University of Utah
Fall Semester 2010
Instructor:
Prof. Vladimir Hlady
Office Hours: Immediately after class or by appoint. 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 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: ?
Lecture: Tues. & Thurs. 12:25-1:45 pm. Room HSEB 3515C
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 the 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):
Week 1 (8/24, 8/26): Proteins and polymers (lecture notes: part A, part B, part C_revised)
readings: K. Dill's paper, D. Chandler's paper
Week 2 (8/31, 9/2): Molecular and mechanical forces (lecture notes)
readings: Chapters 2 and 3 from JH
Week 3 (9/7, 9/9) HW1: Macromolecular conformations (lecture notes)
readings: Chapter 32 from KAD
Week 4 (9/14, 9/16) HW1sol: Measuring molecular forces (lecture notes); QUIZ #1 (QUIZ1_solutions)
readings: Neuman_review, Fernandez_titin, Guntherodt_DNA
Week 5 (9/21, 9/23): Diffusion (lecture notes) and Brownian motion (lecture notes + extras)
readings: Chapter 4 from PN, lecture notes, solved problems
Week 6 (9/28, 9/30): Chemical reactions and association kinetics (lecture notes)
readings: lecture notes, solved problems
Week 7 (10/5, 10/7-out of town) HW2: Polynomials for ligand binding equilibria (lecture notes)
readings: Ch 28 from KAD, solved problems
Week 8 (10/12, 10/14): Fall break
Week 9 (10/19, 10/21) HW2sol: Measuring molecular diffusion in 2D and 3D (lecture notes); QUIZ #2 (QUIZ2_solutions)
readings: Schmidt SMD, Rigler FCS, Schwille FCS review
Week 10 (10/26, 10/28): Biological membranes and proteins (lecture notes); Carrier mediated transport (lecture notes)
readings: lecture notes, solved problems
Week 11 (11/2, 11/4): Osmosis, crowding (lecture notes); cytoskeleton, Einstein polymer (lecture notes), additional pages
readings: lecture notes, solved problems
Week 12 (11/9, 11/11) HW3: Force generation by filaments (lecture notes)
readings: lecture notes
Week 13 (11/16, 11/18) HW3sol: Measuring motor protein forces (lecture notes); QUIZ #3 (QUIZ3_solutions)
readings: Vale paper, Stewart paper, Mehta review on single molecule mechanics
Week 14 (11/23, Thanksgiving): Electrical properties of molecules (lecture notes, and revised and expanded lecture notes)
readings: chapter 20 KAD, solved problems
Week 15 (11/30, 12/2): Polyelectrolytes, coacervates, gels (lecture notes)
readings: lecture notes
Week 16 (12/7, 12/9) HW4: Ion transport (lecture notes); Ion channels (lecture notes)
readings: lecture notes, chapter 17 PoBC, or 12 PN, solved problems
Week 17 HW4sol: Final exam QUIZ#4 (QUIZ4_solutions)(extra Q4 solutions)
Each homework will be posted on-line on Tuesday and will be due in class next Tuesday
Quiz Schedule -
Quiz 1: Thursday, September 9th
Quiz 2: Thursday, October 21st
Quiz 3: Thursday, November 18th
Quiz 4: Friday, December 17th, 10:30 am – 12:30 pm
Grading: 4 Homework assignments 30 %
Protein paper 20 %
3 Quizes and Final exam 50 %
Protein paper: Definition of the assignment, here is an example of the report.
For the first part of web-based predictions, click here, summary of 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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