Biophysics I (BPHS 3090)
York University
Winter 2015 - 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 225)
- Course Syllabus (includes course logistics): here (pdf)
- Instructor: Christopher Bergevin
Office: Petrie 240
Email: cberge [AT] yorku.ca
Office Hours: TBD (and upon 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
- [04.22.15] The final exams have been graded and the HH reports are in the process of being graded. Hopefully final grades will be tallied soon. In the meantime, this article on the brain of Einstein might be of interest.
- [04.15.15] Updates with regard to the final exam:
- The exam will be held on Monday 4/20 from 2-5 PM in TEL 0004.
- The exam will be comprehensive (i.e., the entirety of the semester), though will focus more on material since the class midterm
- 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
- Some relevant problems from the book to focus study on can be found here
- While there have not been HW problems on saltatory conduction (ch.5) or ion channels (ch.6), these topics (within reason) are fair game. To help towards this end, some example problems along these lines can be found here: Set 1, Set 2, and Set 3. You are encouraged to work through these problems!
- 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
- Good luck with your preparations!
- [04.02.15] Due to the strike, we will aim to extend classes until April 17. That is, we will have lectures on April 13, 15, and 17. Once a date for the final exam is known, it will be posted here.
- [03.30.15] As noted below, the HH project has been modified from the syllabus. This pdf has everything you need to know/do. Note that the proposal and report are due on the last day of class (4/17/15).
- [03.23.15] Due to the (on-going) strike and other various considerations, we are going to have to change our course syllabus a bit. In a nutshell, we unfortunately have insufficient time to properly launch the Hodgkin-Huxley (HH) project. So we will instead aim to do the following:
- Reduce emphasis on HH project, such that there will be an extended HW assignment dealing with the HH computations, which will be graded and count for 15% of your final grade (rather than 25%). As such, the HW grade will now count for 30% of your final grade (up from 25%) and the two exams for 55% (up from 50%). There will not be any in-class presentations, and you will only be expected to hand-in a short written report. This assignment will be posted soon, so to allow for ample time to complete before mid-April. See here for a description from last year (for an initial reference point).
- As of today, we still have 11 lectures remaining. We will aim to make the most of that time so to complete the main bulk of the course content. It may become necessary to cancel one (or more) classes and shift those lecture periods to a mutually agreed upon time (e.g., Thursday afternoon). Such will be discussed in class and updates posted here.
- Students are encouraged to voice thoughts/concerns in the midst of the on-going strike via email to the course instructor. Remember that we want to do everything we can to help you guys in the midst of the current challenges.
- [02.27.15] As noted below, due to class cancellations on 2/23 and 2/25, the class midterm will be postponed until Friday 3/6. All other aspects remained unchanged (e.g., test will only cover material up to 2/13, etc.).
- [02.19.15] Reminder that the first exam is coming up following reading week. It will take place in class on Friday 2/27 and will cover all course material through 2/13. 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 the course instructor for (a hard copy of) 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 1/5-2/13 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.
- 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
- 04.17.15 - Summary, Review
- 04.15.15 - Ion channels II
- 04.13.15 - 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
- 04.10.15 - Saltatory conduction
- 04.08.15 - Myelination
- 04.06.15 - Hodgkin-Huxley V
- Notes
- Reading: Vol.2: 4.4.1, 4.4.2, 4.4.8
- 04.03.15 - No class (Good Friday)
- 04.01.15 - 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
- 03.30.15 - 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,
- 03.27.14 - Hodgkin-Huxley II
- 03.25.15 - Hodgkin-Huxley I
- 03.23.15 - Cable Model II
- Notes
- Pre-Problem: Elephant
- Reading: Vol.2: 3.4.2.4-3.4.3.1 3.4.3.3-3.5
- 03.20.15 - Midterm Exam
- See details noted in 'Updates' section above
- 03.18.14 - 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
- 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
- CLASSES POSTPONED
- 03.02.15 - Core Conductor Model II
- 02.27.15 - Core Conductor Model I
- 02.25.15 - CLASS CANCELLED
- 02.23.15 - CLASS CANCELLED
- 02.13.15 - Action potentials, Nonlinearity, Spatial propagation
- 02.11.15 - Electrical properties of cells, Sensory transduction
- 02.09.15 - Active mechanisms: Ion pumps
- 02.06.15 - Resting potential
- 02.04.15 - Electro-diffusion III
- 02.02.15 - Electro-diffusion II
- 01.30.15 - Electro-diffusion I
- 01.28.15 - E&M Review (cont.), Resonance
- 01.26.15 - 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...)
- 01.23.15 - Carrier-mediated transport III
- 01.21.15 - Carrier-mediated transport II
- 01.19.15 - Carrier-mediated transport I
- Notes
- Pre-Problem: i^i
- Reading: Vol.1: 6.1-6.2.1.4
- 01.16.15 - Cellular responses to changes in osmotic pressure
- 01.14.15 - Osmosis
- 01.12.15 - 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
- 01.09.15 - Solutions to the Diffusion Equation, Diffusion processes
- 01.07.15 - Derivation of the Diffusion Eqn.
- 01.05.15 - 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
- HH project: Due 4/17/15
- HW7: Due 4/10/15
- HW6: Due 3/30/15
- HW5: Due 2/25/15
- HW4: Due 2/13/15
- HW3: Due 2/4/15
- HW2: Due 1/26/15
(Note: You will need to download SoftCell and use Matlab for this assignment)
- HW1: Due 1/16/15 (note the lateness policy of the course!)
- Guide to help get you started with plotting in Matlab