BIOEN 6002 Molecular Biophysics

University of Utah

Fall Semester 2017

 

Instructor:

Prof. Vladimir Hlady

Office Hours:  By appoint. in Rm. 108A BPRB, or immediately after class.

e-mail: vladimir.hlady@utah.edu                     phone: 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 cells,

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

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

 

 

TA/Grader:

Ms. Hannah Northrup, (e-mail: hmnorthrup@gmail.com)

 

Lecture: Tues. & Thurs. 12:25-1:45 pm. Room HSEB 5100B

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, so chose one that is close to your research topic. Additional readings come from recent reviews and papers from the literature.

 

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

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

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

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

R. Phillips, J. Kondev, J. Theriot: "Physical Biology of the Cell" Garland Science, 2009

(abbr: PBoC) (ISBN 978-0-8153-4163-5)

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

(abbr: MJB) (ISBN 0-521-62470-3)

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 (8/22, 8/24): Proteins and polymers (lecture notes: part A, part B, part C)

readings: K. Dill's paper, D. Chandler's paper

 

Week 2 (8/29, 8/31): Molecular mechanics, elasticity and viscosity (lecture notes: part A, part B)

readings: Chapters 2 and Chapter 3 from JH

 

Week 3 (9/5, 9/7) HW1; Macromolecular conformations (lecture notes)

readings: Chapter 32 from KAD

 

Week 4 (9/12, 9/14) HW1solutions; Measuring molecular forces (lecture notes); QUIZ #1 (QUIZ1_solutions)

readings: Neuman_review, Fernandez_titin, Guntherodt_DNA

 

Week 5 (9/19, 9/21): Diffusion and Brownian motion (lecture notes: part A, part B), protein assignment, part 1 resource

readings: Chapter 4 from PN, more solved problems

 

Week 6 (9/26, 9/28): Chemical reactions, forces and association kinetics (lecture notes)

readings: lecture notes, extra pages

 

Week 7 (10/3, 10/5) HW2: Polynomials for ligand binding equilibria (lecture notes)

readings: Ch 28 from KAD, solved problems

 

Week 8 (10/8 - 10/15): Fall break

 

Week 9 (10/17, 10/19) HW2solutions: Measuring molecular diffusion in 2D and 3D (lecture notes); QUIZ #2 (QUIZ2_solutions)

readings: Schmidt SMD, Rigler FCS review, Schwille FCS review

 

Week 10 (10/24, 10/26): Biological membranes and receptors (lecture notes); Carrier mediated transport (lecture notes)

readings: lecture notes, solved problems

   
Week 11 (10/31, 11/2): Electrical properties of molecules (lecture notes)
readings: chapter 20 KAD, solved problems,
 

Week 12 (11/7, 11/9) HW3: Electrical properties of molecules (continued); Ion transport (lecture notes)
readings: lecture notes, chapter 17 PoBC, or 12 PN, solved problems
 

Week 13 (11/14, 11/16) HW3solutions: Ion channels (lecture notes)
readings: lecture notes, chapter 17 PoBC, or 12 PN, solved problems
 
Week 14 (11/21, Thanksgiving): QUIZ #3 (QUIZ3_solutions)
readings: lecture notes
 
Week 15 (11/28, 11/30): Osmotic pressure, crowding (lecture notes); Cytoskeleton, Einstein polymer (lecture notes)

readings: lecture notes, (solved problems)
   
Week 16 (12/5, 12/7) HW4 (due on Monday, 12/11 by 3 pm): Force generation by filaments (lecture notes); Motor Forces (lecture notes);

Lecture not covered in 2017: Polyelectrolytes, coacervates, gels (lecture notes)
readings: lecture notes

 

Week 17 (12/12, 10:30 am - 12:30 pm)  Final exam, HW4sol: QUIZ#4 (QUIZ4_solutions)(Extra Q solutions)

 

Each homework will be posted on-line on Tuesday and will be due in class next Tuesday. Here are the histograms of the HWs and Qs.

 

Quiz Schedule -

Quiz 1: Thursday, September 14th

Quiz 2: Thursday, October 19th

Quiz 3: Thursday, November 21st

Quiz 4: Thursday, December 12, 10:30 am - 12:30 pm

 

Grading:                                  4 Homework assignments      30 %

                                                Protein paper        20 %

                                                3 Quizes and Final exam       50 %

For average scores, histograms and progress so far, click here.

Protein paper: Definition of the assignment, here is an example of the report.

For more explanations on the report assigments (click here)

 

General Policy:  All examinations and assignments must be completed in accordance with the University of Utah Student Code.  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 are 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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