

 

Quiz Schedule

Quiz 1: Thursday, January 31st

Quiz 2: Thursday, February 28th

Quiz 3: Thursday, April 3rd

Quiz 4: Thursday, April 30th, 10:30 am - 12:30 pm (QUIZ4_solutions)

 

Grading:                                  4 Homework Assignments      40 %

                                                3 Quizes and Final Exam         60 %

                                               

 

General Policy:  All examinations and assignments must be completed in accordance with the University of Utah Student Code of Ethics (http://www.saff.utah.edu/code.html).  Materials disclosed to the instructor for evaluation must be the original work of the student.  Use of material (such as equations, text or graphics) from the web or any other source without proper citation will be considered academic dishonesty. 

Homework Policy:  4 homework assignments will be required.  Students will be expected to have working knowledge of a mathematical package such as Mathematica, Maple, Matlab or IgorPro and to complete their homework assignments using computer.  Presentation in addition to technical content will constitute part of the grade. (Here is an example of what is expected in homework presentations and format). Late homework generally will not be accepted since solutions will be posted shortly after the due date. 

Exam Policy:  4 open book, open note, 1 hour, written examinations will be given.  Three of the exams will be given during the regularly scheduled class time and the fourth exam will be given during the final exam time. 

 

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