BIOEN 6002 Molecular Biophysics

University of Utah

Fall Semester 2017



Prof. Vladimir Hlady

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

e-mail:                     phone: 801-581-5042



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.





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

Web Site:


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 assignments, part I

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: Ion transport (lecture notes); Ion channels (lecture notes)
readings: lecture notes, chapter 17 PoBC, or 12 PN, solved problems

Week 13 (11/14, 11/16) HW3sol: Osmotic pressure, crowding (lecture notes); QUIZ #3 (QUIZ3_solutions)
readings: lecture notes, solved problems
Week 14 (11/21, Thanksgiving): Cytoskeleton, Einstein polymer (lecture notes);
readings: lecture notes, solved problems
Week 15 (11/28, 11/30): Force generation by filaments (lecture notes), Measuring motor protein forces (lecture notes);
readings: Mehta review, Vale paper, Stewart paper, solved problems
Week 16 (12/5, 12/7) HW4 (due in one week on Friday 11/9 by 3 pm): Polyelectrolytes, coacervates, gels (lecture notes)
readings: lecture notes


Week 17  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 16th

Quiz 4: Thursday, Final exam time ?


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 the update shown in class), 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 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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