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Christopher Bergevin
Home » Biophysics I (BPHS 3090)

Biophysics I (BPHS 3090)

York University

Winter 2014 – 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. [Note: Listed prerequisites are as follows: SC/BPHS 2090 2.00; SC/PHYS 2020 3.00; SC/PHYS 2060 3.00. However, these prereqs. can be waived upon permission of the instructor.]
  • Location & Time: MWF 9:30-10:30 (Bethune College, BC 230)  
  • Course Syllabus (includes course logistics):  here (pdf) 
  • Instructor:  Christopher Bergevin
    Office: Petrie 240 
    Email: cberge [AT] yorku.ca 
    Office Hours: MWF 10:30-11:30 (and upon appointment) 
    Phone: 416-736-2100 ext.33730 
  • TA: Max May 
    Email: maxmay9 [at] gmail.com 
    Recitation: TBD 
  • 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 

  • [04.09.14] A few updates with regard to the final exam:
    • The exam will be held on Sunday 4/13 from 2-5 PM in TEL 0004
    • The exam will be comprehensive (i.e., the entirety of the semester), though will focus on material since the class midterm on 2/28
    • Below in the webpage, all relevant book chapters are noted. Any material from the class notes and HW is fair game, as is anything discussed together in class
    • You will be allowed to bring with you a single double-sided sheet. You can put anything on it you want (e.g., equations), but you must turn it in with your exam
    • Max will be holding a review session today and will also pass out some review materials (as well as hard copies of solutions set for HW 6 and 7)
    • Good luck with your preparations!
  • [03.28.14] The date/location of the final exam will be as follows: Sunday 4/13 from 2-5 PM in TEL 0004. Note that as per the course syllabus, there are no make-up exams (i.e., you are expected to be there on 4/13 and take the exam). Tips for review will be posted here soon.
  • [03.28.14] The final day of class (4/4) will deal with a class discussion on a current scientific paper. See below for more details.
  • [03.24.14] Note that as per the course syllabus, the last day of class (4/4) will focus on a student-centric discussion of a current research paper. The chosen article will be posted here soon. Note that all students are expected to thoroughly read the article, write a one page summary (with discussion questions), attend class and actively participate in the discussion. 
  • [03.17.14] Regarding numerical integration of ODEs as discussed in class today, this wikipedia page may be of interest, especially the one on Runge-Kutta. Some useful basic background on dynamical systems can be found on this wikipedia page and a very useful means (defield and pplane) to explore lower-dimension systems can be found here (a Java version can be run in most browsers, or the Matlab source code can be downloaded).
  • [03.14.14] Regarding regression as discussed in class today, this wikipedia page may be of interest
  • [03.05.14] Details on the HH project are posted and can be found here. Note that the proposal is due on 3/14/14. You are strongly encouraged to discuss ideas along these lines with the course instructors! 
  • [02.24.14] Max has compiled a list of relevant problems from the book that should be of help in terms of preparing for the exam this week (the list can be downloaded here). He is also going to lead a review session on Wednesday (2/26) afternoon for those interested. For specifics of time/location, contact Max directly. Just as a reminder, the midterm will be a 50 min. exam that will cover only material from vol.1 of Weiss (see 1/6-2/14 notes below for relevant chapters). You will be permitted to bring a graphing calculator, along with a single page (one-sided) of notes. You can put anything you want on that page, but you must hand it in with your exam.
  • [02.12.14] Reminder that the first exam is coming up following reading week. It will take place in class on Friday 2/28 and will cover all course material through 2/14. 
  • Max dug up some useful resources regarding ODEs from Zill & Cullen (7th ed.). Email him directly and he will send such your way.
  • Recitation is scheduled for Fridays 10:30-12:30 in PSE 258. All 3090 students are strongly encouraged to come. For those who can not make that time, contact Max May to schedule another time to meet. 
  • Most current version of SoftCell can be downloaded here as a zipped file 
  • Guide to help get you started with plotting in Matlab 
  • Guide to get Matlab running remotely (via York’s internal server). 

In-Class Notes 

  • 04.04.14 – Student-led paper discussion
    • We will discuss the following paper: Physics of nerves (T. Heimburg, 2010)
    • Students are expected to:
      • Thoroughly read the paper (preferably several times)
      • Attend class and be on time on 4/4 (lateness beyond 9:30 will incur a penalty)
      • Submit a written 1 page report at the start of class. This report should contain a salient summary of the paper (indicating a deep understanding of the topics raised and identifying the key biophysical themes) and propose 3-4 questions for discussion
      • Actively engage in the discussion during the class period
      → Note that this discussion composes a significant fraction of your project grade (as per the course syllabus)
  • 04.02.14 – Ion channels II
  • 03.31.14 – Ion channels I
    • Notes
    • Pre-Problem: Fonts
    • Reading: Vol.2: 6.1-6.1.1 6.4-6.4.1.5 6.2-6.2.2 6.5-p407
  • 03.28.14 – HH Student presentations
    • A few salient items to note:
      • You will have 9 minutes for your presentation and 2 minutes for questions. Time limitations will be strictly enforced.
      • Submit your slides (as either pdf or pdf and Powerpoint) to CB by 10 PM on 3/27. This will ensure that your slides will be on the classroom computer on the morning of 3/28.
      • Arrive early to make sure everything works properly. The order of presentations will be randomized and you could be penalized if you are not present at your allotted time.
      • Further updates will be noted here as the date gets closer.
  • 03.26.14 – Saltatory conduction
  • 03.24.14 – Myelination
  • 03.21.14 – HH Project tips 
  • 03.19.14 – Hodgkin-Huxley V 
    • Notes
    • Pre-Problem: Tarragon
    • Some useful basic background on dynamical systems can be found on this wikipedia page and a very useful means (defield and pplane) to explore lower-dimension systems can be found here (a Java version can be run in most browsers, or the Matlab source code can be downloaded)
    • Reading: Vol.2: 4.4.1, 4.4.2, 4.4.8
  • 03.17.14 – Hodgkin-Huxley IV 
    • Notes
    • Pre-Problem: Word jumble
    • Regarding numerical integration of ODEs as discussed in class today, this wikipedia page may be of interest, especially the one on Runge-Kutta
    • Reading: Vol.2: 4.2.3-4.2.3.2, 4.3, 
  • 03.14.14 – Hodgkin-Huxley III 
  • 03.12.14 – Hodgkin-Huxley II 
  • 03.10.14 – Hodgkin-Huxley I 
  • 03.07.14 – Cable Model III, Overview of HH project 
  • 03.05.14 – Cable Model II 
    • Notes
    • Pre-Problem: Elephant
    • Reading: Vol.2: 3.4.2.4-3.4.3.1 3.4.3.3-3.5
  • 03.03.14 – Cable Model I 
    • Notes
    • Pre-Problem: Two turkeys
    • As mentioned in class, ch.6 of Hobbie & Roth (Via YorkU library access) may provide some useful additional reference
    • Reading: Vol.2: ch.3.1-3.2.1 3.3-3.4.2.1
  • 02.28.14 – Midterm Exam 
    • See details noted in ‘Updates’ section above 
  • 02.26.14 – Core Conductor Model II 
  • 02.24.14 – Core Conductor Model I 
  • 02.14.14 – Action potentials, Nonlinearity 
  • 02.12.14 – Electrical properties of cells, Sensory transduction 
  • 02.10.14 – Active mechanisms: Ion pumps 
  • 02.07.14 – Resting potential 
  • 02.05.14 – Electro-diffusion III 
  • 02.03.14 – Electro-diffusion II 
  • 01.31.14 – Electro-diffusion I 
  • 01.29.14 – E&M Review, Resonance 
    • Notes
    • Pre-Problem: Missing cheese
    • Reading: Vol.2: 1.1-1.3 
    • Note: It may be helpful to dig up your freshman physics text, chiefly with regard to the ‘E’ part of E&M as well as electric circuits (e.g., voltage/current relations, capacitance, etc…) 
  • 01.27.14 – Carrier-mediated transport III 
  • 01.24.14 – Carrier-mediated transport II 
  • 01.22.14 – Carrier-mediated transport I 
    • Notes
    • Pre-Problem: i^i
    • Reading: Vol.1: 6.1-6.2.1.4 
  • 01.20.14 – Cellular responses to changes in osmotic pressure 
  • 01.17.14 – Osmosis 
  • 01.15.14 – Measuring membrane diffusion 
  • 01.13.14 – Membrane diffusion 
  • 01.10.14 – Solutions to the Diffusion Equation, Diffusion processes 
  • 01.08.14 – Derivation of the Diffusion Eqn. 
  • 01.06.14 – Course introduction, Math review (e.g., PDEs), Intro. to diffusion 
    • Notes
    • Reading: Vol.1: ch.1 and ch.2 (to get some general background; focus on 1.1-1.2, 1.4, 2.4-2.6) 

HW Assignments 

  • HW7: Due 4/4/14 
  • HW6: Due 3/21/14 
  • HW5: Due 3/10/14 
  • HW4: Due 2/14/14 
  • HW3: Due 2/7/14 
  • HW2: Due 1/27/14 
    (Note: You will need to download SoftCell and use Matlab for this assignment)
  • HW1: Due 1/17/14 (note the lateness policy of the course!)
  • Guide to help get you started with plotting in Matlab