PHY498/598 Topics in Biophysics

Timothy Newman
and guest lecturers

Fall Semester 2006

MWF 11:40:12:30 PSF-462

an overview of modern biology for physicists
(and colleagues from other quantitative disciplines)

Rough outline of lecture course:

Introductory topics
A. What is life?, evolution theory, genetics (6 lectures)
B. Basic concepts of thermodynamics, statistical mechanics, and stochastic processes (3 lectures)
C. Overview of cell biology, both procaryotic and eucaryotic (3 lectures)

Progression through biological scales
D1. (3 lectures) Biochemistry and cell metabolism
D2. (4 lectures) Proteins
D3. (2 lectures) DNA, structure and replication
D4. (3 lectures) Transcription and translation
D5. (3 lectures) Cell membrane
D6. (4 lectures) Mitochondria, cytoskeleton, cell cycle
D7. (5 lectures) "Multicellular" biology
D8. (2 lectures) Population biology

D1-D4 will be covered in detail. D5-D8 will focus on the main points.

Recommended texts:

Main text: Molecular Biology of the Cell (4th edition), Bruce Alberts et al (Garland Publishing)

Some additional recommendations:
For A, Maynard Smith (Problems of biology) and Mayr (This is evolution)
For B, Adkins (Equilibrium thermodynamics), Mandl (Statistical physics), and Reichl (A modern course in statistical physics)
For C, Alberts et al (Molecular biology of the cell, 3rd or 4th edition), chapter 1
For D1-6, Alberts et al (Ch. 2-18)
For D7, Alberts et al (Ch. 19-21) and Wolpert et al (Principles of development)
For D8, Roughgarden (Theory of population genetics and evolutionary ecology)
Also of interest are two recent biophysics textbooks:
"Biological physics: energy, information, life" by Philip Nelson
"Biophysics: an introduction" by Rodney Cotterill

Projected calendar of lectures (in MWF groups):

(class use only) indicates a lecture with copyrighted images - these webpages may only be used for students enrolled in PHY 498/598

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8/21 A(L1) What is life?
8/23 A(L2) Darwin's theory of evolution
8/25 A(L3) Darwin's theory of evolution (cont) (Glossary of terms used in discussing evolution and genetics)

8/28 A(L3) Mendelian genetics
8/30 A(L3) Mendelian genetics (cont)
9/01 A(L3) Mendelian genetics (cont)

9/04 No Class (Labor Day)
9/06 B(L1) Thermodynamics and equilibrium/non-equilibrium statistical mechanics
9/08 B(L2) Random walks and stochastic processes

9/11 B(L2) Random walks and stochastic processes (continued)
9/13 C(L1) Origins of life - the "prebiotic soup"
9/15 C(L2) Basics of procaryotic cells

9/18 C(L3) Basics of eucaryotic cells
9/20 C(L3) Basics of eucaryotic cells (continued)
9/22 Class presentations (Jen Glass, Tyler Glembo, and Hermann Azemtsa Donfack)

9/25 D1 Introduction to biochemistry and metabolism (class use only)
9/27 D1 Introduction to biochemistry and metabolism (continued)
9/29 D1 Introduction to biochemistry and metabolism (continued)

10/02 D2 Proteins - structure (class use only)
10/04 D2 Proteins - structure (continued)
10/06 D2 Proteins - function (class use only)

10/09 D2 Proteins - function (continued)
10/11 D3 DNA - structure and storage (class use only)
10/13 D3 DNA - replication (class use only)

10/16 D4 Transcription (class use only)
10/18 D4 Translation (class use only)
10/20 D4 Protein folding (class use only)

10/23 D5 Membrane structure (class use only)
10/25 D5 Membrane transport (class use only)
10/27 D5 Membrane transport (continued)

10/30 D6 Mitochondria (class use only)
11/01 D6 Cytoskeleton (class use only)
11/03 D6 Cytoskeleton (continued)

11/06 D6 Cell Cycle (class use only)
11/08 D6 Cell Cycle (continued)
11/10 No class (Veteran's Day)

11/13 Guest lecture: Prof. John Nagy, Department of Biology, SCC: Cancer biology
11/15 D7 Germ cells (class use only)
11/17 D7 Fertilization (class use only)

11/20 Guest lecture: Dr. Felisa Wolfe-Simon, School of Earth and Space Exploration, ASU: Marine phytoplankton
11/22 D7 Developmental biology (class use only)
11/24 No class (Thanksgiving)

11/27 Guest lecture: Prof. Paul Davies, Institute for Fundamental Science, ASU: Early life
11/29 D7 Developmental biology (cont)
12/01 D8 Population biology

12/04 D8 Population biology (cont)

Assignments

There will be two research assignments. Grades will be determined based on the quality of the written presentations associated with these assignments.

Assignment 1: Transitions during the evolution of early life on Earth

Assignment 2: Dynamics of tumor growth, invasion, and metastasis

For more information about the class please contact Timothy Newman