RUTGERS UNIVERSITY
Department of Physics and Astronomy
750:567 Physics of Living Matter (3 credits), Spring
2019
Professor: Sang-Hyuk Lee
Office
Location: Center for Integrative Proteomics Research (CIPR) 308A
Office
Phone: (848) 445 5286
Email:
shlee@physics.rutgers.edu
Class Timings: Tuesday
*4:00-5:20pm and Friday at 12:00-1:20 pm (*revised schedule)
Class Location: Proteomics
306 (revised classroom)
Course Description: This course is designed to
introduce biophysics to upper-level physics undergraduate and graduate students.
The course will start with a review of big ideas in modern molecular/cellular
biology to familiarize physics students with the language used in life science.
Thereafter, basic physical principles underling structure and dynamics of
macromolecules, such as diffusion, random walks, low Reynolds-number
hydrodynamics, entropic force, and osmotic pressure, will be discussed in the
light of soft matter physics. Life cannot persist without constant mechanical
work of numerous molecular machines inside cells. The working principles of
these molecular machines will be studied in more detail through enzyme kinetics
and mechano-chemical coupling. Recent developments in
biophysical methods that have enabled testing of many physical models in
biology will be covered as well.
TEXTBOOK (required for this course)
P. Nelson, Biological
Physics: 1st Ed., Freeman (2004).
SUPPLEMENTARY TEXTS
B. Alberts and D. Bray, The Essential Cell Biology, 4th
Ed., Garland Science (2013).
B. Alberts and A. Johnson, The Moleculear
Biology of the Cell, 6th Ed (2014).
R. Phillips and J. Kondev, Physical Biology of the Cell, 2nd
Ed (2012).
PREREQUISITES
Linear Algebra, Differential Equations, Thermodynamic, Statistical
Mechanics and Classical Physics (at the junior level)
GRADING POLICY
The course grade will be determined as follows:
Attendance: 30%
Homework: 30%
Research
Paper: 30%
Final
Presentation: 10%
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Course Schedule (Spring
2019) |
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Lecture |
Week |
Topic |
Reading
(Nelson) |
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|
1 |
week 1 |
Intro
to cell molecular / cellular biology I |
Ch 2 |
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2 |
Intro
to cell molecular / cellular biology II |
Ch 2 |
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|
3 |
week 2 |
Intro
to cell molecular / cellular biology III / Molecular Dance I |
Ch 3.1 |
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|
4 |
Molecular
Dance II |
Ch 3.2-3 |
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|
5 |
week 3 |
Randlom Walks I |
Ch 4.1-3 |
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6 |
Random
Walks II |
Ch 4.4-6 |
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|
7 |
week 4 |
Random
Walks III / Hydrodynamics at low Reynolds-Number I |
Ch 5.1 |
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|
8 |
Hydrodynamics
at low Reynolds-Number II |
Ch 5.2 |
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|
9 |
week 5 |
Hydrodynamics
at low Reynolds-Number III |
Ch 5.3 |
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|
10 |
Entropy,
Temperature, and Free Energy I |
Ch 6.1-3 |
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|
11 |
week 6 |
Entropy,
Temperature, and Free Energy II |
Ch 6.4-6 |
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|
12 |
Entropy,
Temperature, and Free Energy II / Entropic Force I |
Ch 7.1 |
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|
13 |
week 7 |
Entropic
Force II |
Ch 7.2-3 |
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|
14 |
Entropic
Force III |
Ch 7.4-5 |
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|
15 |
week 8 |
Chemical
Forces and Self-Assembly I |
Ch 8.1-3 |
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|
16 |
Chemical
Forces and Self-Assembly II |
Ch 8.4-6 |
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|
17 |
week 9 |
Chemical
Force III / Cooperative Transitions in Macromolecules I |
Ch 9.1 |
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18 |
Cooperative
Transitions in Macromolecules II |
Ch 9.2 -
9.5.2 |
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|
19 |
week 10 |
Cooperative
Transitions in Macromolecules III |
Ch 9.5.3
- 9.6 |
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|
20 |
Enzymes
and Molecular Machines I |
Ch 10.1-2 |
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|
21 |
week 11 |
Enzymes
and Molecular Machines II |
Ch 10.3 |
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|
22 |
Enzymes
and Molecular Machines III |
Ch 10.4 |
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23 |
week 12 |
Machines
in Membranes I |
Ch 11.1-2 |
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24 |
Machines
in Membranes II |
Ch 11.3-4 |
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25 |
week 13 |
Biophysical
Methods I |
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25 |
Biophysical
Methods II |
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27 |
week 14 |
Final
Presentation |
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28 |
Final
Presentation |
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