Biophysics I (BPHS 4080)

York University

Winter 2016 - 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 1:30-2:30 (Ross S201)
  
  
• Course Syllabus (includes course logistics): here (pdf)
  
  
• Instructor: Christopher Bergevin
  Office: Petrie 240
  Email: cberge [AT] yorku.ca
  Office Hours: W 2:45-4:30 (try to email ahead of time if possible) and by appointment
  
  
• 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

• [04.11.16] A few updates with regard to the final exam:
  • The exam will be held on Monday April 18 from 9-12 AM in TEL 0004
  • Note that as per the course syllabus, there are no make-up exams (i.e., you are expected to be there and take the exam)
  • The exam will be comprehensive (i.e., the entirety of the semester), though will focus on material since the class midterm
  • 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
  • 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
  • A good strategy for studying is to practice problems/exercises at the ends of the chapter in Weiss. Try not to look at solutions (they aren't hard to find, thank you Google!), at least until you have really spent a decent chunk of time w/ a problem
  • Good luck with your preparations!
• [03.18.16] Some interesting/useful historical notes (re HH) from Domenica Karavitaki.
• [03.16.16] Here is a nice overview of the HH model from an undergraduate student's perspective (courtesy of Gantumur Tsogtgerel at McGill).
• [03.15.16] The final exam will take place on Monday April 18 from 9-12 AM in TEL 0004.
• [03.08.16] Now that the 2016 Biophysics Week is officially upon us, here are a few quick/interesting reads via the newest issue of the Biophysical Journal:
  • Introduction to Biophysics Week: What is Biophysics?
  • Cellular Biophysics
  • Systems Biophysics: Multiscale Biophysical Modeling of Organ Systems
  • Optogenetics: Turning the Microscope on Its Head
  • Probing Natures Nanomachines One Molecule at a Time
  • The Current Revolution in Cryo-EM
  • Making Sense of Intrinsically Disordered Proteins
  • Inherited Arrhythmias: Of Channels, Currents, and Swimming
  • How Viruses Invade Cells
• [03.08.16] Whose doing which paper can be found on this updated list.
• [03.05.16] Detailed instruction on the course project component can be found here. Groups for both components can be found in this updated list. Look over the papers listed below and see if you have a strong preference for anyone in particular, otherwise you will be assigned one by 3/7.
• [02.28.16] Remember that the class midterm will take place tomorrow (2/29) during the regularly scheduled class time. You are allowed a one-page sheet which you must turn with your exam. Also, solutions to the HWs and review problems are available in the main physics office (ask Marlene or Janaki; they are in my mailbox). Note that there is only one copy of the review prob. solutions; you can peruse it there in the office only (i.e., do not take it or copy it). Good luck!
• [02.17.16] Note that HW5 has been posted and can be handed into the physics main office by the end of the day on 2/26. Also note that the first exam is coming up. It will take place in class on Monday 2/29 and will cover all course material through 2/12, as well as topics discussed in class during the week of 2/22. Here is a compiled 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). Feel free to ask Janaki in the main office to look at a hard copy of the solutions to these problems. Just as a reminder, the midterm will be a 50 min. exam that will cover only material from vol.1 of Weiss (see 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.
• [02.11.16] The class has a project component consisting of two parts. More details will be provided soon (right after the midterm), but preliminaries will be given here such that you can start mentally preparing. The two components are as follows:
  • Numerical simulation of the Hodgkin-Huxley (HH) model. It will be similar in nature to that of 2015 (for reference, here is the description), with students working together in randomized pairs.
  • Students will do a critical review of a current scientific paper (also working together in randomized pairs). There will be a short write up and in-class discussion. Papers will be chosen from the following:
    • Drion et al PNAS 2015
    • Hamilton et al Nature 2016 (background provided here)
    • Hoshi & Armstrong BJ 2015 (original paper; this was the very first article to appear in the Biophysical Journal!)
    • Jung et al PNAS 2016
    • Licata et al BJ 2016
    • Moore BJ 2015 (original paper, similar to Hoshi & Armstrong)
    • Rodrigues et al PNAS 2016
• [02.11.16] There will be no classes held during Reading Week (Feb.15-19). Also, the instructor will be out of town the following week (Feb.22-26), though classes will still be held (details to be posted). Also keep in mind that the midterm will be held in class on Monday (Feb.29). Notes regarding study tips/strategies will be posted on the website, but in short: anything covered as of 2/12 (and potentially of the week Feb.22-26) in class, on HW, or via assigned reading is fair game. There will also be one more HW assignment beyond what is currently assigned.
• [02.08.16] Tentative time/date for the final exam is Monday, April 18 from 9-12.
• [01.27.16] No office hours this afternoon. But feel free to email course instructor.
• [01.22.16] Article from current issue of Physics Today mentioned in class (here is a link to the book alluded to in the article)
• [01.04.16] First day of class. Note that the York bookstore does not have the books currently in stock. So I tried to make sure that there are two copies on (2 hour) reserve in the science library (Steacie) for both volumes. Buying options include the MIT Press directly ( here, though only v.1 appears to be available) or via amazon.ca.
• 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

• 04.04.16 - Ion channels II
  • Notes
  • Pre-Problem: Pics + Eqns. = ???
  • Reading: Vol.2: p407-416 6.3.2-6.3.6, 6.6.1-6.6.3, 6.7
• 04.01.16 - Student HH presentations
• 03.30.16 - 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
• 03.28.16 - Myelination & Saltatory conduction
  • Notes
  • Reading: Vol.2: 5.1-5.2.4.4
• 03.25.16 - No class (Good Friday)
• 03.23.16 - Hodgkin-Huxley V
  • Notes (cont. from 3/21)
  • Pre-Problem: Records (a related wikipedia page is of interest...)
  • Reading: Vol.2: 5.1-5.2.4.4
• 03.21.16 - Hodgkin-Huxley IV
  • Notes
  • Pre-Problem: Word jumble
  • 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
• 03.18.16 - Hodgkin-Huxley III
  • Notes
  • Nonlinear regression is relevant here, thus this wikipedia page may be of interest
  • Similarly for numerical integration of ODEs, 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,
• 03.16.16 - Hodgkin-Huxley II
  • Notes
  • Reading: Vol.2: 4.2.3-4.2.3.1
• 03.14.16 - Hodgkin-Huxley I
  • Notes
  • Pre-Problem: Colors (this wikipedia page may be of interest)
  • Reading: Vol.2: 4.1-4.1.2.3 4.2-4.2.2.2
• 03.11.16 - Cable Model II
  • Notes
  • Pre-Problem: Pointilism
  • Reading: Vol.2: 3.4.2.4-3.4.3.1 3.4.3.3-3.5
• 03.09.16 - Cable Model I
  • Notes
  • Pre-Problem: Elephant
  • Ch.6 of Hobbie & Roth (Via YorkU library access) may provide some useful additional reference
  • Related to the topic of capacitance discussed in class, this Slate article is of relevant interest (if you ever wondered how your touch screen works)
  • Reading: Vol.2: ch.3.1-3.2.1 3.3-3.4.2.1
• 03.07.16 - Core Conductor Model II
  • Notes
  • Pre-Problem: Hidden giant
  • Reading: Vol.2: ch.2.4.3-2.5
• 03.04.16 - Core Conductor Model I
  • Notes
  • Pre-Problem: Uranus orbiting
  • Reading: Vol.2: ch.2.1-2.4.2
• 03.02.16 - Class postponed
  • NOTE: Class postponed due to travel/weather
  • Reading: Vol.2: ch.2.1-2.4.2
• 02.29.16 - Midterm
  • See notes above in Updates section
• 02.22-24.15 - Historical interlude
  • Lectures by Jill Lazenby will focus on this article by Grote (Surfaces of action: cells and membranes in electrochemistry and the life sciences, 2010)
  • Notes
• 02.15-19.16 - Reading week (no lectures)
• 02.12.16 - Action potentials, Nonlinearity, Spatial propagation
  • Notes
  • Pre-Problem: Circuit??
  • Short article with a bit of historical perspective…
  • Jan.2016 Nature articles on “deep learning”: Editorial, Overview, Article
  • Reading: Vol.2: ch.1
• 02.10.16 - Electrical properties of cells, Sensory transduction
  • Notes
  • Pre-Problem: Geography 101
  • Reading: Vol.2: ch.1
• 02.08.16 - Active mechanisms: Ion pumps
  • Notes
  • Pre-Problem: Star lines
  • Reading: Vol.1: 7.6-7.8
• 02.05.16 - Resting potential
  • Notes
  • Pre-Problem: Daisy, the cow
  • Reading: Vol.1: 7.5
• 02.03.16 - Electro-diffusion II
  • Notes
  • Pre-Problem: Daisy, the cow
  • Reading: Vol.1: 7.5
• 02.01.16 - Electro-diffusion I
  • Notes
  • Pre-Problem: Playing w/ matches II
  • Reading: Vol.1: 7.2.1 7.2.3 7.2.4.1 7.4
• 01.29.16 - Resonance in cell physiology, Intro. to electro-diffusion
  • Notes
  • Pre-Problem: Perspectives & distance...
  • Links for papers referenced in class:
    • Crawford & Fettiplace (1985)
    • Ramanathan et al (1999)
    • Fettiplace & Fuchs (1999)
    • Ramanathan & Fuchs (2002)
    • Fettiplace & Kim (2014)
• 01.27.16 - E&M Review
  • 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...)
  • Here are some reference slides dealing with the mathematics of the linear harmonic oscillator
• 01.25.16 - Carrier-mediated transport III
  • Notes
  • Pre-Problem: Liberty
  • Reading: Vol.1: 6.4.2-6.4.3
• 01.22.16 - Carrier-mediated transport II
  • Notes
  • Pre-Problem: Hip to be square
  • Reading: Vol.1: 6.4-6.4.1.4
• 01.20.16 - Carrier-mediated transport I
  • Notes
  • Pre-Problem: i^i
  • Reading: Vol.1: 6.1-6.2.1.4
• 01.18.16 - Cellular responses to changes in osmotic pressure
  • Notes
  • Pre-Problem: Some call him....
  • Reading: Vol.1: 4.7.2-p.230; Fig.4.26; Fig.4.28; 4.8.2-4.8.3
• 01.15.16 - Osmosis
  • Notes
  • Pre-Problem 1: What color is the bear?
  • Pre-Problem 2: Bear problem v.2.0
  • Reading: Vol.1: 4.1-4.3.2.3; 4.4-4.5.1.2
• 01.13.16 - Membrane diffusion, Measuring membrane diffusion
  • Notes
  • Pre-Problem: Pattern??
  • Reading: Vol.1: 3.6-3.6.1.2; 3.7-3.7.2, 3.8-3.8.5
• 01.11.16 - Solutions to the Diffusion Equation, Diffusion processes
  • Notes
  • Pre-Problem: Playing w/ matches
  • Reading: Vol.1: 3.5-3.5.2.1
  • Here is a link to the BPHS 2090 (F15), which contains slides that may be useful (e.g., aspects of micro- vs. macroscopic, the diffusion constant)
• 01.08.16 - Derivation of the Diffusion Eqn. (cont)
  • Notes (same as 1/6)
  • (solved) Sample problems
• 01.06.16 - Derivation of the Diffusion Eqn.
  • Notes
  • Pre-Problem: Panda bear, panda bear, what do you see?
  • Reading: Vol.1: 3.1-3.1.5; 3.2-3.2.2;
• 01.04.16 - 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 3/25/16
• HW6: Due 3/14/16
• HW5: Due 2/26/16
• HW4: Due 2/17/16 (Note 2-day extension)
• HW3: Due 2/8/16
• HW2: Due 1/29/16
• HW1: Due 1/15/16 (note the lateness policy of the course!)
• Guide to help get you started with plotting in Matlab