PY 571 Biophysics,   Spring 2019


This is the website for PY 571, Biological Physics. This website will be updated with lecture notes and homework assignments.

General course information:
We meet TH 11-12:20 in SCI 328.

Syllabus pdf .

Textbooks worth reading:

Bill Bialek's Biophyics: Searching for Principles. A draft of this is available from his website here. The finished book is well worth owning.

Phil Nelson's Biological Physics

Rob Phillips, Jane Kondev, Julie Theriot, Hernan Garcia. Physical Biology of the Cell

Rob Phillips, Ron Milo. Cell Biology by the Numbers

Anirvan Sengupta Modeling Molecular Networks (draft of book is available here) .

Readings, Homeworks and handouts:

Weeks 1

Recommended Reading:
Berg + Purcell, Physics of Chemoreception .
Von Neumann Hixon Symposium
Schronginder's What is Life.
A Molecular Biology crash course/refresher from Anirvan Sengupta's wonderful forthecoming book "Modeling Molecular Networks" (I am also a co-author but did not do much)

Code: We will be using the followingPython Notebook which you can download from Jake VanderPlas' Pythonic Perambulations blog

Notes: Lecture 1: Asking Big Questions

Homework #1: See end of Notes for HW. Due Jan 31st.

Weeks 2

Recommended Reading:
There will be a journal club on Growth Laws and see short review here.
Any elementary thermodynamics books and in the notes based on this chapter.
Notes: Lecture 2: Growth Laws, Lecture 3: Primer on Thermodynamics

Weeks 3

Recommended Reading:
You can get an introduction to kinetics in the Chapter 2 of Sengupta here (please do not circulate) and notes below.
There will be Jounral Club on Hopfield's Classical KPR paper
Notes: Lecture 4: Enyzme kinetics: from Michaelis-Menten to Thermodynamics, Lecture 5: Kinetic Proof Reading
Homework #2: Due all HW problems in Lectures 3, all problems in Lecture 4 including HW, and HW problems in Lecture 5. Due Feb. 19th.