APH 161

General Information


Physical Biology of the Cell

Physical Biology of the Cell (2nd ed)
by Phillips, Kondev, Theriot and Garcia

ISBN: 0815344503

Cell Biology by the Numbers
by Ron Milo and Rob Phillips

This book is in the final stages of completion and will be published at the end of 2015. You can find the most current draft here.  Several readings will be assigned from this book as part of the homework.


Tentative Syllabus

Monday, Jan. 5 Lecture 1: Course introduction, biological numeracy and discoveries about the living world, A feeling for the numbers part 1. E. coli by the numbers. Streetfighting Mathematics

The End of Theory: The Data Deluge Makes the Scientific Method Obsolete

Nature 1902
Wednesday, Jan. 7 Lecture 2: A feeling for the numbers part 2. Rates in the central dogma, diffusion and diffusive time scales, flies by the numbers. Superresolution Imaging of Ribosomes and RNA Polymerase in live E. coli cells

Drosophila Brainbow

Li et. al. 2014

Gregor et. al. 2007
HW1 out
Friday, Jan. 9 Lecture 3: Wetware! Biological computation. Examples including enzymes, ion channels and transcription factors. Statistical mechanics of binding.
Monday, Jan. 12 Lecture 4: Immunological computation. Chemotaxis part 1.
Wednesday, Jan. 14 Lecture 5: Chemotaxis part 2. HW1 due HW2 out
Friday, Jan. 16 Lecture 6: The Monod-Wyman-Changeux model and enzyme action.
Monday, Jan. 19 no class, MLK day
Wednesday, Jan. 21 Lecture 7: MWC enzymes, bioelectricity and light. Cell signaling and statistical mechanics. Bray ; Sourjik HW2 due HW3 out
Friday, Jan. 23 Lecture 8: Introduction to gene expression.
Monday, Jan. 26 Lecture 9: Gene expression in bacteria
Wednesday, Jan. 28 Lecture 10: Gene expression in development of multicellular organisms HW3 due HW4 out
Friday, Jan. 30 Lecture 11: Biological order in one-, two- and three-dimension. Biological polymerization and biological fidelity. Howard,Grill,Bois review
Monday, Feb. 2 no class, RP out of town
Wednesday, Feb. 4 no class, RP out of town HW4 due HW5 out
Friday, Feb. 6 no class, RP out of town
Monday, Feb. 9 Lecture 12: The cytoskeleton, part 1.
Wednesday, Feb. 11 Lecture 13: The cytoskeleton, part 2. How are cytoskeletal lengths controlled. Frank HW5 due HW6 out
Friday, Feb. 13 no class, RP out of town
Monday, Feb. 16 no class, President's Day
Wednesday, Feb. 18 Lecture 14: chromosome geography and ordering the DNA. HW6 due No HW this week
Friday, Feb. 20 Lecture 15: organization at membranes
Monday, Feb. 23 Lecture 16: organization of cells - organellar structure and size control, multicellular structures
Wednesday, Feb. 25 Lecture 17: Special Lecture: Adventure in Science HW7 out
Thursday, Feb. 26 Lecture 18: Thursday evening, pizza dinner and make up lecture - special lecture on evolution and population genetics, physical biology at larger space and time scales. Is the earth old? Is the earth big?
Friday, Feb. 27 Lecture 19: Last day of class. Course summary and what we want you to remember. Hologenomic Basis
Friday, Mar. 6 HW7 due