General Information


Textbooks

Physical Biology of the Cell

Physical Biology of the Cell
by Phillips, Kondev, Theriot, and Garcia

ISBN: 0815341636

Guesstimation: Solving the World's Problems on the Back of a Cocktail Napkin

by Weinstein and Adam

ISBN: 0691129495



 

Syllabus


DATE TOPIC

RELEVANT READINGS (papers are linked below and can also be found on the Files page)

Monday, 8/5 Course introduction and a feeling for the numbers in biology. Introduction to Matlab

Cell SnapShot

Feeling for the numbers in Biology

Tuesday, 8/6 A feeling for the numbers: rates and the central dogma.

Molecular brakes in DNA replication

rRNA transcription rate

Wednesday, 8/7 Diffusion time scales. An introduction to statistical mechanics.

Protein transport in axons

First exposure to stat mech in Biology

Thursday, 8/8 Using statistical mechanics with states and weights. Simple ligand-receptor binding. Thermodynamics of simple repression.

Transcriptional regulation by the numbers: models

Dissection of simple repression

Friday, 8/9 Genetic switches. The spring constant of an optical trap.
Monday, 8/12 Pattern formation in fly embryos.

Bicoid dosage in fly patterning

The clock-wavefront in developing zebrafish

Diffusion and scaling during embryonic pattern formation

Tuesday, 8/13 The physics of genome management - DNA packing in viruses and cells.

DNA-encoded nucleosome organization

Mechanism of protein access to specific DNA sequences in chromatin

Packaging DNA in viruses

Wednesday, 8/14 Random walks, polymer physics, and the cytoskeleton.
Thursday, 8/15 Dynamic control of microtubule length and concluding thoughts.

Kinesin depolymerizes microtubules

Length dependence of microtubule depolymerization

 

Assignments