As the course progresses, we will post links to treadings relevant to what we've talked about in class

Useful links

Physical Biology of the Cell @ Caltech Recorded lectures and videos from the Caltech offering.
Physical Biology of the Cell @ Berkeley YouTube Channel Compilation of recorded lectures on Physical Biology.
Introduction to Data Analysis in the Biological Sciences @ Caltech (BE/Bi 103) Comprehensive course on Python and data analysis in the biological sciences (Justin Bois).
W3Schools Python Tutorial Quick Python refresher / on-ramp for beginners.

Daily Suggested Reading

Physical Biology of the Cell, 2nd Edition by Phillips, R. et al. (2012) Our course will be loosely based on this textbook. Note that we are actively working on the 3rd edition and may share draft chapters as we visit topics in lecture.
A Student’s Guide to Python for Physical Modeling: Updated Edition by Kinder, J. and Nelson, P. (2018) A great introduction to programming in Python; useful throughout the course.
Molecular Biology of the Cell by Alberts, B. et al. (2014) Useful refresher for core cell biology.
Cell Biology by the Numbers by Milo, R. and Phillips, R. (2015) A reference source for biological numeracy. Companion site: book.bionumbers.org.
Street-Fighting Mathematics: The Art of Educated Guessing and Opportunistic Problem Solving by Mahajan, S. (2010) Fantastic resource for estimation and approximation.
Guesstimation: Solving the World’s Problems on the Back of a Cocktail Napkin by Weinstein, L. and Adam, J. A. (2008) More estimation practice and philosophy.

What is the total number of protein molecules per cell volume? A call to rethink some published values by Ron Milo (2013) This paper is one of the most systematic places to examine the question of how many proteins are found per micron cubed of cytoplasmic material. Ron’s table 1 summarizes the situation for a number of different cell types across the tree of life.
The quantitative and condition-dependent Escherichia coli proteome by Alexander Schmidt, Karl Kochanowski, Silke Vedelaar, Erik Ahrné, Benjamin Volkmer, Luciano Callipo, Kèvin Knoops, Manuel Bauer, Ruedi Aebersold, and Matthias Heinemann (2016) This paper describes a mass spectrometry study of the protein contents of E. coli for 22 different growth conditions. Their results are a gold-standard to compare our estimates of the cell as a bag of proteins to.
Fundamental limits on the rate of bacterial growth and their influence on proteomic composition by Nathan M. Belliveau, Griffin Chure, Christina L. Hueschen, Hernan G. Garcia, Jane Kondev, Daniel S. Fisher, Julie A. Theriot, and Rob Phillips (2021) This paper brings together proteomic studies of E. coli from a number of different sources and attempts to carefully unify the data under many growth conditions with simple estimates like those to be carried out in class.

Duration of urination does not change with body size by Patricia J. Yang, Jonathan Pham, Jerome Choo, and David L. Hu (2014) Mammals heavier than ~3 kg have an approximately constant urination time (~21 ± 13 s): flow rate is gravity-dominated so T ≈ V/Q. For smaller mammals, capillary and viscous forces complicate the scaling.
On Biomolecular Layers of lipoids on the Chromocytes of the Blood by E. Gorter, F. Grendel. (1924) Found the height of biolayers of red blood cells and lipids.

Ordered Phases of DNA in Vivo and in Vitro by F. Livolant (1991) DNA in packed as spirals in macrophages.
Entangled polymers by Pierre-Gilles de Gennes (1983) About the entanglment of polymers. When the DNA forms knots.
A universal polymer signature in Hi-C resolves cohesin loop density and supports monomeric extrusion by K. Polovnikov, D. Starkov (2025)

Models in biology; ‘accurate descriptions of our pathetic thinking’ by Jeremy Gunawardena (2014) An excellent piece touching on the utility of models in biology.

A First Exposure to Statistical Mechanics for Life Scientists by Hernan G. Garcia, Jane Kondev, Nigel Orme, Julie A. Theriot, Rob Phillips (2018) Great introduction to Statistical Mechanics.
Polymer physics of intracellular phase transitions by Clifford P. Brangwynne, Peter Tompa and Rohit V. Pappu (2015) Phase transition in biology.