91亚色
Winter 2018 - 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: MWF 1:30-2:30 (CC 335)
- Course Syllabus (includes course logistics): (pdf)
- Instructor:
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)
鈫 Via 91亚色U, you may be able to access another useful text online
Updates and useful bits
- [2018.03.25] Fixed mix-up below (my error) re the J&L paper choice
- [2018.03.23] Papers for the 3/26 "Jclub" can be accessed here:
- (Jordan & Leo)
- (Kevin & Nader)
- (Neil & Samal)
- [2018.03.09] Firmed up details involving the 4080 project can be found
- [2018.02.28] Final exam date is now determined: Monday April 16th at 9 AM (Note: Classes end on April 6th)
- [2018.02.26] The class has a project component consisting of two parts. Further details will be discussed (soon) in class, 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 and 2016 (for reference, here is the ), with students working together in pairs.
- Students will do a critical review of a current scientific paper (again, working in pairs, but w/ different partners). There will be a short write up and in-class discussion. Examples of papers will be along the lines (and I'll update here w/ more recent papers):
- (background provided
- (original ; this was the very first article to appear in the Biophysical Journal!)
- (original , similar to Hoshi & Armstrong)
- [2018.02.02] The midterm will not cover electrodiffusion. The primary focus will be diffusion, osmosis, and carrier models (and all material covered in class and the assigned reading tied to those topics).
- [2018.01.26] The class midterm will take place on Friday 2/9 during the regularly scheduled class time. You are allowed a one-page double-sided sheet which you must turn with your exam.
- [2018.01.26] Apologies for the cancelled class on 1/24. Was quite a bit under the weather. And still am a bit. Nonetheless, we will have class today as usual. I may just be a bit (relatively) subdued.... 馃槈
- [2018.01.05] First day of class. Welcome!
- Most current version of SoftCell can be downloaded as a zipped file
- to help get you started with plotting in Matlab
- to get Matlab running remotely (via 91亚色's internal server).
In-Class Notes
- 2018.01.05 - Course introduction, Math review (e.g., PDEs), Intro. to diffusion
- 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)
- 2018.01.08 - Derivation of the Diffusion Eqn.
- Reading: Vol.1: 3.1-3.1.5; 3.2-3.2.2;
- 2018.01.10 - Solutions to the Diffusion Equation, Diffusion processes
- Reading: Vol.1: 3.5-3.5.2.1
- Here is a to the BPHS 2090 (F15), which contains slides that may be useful (e.g., aspects of micro- vs. macroscopic, the diffusion constant)
- 2018.01.12 - Membrane diffusion, Measuring membrane diffusion
- Reading: Vol.1: 3.6-3.6.1.2; 3.7-3.7.2, 3.8-3.8.5
- 2018.01.15 - Osmosis
- Pre-Problem 1:
- Pre-Problem 2:
- (2006) on "forward" osmosis
- Reading: Vol.1: 4.1-4.3.2.3; 4.4-4.5.1.2
- 2018.01.17 - Cellular responses to changes in osmotic pressure
- Reading: Vol.1: 4.7.2-p.230; Fig.4.26; Fig.4.28; 4.8.2-4.8.3
- 2018.01.19 - Carrier-mediated transport I
- Reading: Vol.1: 6.1-6.2.1.4
- 2018.01.22 - Carrier-mediated transport II
- Reading: Vol.1: 6.4-6.4.1.4
- 2018.01.24 - CLASS CANCELLED
- 2018.01.26 - Carrier-mediated transport III
- Reading: Vol.1: 6.4.2-6.4.3
- 2018.01.29 - E&M Review
- 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 dealing with the mathematics of the linear harmonic oscillator
- 2018.01.31 - Resonance in cell physiology, Intro. to electro-diffusion
- Pre-Problem:
- Links for papers referenced in class:
- (1985)
- (1999)
- (1999)
- (2002)
- (2014)
- 2018.02.02 - Electro-diffusion
- Pre-Problem:
- Reading: Vol.1: 7.2.1 7.2.3 7.2.4.1 7.4
- 2018.02.05 - Resting potential
- Pre-Problem:
- Reading: Vol.1: 7.5
- 2018.02.07 - Review
- In-class review led by 4080 alum
- 2018.02.09 - Midterm
- See announcements up top for more info
- 2018.02.12 - No Class
- 2018.02.14 - Membrane resting potential
- Reading: Vol.1: 7.5
- 2018.02.16 - Active mechanisms: Ion pumps
- Reading: Vol.1: 7.6-7.8
- 2018.02.26 - Action potentials, Nonlinearity, Spatial propagation
- Pre-Problem:
- Short with a bit of historical perspective芒聙娄
- Jan.2016 Nature articles on "deep learning"聙聺: , ,
- Reading: Vol.2: ch.1
- 2018.02.28 - Core Conductor Model I
- Reading: Vol.2: ch.2.1-2.4.2
- 2018.03.02 - Core Conductor Model II
- Pre-Problem:
- Reading: Vol.2: ch.2.4.3-2.5
- 2018.03.05 - Cable Model I
- Pre-Problem:
- Ch.6 of (Via 91亚色U library access) may provide some useful additional reference
- Related to the topic of capacitance discussed in class, this 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
- 2018.03.07 - Cable Model II
- Pre-Problem:
- Reading: Vol.2: 3.4.2.4-3.4.3.1 3.4.3.3-3.5
- 2018.03.09 - Hodgkin-Huxley I
- Project
- Pre-Problem: (this may be of interest)
- Reading: Vol.2: 4.1-4.1.2.3 4.2-4.2.2.2
- 2018.03.12 - Hodgkin-Huxley II
- Reading: Vol.2: 4.2.3-4.2.3.1
- 2018.03.14 - Hodgkin-Huxley III
- Nonlinear regression is relevant here, thus this may be of interest
- Similarly for numerical integration of ODEs, this may be of interest, especially the one on
- Reading: Vol.2: 4.2.3-4.2.3.2, 4.3,
- 2018.03.16 - Hodgkin-Huxley IV
- Reading: Vol.2: 4.4.1, 4.4.2, 4.4.8
- 2018.03.19 - Hodgkin-Huxley V
- Some useful basic background on dynamical systems can be found on and a very useful means (defield and pplane) to explore lower-dimension systems can be found (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
- 2018.03.21 - Myelination & Saltatory conduction I
- Draft (Matlab) discussed in class re exploring foundations of HH model
- Reading: Vol.2: 5.1-5.2.4.4
- 2018.03.23 - Myelination & Saltatory conduction II
- Pre-Problem:
- Reading: Vol.2: 5.1-5.2.4.4
- 2018.03.26 - Student "Jclub" presentations
- (Jordan & Leo)
- (Kevin & Nader)
- (Neil & Samal)
- 2018.03.28 - Ion channels I
- Reading: Vol.2: 6.1-6.1.1 6.4-6.4.1.5 6.2-6.2.2 6.5-p407
- 2018.04.02 - Ion channels II
- Reading: Vol.2: 6.1-6.1.1 6.4-6.4.1.5 6.2-6.2.2 6.5-p407
- 2018.04.04 - Ion channels III
- Reading: Vol.2: p407-416 6.3.2-6.3.6, 6.6.1-6.6.3, 6.7
- 2018.04.06 - Student HH presentations
HW Assignments
- : Due 2018.01.12 ()
- : Due 2018.01.22 ()
- : Due 2018.02.02 ()
- : Due 2018.02.26 ()
- : Due 2018.03.07 ()
- to help get you started with plotting in Matlab