Here you will find papers, vignettes, and other resources mentioned in the class. They will be added as the course progresses.
Vignettes
PBOC Youtube channel This series of vignettes expands on topics we will cover in the course. Specific suggestions for vignettes to watch will be given during the course.
| Date | Topic |
|---|
In-Class Readings
Reading assignments
Cell Biology by the Numbers by Milo & Phillips. This book describes many of the estimates we will do in class and is a useful resource for finding key numbers that characterize biological phenomena.
Street Fighting Mathematics by Sanjoy Mahajan.
Day 1 (April 20th)
Torque dependent remodelling of the bacterial flagellar motor by Wadhwa, Phillips, Berg PNAS 2019.
Fundamental limits on the rate of bacterial growth and their influence on proteomic composition by Belliveau, et al. Cell Systems 2021. This paper goes into more detail on the cell growth limits we discussed in class.
Day 2 (April 21st)
The bioenergetic costs of a gene by Marinov & Lynch PNAS 2015.
Models in biology: ‘accurate descriptions of our pathetic thinking’ by Jeremy Gunawardena BMC Biology 2014.
Day 3 (April 22nd)
Theory in Biology: Figure 1 or Figure 7? by Rob Phillips CellPress 2015.
Day 4 (April 23rd)
Intraflagellar transport balances continuous turnover of outer doublet microtubules: implications for flagella length control by Marshall and Rosenbaum JCB 2001.
Organelle growth control through limiting pools of cytoplasmic components by Goehring and Hyman Current Biology 2012.
Dynamics of the IFT machinery at the ciliary tip by Chien et al.2017.
Synthetic reconstruction of the hunchback promoter specifies the role of Bicoid, Zelda, and Hunchback in the dynamics of its transcription by Fernandes et al. eLife 2022.
The time needed to set up a gradient: Detailed calculations by Munro and Crick Symp Soc Exp Bio 1971.
Day 5 (April 25th)
What I’d like to know about 2105 by David Mermin2005.
Key biology you should have learned in physics class: Using ideal-gas mixtures to understand biomolecular machines by Daniel M. Zuckerman American Journal of Physics 2020.
Kinetic proofreading: A new mechanism for reducing errors in biosynthetic processes requiring high specificity by J. J. Hopfield PNAS 1974.
Kinetic proofreading of enzyme discrimination by Jacques Ninio Biochimie 1975.
Day 7 (April 27th)
The birth of the operon by Francois Jacob Science 2011.
Molecular ‘vitalism’ by Kirschner, Gerhart, and Mitchison Cell 2000.
miscellaneous
Jane’s notes – stat mech and diffusion
Jane’s notes – poisson distribution
Here are links to homeworks involving order of magnitude estimates: BE161: Homework 1, BE161: Homework 2.