PHY498/598 Topics in Biophysics

Timothy Newman

Fall Semester 2007

MWF 11:40:12:30 PSF-462

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

Note: for 2007 only, this class will be taught via a weblink
Depending on the number of students enrolled, the classroom setting may not be used
More information will be available soon

Rough outline of lecture course:

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

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

Lecture Notes:
(The lecture schedule from 2006 is available here)

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

If using Microsoft Internet Explorer, in order to view these notes with correct fonts, select View - Encoding - Western European

A1 What is life?
A2 Darwin's theory of evolution (Glossary of terms used in discussing evolution and genetics)
A3 Mendelian genetics

B1 Thermodynamics and equilibrium/non-equilibrium statistical mechanics
B2 Random walks and stochastic processes

C1 Origins of life - the "prebiotic soup"
C2 Basics of procaryotic cells
C3 Basics of eucaryotic cells

D1 Introduction to biochemistry and metabolism (class use only)

D2 Proteins - structure (class use only)
D2 Proteins - function (class use only)

D3 DNA - structure and storage (class use only)
D3 DNA - replication (class use only)

D4 Transcription (class use only)
D4 Translation (class use only)
D4 Protein folding (class use only)

D5 Membrane structure (class use only)
D5 Membrane transport (class use only)

D6 Mitochondria (class use only)
D6 Cytoskeleton (class use only)
D6 Cell Cycle (class use only)

D7 Germ cells (class use only)
D7 Fertilization (class use only)
D7 Developmental biology (class use only)

D8 Population biology

Assignments

There will be two research assignments.

Assignment 1:
Assignment 2:

For more information about the class please contact Timothy Newman