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.

Weeks 4-5

Recommended Reading:
You can get an introduction to these ideas in Hill's Free Energy Transduction book. I have also extensively consulted Hong Qian's review here. and notes below.
There will be Jounral Club on 2/28 on Noise in Gene expression . Please also read the SI.
Notes: Lecture 6: Free Energy Transduction and temporary scanned notes.
Lecture 7: Basic Probability
Homework #3: Due all HW problems in Lectures 6, all exercises in Lecture 7 Due March 5th.

Weeks 8-9

Recommended Reading:
Please read this chapter from Anirvan's book Chapter. Please use this notebook for class on birth-death processes. Please also look at this wonderful notebook/discussion on implementing the Gillespie algorithm and how to optimize this in Python.

Notes: Lecture 9: Random walks, Birth Death Processes, and the Gillespie Algorithm

Homework #4: Due all HW problems in Lecture 9, all exercises in Birth-death notebook Due April 2nd.

Weeks 10

Recommended Reading:
Please read this chapter from Anirvan's book Chapter. We will be doing Journal Club on these papers Paper 1 and Paper 2. Please also read SI: SI1 and SI2. The powerpoint summarizing experiments is here pdf

Notes: Lecture 10: Single-molecule transcription

Weeks 11-12

Recommended Reading:
There are readings scattered through out notes. Please check them. For next week Tuesday 4/16, please read this short review on chemotaxis to get some biological background. The main discussion will be on these papers on perfect adaptation: Barkai and Leibler Nature 1997, a short experimental followup Alon et al , and a simple molecular explanation Keymer et al PNAS 2006.

Notes: Lecture 12: Berg-Purcell Revisited

Weeks 13

Recommended Reading:
Here is a list of papers on the Motor I used to make lecture Motor Papers. I also used the discussion of the Nerst potential from Chapter 4 or Phil Nelson's Biophysics book and the discussion of thermal rachets from Chapter 9.

Notes: Lecture 13: Bacterial Motor

Final Homework:This is comprehensive HW instead of exam and project Final HW.Due Wed. May 8th.