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This is the website for PY 571, Biological Physics. This website will be updated with lecture notes and homework assignments. |
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General course information: |
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Syllabus pdf . |
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Textbooks worth reading: |
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Readings, Homeworks and handouts: |
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Weeks 1
Required Reading: Von Neumann Hixon Symposium Read section "The Concept of Complication: Self-Reproduction" p.312-318 (but worth reading whole thing) Recommended Reading: 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 Slides on basics of transcription, translation, and replication. Movies/animations are from CSHL DNA learning center. Homework #1: See end of Notes for HW. Due Thursday Feb 4th. |
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Weeks 2 This week we will be thinking about reproduction and reading papers on recently discovered "Growth Laws" as well introducing relationship between chemical kinetics and thermodynamics. Recommended Reading: There will be a journal club on Tuesday Feb. 2nd on this paper Growth Laws . For context, see this very short review here. There is also background reading on kinetics and thermodynamics from Chapter 2 of Sengupta here (please do not circulate) and these notes on thermodynamcs:Lecture 3: Primer on Thermodynamics Notes: , Lecture 2: Growth Laws Worksheet: Lecture 4: Enyzme kinetics: from Michaelis-Menten to Thermodynamics. |
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Weeks 3
Worksheet: Continue Lecture 4: Enyzme kinetics: from Michaelis-Menten to Thermodynamics. Journal Club Paper:There will be Journal Club on Hopfield's Classical KPR paper on Thursday Feb 11th. Notes: Lecture 5: Kinetic Proof Reading (Not written yet except HW) Homework #2: Do all HW problems in Lecture 1.5: Getting a feel for BioNumbers (ignore group +individual prompts) and all problems in Lecture 4 including HW. Due Tuesday Feb. 16th. |
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Weeks 4-5
Notes: Lecture 6: Free Energy Transduction . Fixed and expanded. Worksheet: Understanding Molecular Machines. Do this in class. Journal Club on February 25th. Start by watching this 1 minute video on microtubules and cytoskeletons and looking at Wikipedia entry on kinesins . Then, read this amazing experimental paper from 1994 on the molecular motors by Svoboda and Steven Block: Svoboda et al. This paper is among the first really impressive experimental demonstration of optical traps -- something that has now become standard in many physics fields. The correspondingtheory paper by David Huse and Stan Leibler used to interpret experiments is found here. Readings: Hong Qian's review and our reviewon energy consumption and information processing in biochemical networks. This review on molecular motor summarizes the current state of the field and open questions. You can also read Chapter 10 of Phil Nelson's Biological Physics book. Homework #3 Do all HW problems in Lecture 5: Kinetic Proof Reading and Lecture 6: Free Energy Transduction Due Tuesday March 2nd. |
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Weeks 6
Notes: Lecture 7: Polymers . New. Readings: 2012 Boulder Summer School lectures, Levitov's notes on polymers, Chapter 1 of De Genne's Scaling Concepts in Polymer Physics, Intro. to Flory theory. |
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Weeks 6
Notes: Lecture 7: Polymers . New. Readings: 2012 Boulder Summer School lectures, Levitov's notes on polymers, Chapter 1 of De Genne's Scaling Concepts in Polymer Physics, Intro. to Flory theory. |
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Weeks 7
Notes: Lecture 8: Neuroscience (will add powerpoint and handwritten notes soon at this link) Readings: Chapter 1 of Dynamical Systems in Neuroscience and Section 5.2 of Bialek's Biophysics Boook Homework #4 Read sections 9.2-9.5 of this early draft of Nelson's biophysics book (worth owning the final version if you have any interest in biophysics!) Do HW problems 9.5 and 9.6. Due Tuesday March 30th. |
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Weeks 8
Notes: Readings: Lecture 2, Lecture 4, and Lecture 7 from this wonderful class from Dmitri Kartofelev and Scholarpedia article on FHN. Journal Club Paper:There will be Journal Club on Hopfield's Classical Paper on Thursday April 1st. Homework #4 Read sections 9.2-9.5 of this early draft of Nelson's biophysics book (worth owning the final version if you have any interest in biophysics!) Do HW problems 9.5 and 9.6. Due Tuesday March 30th. |
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Weeks 9
Journal Club Paper:There will be Journal Club on Hopfield's Classical Paper on Tuesday April 6th. Journal Club Papers: There will be a Journal Club on Thursday 4/8 we will discuss these foundational papers on information theory and neuroscience. .pdf and .pdf |
Weeks 10+11
Readings: Ben Good's Notes for his class, especially Lectures 1-5 and also Chapter 1 of his thesis. Another very physics source are Daniel Fisher's 2007 Les Houche Notes. A good overview of Genealogical trees and coalescent theory can be found here. The NextStrain website for visualizing virus evolution is here. Finally, this is the applied evolutionary biology review that I talked about in class. I also talked about this paper on Fisher Waves. Homework #5 Please do Homework 5. Due Thursday April 22nd. |
Weeks 12
Journal Club: There will be Journal Club on Thursday April 27th on the following papers that explain Next Strain: Background Theory and main paper. It might be helpful to start with this short commentary on paper, then read main paper and theory paper. Homework #6 Please do Homework 6. Due Thursday May 6th (no extensions). This may take 4-8 hours depending on your programming skills. This link might be useful for Problem 2. Data file for problem 1 from NextStrain that I downloaded. This is all 465 sequences we have from India. Notice each sequence has Pangolin strain number and date collected. Use this to make frequency plot as a function of time and try to fit selection coefficient. If this is taking you a long time, feel free to skip the question. It's just for fun :). |