York University
Winter 2020 - 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 (if time permits) 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: MF 1:30-2:45 (Stong 203)
- Course Syllabus (includes course logistics): here (pdf)
- Instructor: Christopher Bergevin
Office: Petrie 240
Email: cberge [AT] yorku.ca
Office Hours: TBD 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
- [2020.03.30] Apologies for the delayed update. I hope you are doing well in these turbulent times. To keep the 4080 ball rolling, here are a few items:
- Some new readings and slides should now be posted below. These wrap up HH, and cover myelination and ion channels. Consider that the "end" of the course content-wise.
- HW6 is now posted and has a fairly liberal due date. So don't sweat that.
- Project-wise, we will scrap the Jclub component. So focus solely on the HH project/presentation for end of April. I will provide further updates a bit further down stream.
- We will nail down a date for the final exam. I'll propose 4/21 (~3 weeks from now). Let me know if you have any objections and we can take it from there.
- Otherwise, please stay safe and sane, and feel free to get in touch w/ thoughts/questions. My internet is terrible, but will do my best to be responsive! And for what it is worth, I miss you guys!
- [2020.03.23] First (and most importantly), my best wishes to all is these unprecedented times. I hope all are well, and I trust you are doing all you can to keep a calm/rational head and take care of those around you. I am holed up w/ my family, doing the best we can to work towards the collective efforts to help stem the flow of infections (and "home school" the kids). Second, apologies for the delay in the update here. I know things have been crazy for EVERYONE, but it is important to do our best to keep the ball rolling forward. You guys are the future, so we need to do the best job we can realizing that.
Below is an outline to help us work towards wrapping up the semester. The reality is, the current situation affects us all in a multitude of ways, and I get that. For what it is worth, take comfort in that you can count on me to be on your side and do everything I can to help. If you are willing to work and want to do well, you'll navigate through this (2010 included). One drawback for me though is that my internet is limited (we live rural), and it has gotten fairly iffy of late given increased demand (as I suspect it has for many of you too). Such practically limits teaching-at-a-distance plans (e.g., I don't think zoom lectures are much of an option).
So with all that, let's delve into some specifics:- The semester will carry on, trying to maintain dates as per York. However, we will be in a somewhat limited form in that course content will consist of slides and readings posted here (see below), as well as problems/solutions. I think it prudent to have one more homework (HW6) that I'll aim to get posted soon. Further, we will continue w/ the final exam and project (see next points).
- Assuming things don't change, we will aim to have a final exam for 4080. At the moment, it is scheduled to take place on Tuesday April 7. That seems crazy to me. Assuming no objections, I propose we push back until mid/late April, date TBD. Let me know if you object. Details will be posted, but the plan at the moment is that it'll be open note/book. I'll post a pdf here at a specified time, and then you'll have five hours to submit a single pdf w/ your (scanned) solutions. As you might expect, all stipulations re academic honesty will apply! 😉
- The project will continue too, but now w/ a different name: Final Exam Part 2! That way we can extend the due date until the end of the final exam period (i.e., 4/25). Continue as is w/ your group. The aim will be the end point is a pdf of the presentation you submit come 4/25. I'll provide further updates as time progresses, but at least you got an anchor point.
- Hopefully in the next day or two, I'll get some materials posted. In the meantime, see the book readings noted below.
- Feel free to get in touch via email (or even phone if need be). I am likely to be slow in responding, but I want to do what i can to help you guys navigate this tricky/important stage in your physics education. Biophysics rules! 😉
- [2020.03.17] So, the state of flux continues (and will likely keep doing such)! I realize how disruptive current circumstances are for all. We all have a lot on our plates, and the last thing we need is to worry about school. So for the moment, let me assure you that you do not need to worry about class/grades. First and foremost, take care of yourself. Only then can you help take care of those around you. And follow the guidelines out there: respect the communal need for "social distancing", so to limit exposure for all.
For the moment, consider any course-related deadline suspended. We all need a bit of time for things to settle a bit further before we collectively figure out how to proceed. I am greatly heartened that York is showing strong leadership w/ setting a solid foundation looking ahead, while not ignoring the gravity of circumstances. I will follow their lead and help us move forward in a positive way.
On that note, even w/ the need to spend a bit more time to come up w/ a battleplan (e.g., use of zoom, etc), I appreciate the importance of hashing out some steps to keep you occupied in the meantime. So let me highlight some text-related focal points, as well as some problems to keep you (pleasantly) occupied:- Weiss Vol.2: 4.2.3-4.2.3.2, 4.3
- Weiss Vol.2: 4.4.1, 4.4.2, 4.4.8
- Weiss Vol.2: 4.4.1, 4.4.2, 4.4.8
- Some useful basic background on dynamical systems can be found on this wikipedia page and a very useful means (dfield 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)
Will try to get HW6 posted shortly so to keep you busy! As well as HW5 solutions. And make sure to keep working on your HH projects.
Feel free to reach out to me as needed. My delay time is not insignificant (and my internet at home is amazingly slow/iffy), but I will do my best to stay in regular communication. Lastly, try not to follow the news too much. As there is a lot of doom & gloom there. However, if you can't resist, here are two NYT bits w/ (what I think is) good news: Lessons from Singapore and Advancing treatment possibilities (I really like this last one a lot, in that I see people like our BPHS majors leading the charge!!)
- [2020.03.16] A quick update to students. First and foremost, I realize how crazy times are at the moment. There are many substantial changes in our lives that will profoundly affect things in many ways downstream. But one step at a time. Second, let me try to assure that we will do our best to finish this semester in a solid and fair way, despite no more in-person classes. You guys will continue to grow and thrive, and I am dedicated to seeing that through. How we will best proceed though requires a bit more time. Personally, the disruption to daycare/school is keeping me overly occupied at the moment (we have three young kids). So I need a bit of time to come up w/ a plan. Plus, you guys have a LOT on your plates at the moment too. Which brings me to the third point: Let's hit the pause button for a few days. Consider all due dates for the moment as tentatively postponed. I'll aim to update you guys here soon w/ a battleplan, including course content (e.g., slides, problems to solve, solved problems, skype/zoom times, etc...).
In the meantime, continue reading the textbook (it is a valuable resource) and do your best to stay intellectually stimulated/challenged (I'll aim to hack together a new HW assignment; great time to polish up on computer coding too!). Such will help keep you sane in these trying times. And most importantly, take care of yourself and those around you. You got this! 😉 - [2020.03.05] In case you have not yet stumbled across this, a useful reference for Softcell
- [2020.03.05] HW5 is now posted. For 3/6, we will spend class time talking about HH and finish up the cable model on 3/9.
- [2020.02.28] Zipped folder containing pdfs of potential project paper (re "journal club") can be accessed here
- [2020.02.28] Solutions to the midterm exam can be accessed here
- [2020.02.20] HW #4 is now posted (see below).
- [2020.02.20] Details on the course projects can be found here. Please note that there are two components: the HH simulations and the "journal club". We will discuss both aspects in class on 2/24 (including an overview of possible papers).
- [2020.02.20] The midterms have been graded. Raw scores saw a min of 38 and a max of 96. I am going to add 4 to shift things up (i.e., the highest score will thus be 100). As such, the mean score is 72% with a std of 19. Will hand them back on 2/24.
- [2020.02.03] The class midterm will take place on Friday 2/14 during the regularly scheduled class time. For the 75 min. exam, you are allowed a one-page double-sided sheet which you must turn with your exam. The midterm will include electrodiffusion, as well as preceding topics: diffusion, osmosis, carrier models, etc... (and all material covered in class and the assigned reading tied to those topics). To help prepare and provide a reference point, here is a link to the 2018 4080 midterm (Note: That 60 min. exam did not include electrodiffusion).
- [2020.01.16] Tis official, our new classroom will be Stong 203. See you there tomorrow at 1:30.
- [2020.01.13] Looking ahead (i.e., Friday 1/17 and beyond), our new room will be Stong 203. I am waiting for confirmation on that at the moment. Will also get HW#2 posted shortly....
- [2020.01.07] Schedule change. Effective immediately, the new lecture schedule will be MF 1:30-2:45 and Th 12-1 (special 4080 "office hour", anyone/everyone is welcome). Additionally, we will have office hours T 12-1 and Th 2-3. At the moment, we do not have a new classroom. But fortunately, for the meantime, we can use my lab (Farquharson 103), which should suit our purposes fine until something else gets lined up. So to summarize:
- No lecture tomorrow (Wednesday 1/8) or any Wednesday here on out
- Feel free to come by my office this Thursday (1/9) at 12 to chat
- Our 2nd lecture will be Friday (1/10) at 1:30 in Farquharson 103
- [2020.01.06] First day of class. Welcome!
- 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
- 2020.01.06 - Course introduction, Math review (e.g., PDEs), Intro. to diffusion
- Notes
- Reading: Vol.1: ch.1 and ch.2 (general background; focus on 1.1-1.2, 1.4, 2.4-2.6)
- 2020.01.10 - Derivation of the Diffusion Eqn.
- Notes
- Reading: Vol.1: 3.1-3.1.5; 3.2-3.2.2;
- 2020.01.13 - Membrane diffusion, Measuring membrane diffusion
- Notes
- Reading: Vol.1: 3.5-3.5.2.1; 3.6-3.6.1.2; 3.7-3.7.2, 3.8-3.8.5
- 2020.01.17 - Water Transport: Osmosis, Cellular responses to changes in osmotic pressure
- Notes
- Reading: Vol.1: 4.1-4.3.2.3; 4.4-4.5.1.2; 4.7.2-p.230; Fig.4.26; Fig.4.28; 4.8.2-4.8.3,
- 2020.01.20 - Carrier-mediated transport I
- Notes
- Reading: Vol.1: 6.1-6.2.1.4; 6.4-6.4.1.4
- 2020.01.24 - Carrier-mediated transport II
- Notes
- Reading: Vol.1: 6.4.2-6.4.3
- 2020.01.27 - Cell Electrophysiology, E&M Review
- Notes
- Reading: Vol.1: 7.1; Vol.2: 1.1-1.3
- 2020.01.31 - Electro-diffusion
- Notes
- Reading: Vol.1: 7.2.1 7.2.3 7.2.4.1 7.4
- 2020.02.03 - Membrane resting potential
- Notes
- Pre-Problem: Daisy, the cow
- Reading: Vol.1: 7.5
- 2020.02.07 - Active mechanisms: Ion pumps
- Notes
- Reading: Vol.1: 7.6-7.8
- 2020.02.10 - Action potentials, Nonlinearity, Spatial propagation
- 2020.02.14 - Midterm
- See announcements up top for more info
- 2020.02.17 & 21 - NO CLASS (Reading Week)
- 2020.02.24 - NO CLASS (instructor sick)
- 2020.02.28 - Core Conductor Model I
- Notes
- Reading: Vol.2: ch.2.1-2.4.2
- 2020.03.02 - Core Conductor Model II, Cable Model I
- Notes
- Reading: Vol.2: ch.2.4.3-2.5, 3.1-3.2.1 3.3-3.4.2.1
- 2020.03.06 - HH Intro/Overview
- Notes
- Reading: Vol.2: 4.1-4.1.2.3
- 2020.03.09 - Cable Model II
- Notes
- Reading: Vol.2: ch.ch.3.4.2.4-3.4.3.1 3.4.3.3-3.5
- 2020.03.13 - HH I
- Notes
- Reading: Vol.2: ch.4.2-4.2.2.2
- 2020.03.23 - Hodgkin-Huxley II
- Notes
- Reading: Vol.2: 4.2.3-4.2.3.1, 4.2.3-4.2.3.2
- 2020.03.25 - Hodgkin-Huxley III
- Reading: Vol.2: 4.3, 4.4.1, 4.4.2, 4.4.8
- 2020.03.30 - Hodgkin-Huxley IV
- Notes
- Some useful basic background on dynamical systems can be found on this wikipedia page and a very useful means (dfield 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
- 2020.04.01 - Myelination & Saltatory conduction
- Notes
- Reading: Vol.2: 5.1-5.2.4.4,
- 2020.04.01 - Ion channels
- Notes
- Reading: Vol.2: 6.1-6.1.1 6.4-6.4.1.5 6.2-6.2.2 6.5 p407-416, 6.3.2-6.3.6, 6.6.1-6.6.3, 6.7,