RUTGERS UNIVERSITY

Department of Physics and Astronomy

 

750:567 Physics of Living Matter (3 credits), Spring 2018

 

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 and Friday at 3:20-4:40 p.m.

Class Location: ARC-205

 

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% 

 

 

 

 

 

 

 

 

Course Schedule (Spring 2018)

          Lecture

Week

Topic

Reading

1

week 1

Intro to cell molecular / cellular biology I

Ch 2

2

Intro to cell molecular / cellular biology II

Ch 2

3

week 2

Intro to cell molecular / cellular biology III / Molecular Dance I

Ch 3.1

4

Molecular Dance II

Ch 3.2-3

5

week 3

Randlom Walks I

Ch 4.1-3

6

Random Walks II

Ch 4.4-6

7

week 4

Random Walks III / Hydrodynamics at low Reynolds-Number I

Ch 5.1

8

Hydrodynamics at low Reynolds-Number II

Ch 5.2

9

week 5

Hydrodynamics at low Reynolds-Number III

Ch 5.3

10

Entropy, Temperature, and Free Energy I

Ch 6.1-3

11

week 6

Entropy, Temperature, and Free Energy II

Ch 6.4-6

12

Entropy, Temperature, and Free Energy II / Entropic Force I

Ch 7.1

13

week 7

Entropic Force II

Ch 7.2-3

 

14

Entropic Force III

Ch 7.4-5

15

week 8

Chemical Forces and Self-Assembly  I

Ch 8.1-3

16

Chemical Forces and Self-Assembly  II

Ch 8.4-6

17

week 9

Chemical Force III / Cooperative Transitions in Macromolecules I

Ch 9.1

18

Cooperative Transitions in Macromolecules II

Ch 9.2 - 9.5.2

19

week 10

Cooperative Transitions in Macromolecules III

Ch 9.5.3 - 9.6

20

Enzymes and Molecular Machines I

Ch 10.1-2

21

week 11

Enzymes and Molecular Machines II

Ch 10.3

22

Enzymes and Molecular Machines III

Ch 10.4

23

week 12

Machines in Membranes I

Ch 11.1-2

24

Machines in Membranes II

Ch 11.3-4

25

week 13

Biophysical Methods I

25

Biophysical Methods II

27

week 14

Final Presentation

28

Final Presentation