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Christopher Bergevin
Home » Biophysics I (BPHS 3090)

Biophysics I (BPHS 3090)

York University

Winter 2013 - Course Website

Basic Information 

  • Course Description: This course will focus on physics relevant to cellular dynamics and transport. Basic principles will include: electrodynamics (e.g., charge transport across cells, Nernst potentials), diffusion, osmosis, and wave propagation. Salient biological topics will be approached in a rigorous mathematical fashion and include those such as: cellular homeostasis, the Hodgkin-Huxley model for action potentials, molecular biology of ion channels, and molecular motors (e.g., motion in low Reynolds-number regimes). The objective of the course is to help students to integrate the knowledge gained in second and third year biology and physics courses and to use methods of physics to study biological processes. One term. Three credits. Prerequisites: SC/BPHS 2090 2.00; SC/PHYS 2020 3.00; SC/PHYS 2060 3.00. 
  • Location & Time: TTh 11:30-1 (Calumet College, CC 335)  
  • Course Syllabus (includes course logistics):  here (pdf) 
  • Instructor:  Christopher Bergevin
    Office: Petrie 240 
    Email: cberge [AT] yorku.ca 
    Office Hours: TBD 
    Phone: 416-736-2100 ext.33730 
  • TA: Kevin Cross 
    Email: kc777 [AT] yorku.ca 
    Recitation: M 1-2 (BSB 203) 
  • Text  Cellular Biophysics vols. 1 and 2, by T.F. Weiss (MIT Press) 
    → Via YorkU, you may be able to access another useful text online here

Updates and useful bits 

  • The final exam for the class will take place tomorrow (Thursday, 4/11) from 9 AM-12 PM in Chemistry (CB) 120. The exam will chiefly cover material from vol.2 of Weiss. Some concepts from vol.1 (e.g., ch.7) are highly relevant, but will not be tested directly. A good strategy for preparing is closely reviewing the course notes and HW, as well as re-reading pertinent chapters from vol.2 of the text. Also remember that you will be allowed to bring a single-sided sheet with you containing any formulae/info you think is relevant (you will have to turn this in with your exam). You may also want to bring a ruler and a calculator (though neither are required). You'll have the full 3 hours to complete the exam, though it will likely take you less time than that. As a heads up, the test has several extra credit problems, meaning that it is possible to score up to 135%.
  • A new HW assignment (HW6) has been posted (link at bottom of page) and is due on 3/26. This assignment should ultimately help with respect to the HH project, for which the presentations are on 3/28. Also note that we will have one final HW assignment (yet to be posted) that will be due on 4/4 (the last day of class, and the same day as the in-class paper discussion). 
  • The 2nd part of the project component to the course involves an in-class discussion on a recent scientific paper. The paper will be Debanne et al. (2012, Nat. Rev. Neurosci.) and can be downloaded here. The class discussion will take place on Thursday April 4th (4/4/13). Note the requirements as listed in the course syllabus. Specifically, each student will be expected to 
    • Read the article carefully/critically 
    • Turn in on 4/4 at the start of class a 1-page concise/clearly written summary that a. summarizes the key theme of the paper, b. identifies key biophysical themes present, and c. poses several probing questions stemming from it)
    • Participate and make significant contributions to the in-class discussion on the paper
    Note the the discussion should be primarily led by the students (i.e., 4/4 will not be a lecture on the paper!). 
    → Give yourself plenty of time on this and do not put it off until the last minute (e.g., you'll likely need to reread the paper at least several times before things start to sink in). 
  • Details on the Hodgkin-Huxley project can be found here
  • New HW assignment (#5) posted on 3/4 and due on 3/14. Also, details on the Hodgkin-Huxley project will be discussed in class this week. 
  • The first exam will be on 2/26/13. As per the syllabus, there are no makeups. You will be allowed to bring a single one-sided sheet you make with anything on it (e.g., formulae, diagrams, etc...) that you'll need to turn in with your exam. The exam material comes from the class notes (everything up to 2/14) and HW (incl. HW4) and only from vol.1 of the texts. Problems will be similar in nature to the HW. Salient topics are: membrane diffusion, water transport, carrier-mediated transport, electro-diffusion, and membrane circuit analogs. 
  • As a random sampling, here are some class-relevant articles from the Feb. 2013 issue of the Biophysical Journal 
  • There was a bit of an error in the wording of problem 7 in HW#2. That has been corrected in the online version. 
  • Note that HW assignments will regularly be updated below (so make sure to check regularly!) 
  • Recitation is now scheduled weekly on Mondays from 1-2 in BSB 203. The first meeting will take place on 1/14 and then weekly from there on out unless noted otherwise. Contact Kevin if you have questions. All 3090 students are strongly encouraged to come. 
  • Most current version of SoftCell can be downloaded here as a zipped file 
  • Guide to help get you started with plotting in Matlab 

In-Class Notes 

HW Assignments 

  • HW7: Due 4/4/13 at 11:30
  • HW6: Due 3/26/13 at 11:30
  • HW5: Due 3/14/13 at 11:30
  • HW4: Due 2/26/13 at 11:30
  • HW3: Due 2/12/13 at 11:30
  • HW2: Due 1/31/13 at 1:00 
  • HW1: Due 1/22/13 at 1:00 (note the lateness policy of the course!)
  • Guide to help get you started with plotting in Matlab