University of Utah
Fall Semester 2017
Prof. Vladimir Hlady
Office Hours: By appoint. in Rm. 108A BPRB, or immediately after class.
e-mail: firstname.lastname@example.org 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.
Ms. Hannah Northrup, (e-mail: email@example.com)
Lecture: Tues. & Thurs. 12:25-1:45 pm. Room HSEB 5100B
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):
readings: Chapter 32 from KAD
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
readings: Ch 28 from KAD, solved problems
Week 8 (10/8 - 10/15): Fall break
readings: lecture notes, 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)
Lecture not covered in 2017: Polyelectrolytes, coacervates, gels (lecture notes)
readings: lecture notes
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.
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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