University of Utah
Fall Semester 2019
Instructors:
Profs. Vladimir Hlady and Tamara Bidone
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 solutions of biomedical engineering problems.
TA/Grader:
Mr. Douglas Steinhauff, Ms. Annie White
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)
Selected readings from these books are available on the course website (see the reading links below):
Week 1 (8/20, 8/22): Proteins and polymers (lecture notes: part A, part B, part C)
readings: K. Dill's paper, D. Chandler's paper
Week 2 (8/27, 8/29): Molecular mechanics, elasticity and viscosity (lecture notes: part A, part B)
readings: Chapters 2 and Chapter 3 from JH
Week 3 (9/3, 9/5) HW1; Macromolecular conformations (lecture notes)
readings: Chapter 32 from KAD
Week 4 (9/10, 9/12) HW1solutions; Measuring molecular forces (lecture notes); QUIZ #1 (QUIZ1_solutions)
readings: Neuman_review, Fernandez_titin, Guntherodt_DNA
Week 5 (9/17, 9/19): 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 (9/24, 9/26): Chemical reactions, forces and association kinetics (lecture notes)
readings: lecture notes, extra pages
Week 7 (10/1, 10/3) HW2: Polynomials for ligand binding equilibria (lecture notes), Extra lecture notes (extra notes)
readings: Ch 28 from KAD, solved problems
Week 8 (10/6 - 10/13): Fall break
Week 9 (10/15, 10/16) 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 (10/22, 10/24): Biological membranes and receptors (lecture notes); Carrier mediated transport (lecture notes)
readings: lecture notes, solved problems
Week 11 (10/29, 10/31): Electrical properties of molecules (lecture notes); Ion at dielectric interface (extra page)
readings: chapter 20 KAD, solved problems
Week 12 (11/5, 11/7) HW3 Ion transport (lecture notes)
readings: lecture notes, chapter 17 PoBC, or 12 PN, solved problems
Week 13 (11/12, 11/14) HW3solutions: Ion channels (lecture notes) Updated lecture notes (lecture notes) QUIZ #3 (QUIZ3_solutions)
readings: lecture notes, chapter 17 PoBC, or 12 PN
Week 14 (11/19, 11/21): Osmotic pressure, crowding (lecture notes) Cytoskeleton, Einstein polymer (lecture notes)
readings: lecture notes, solved problems
Week 15 (11/26, Thanksgiving): Force generation by filaments (lecture notes)
readings: lecture notes
Week 16 (12/3, 12/5) HW4 (due on Tuesday, 12/10 by 3 pm): Motor Forces (lecture notes);
readings: lecture notes
Week 17 (12/9 - 12/13) 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.
Quiz Schedule -
Quiz 1: Thursday, September 12th
Quiz 2: Thursday, October 17th
Quiz 3: Thursday, November 14th
Quiz 4: Thursday, December 12th, 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 assignments click here: Assignment Update
Your protein paper is due at latest at the time of the final exam (12/10/19, 10:30 am).
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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