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Christopher Bergevin
Home » Biophysics I (BPHS 4080)

Biophysics I (BPHS 4080)

York University

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):  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 

  • [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:You should come prepared to not only discuss your own paper, but the others as well (e.g., look them over carefully ahead of time and come prepared to discuss/ask questions!). Feel free to aim to use the monitor for your “presentation” too.
  • [2018.03.09] Firmed up details involving the 4080 project can be found here
  • [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:
  • [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…. 😉
  • [2018.01.05] 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 

  • 2018.01.05 – 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) 
  • 2018.01.08 – Derivation of the Diffusion Eqn. 
    • Notes
    • Reading: Vol.1: 3.1-3.1.5; 3.2-3.2.2; 
  • 2018.01.10 – Solutions to the Diffusion Equation, Diffusion processes 
    • Notes
    • 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) 
  • 2018.01.12 – Membrane diffusion, Measuring membrane diffusion 
    • Notes
    • Reading: Vol.1: 3.6-3.6.1.2; 3.7-3.7.2, 3.8-3.8.5
  • 2018.01.15 – Osmosis 
  • 2018.01.17 – Cellular responses to changes in osmotic pressure 
    • Notes
    • 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 
    • Notes
    • Reading: Vol.1: 6.1-6.2.1.4 
  • 2018.01.22 – Carrier-mediated transport II 
    • Notes
    • Reading: Vol.1: 6.4-6.4.1.4 
  • 2018.01.24 – CLASS CANCELLED 
  • 2018.01.26 – Carrier-mediated transport III 
    • Notes
    • Reading: Vol.1: 6.4.2-6.4.3 
  • 2018.01.29 – E&M Review 
    • Notes
    • 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
  • 2018.01.31 – Resonance in cell physiology, Intro. to electro-diffusion
  • 2018.02.02 – Electro-diffusion 
  • 2018.02.05 – Resting potential 
  • 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 
    • Notes
    • Reading: Vol.1: 7.5 
  • 2018.02.16 – Active mechanisms: Ion pumps 
    • Notes
    • Reading: Vol.1: 7.6-7.8 
  • 2018.02.26 – Action potentials, Nonlinearity, Spatial propagation 
  • 2018.02.28 – Core Conductor Model I 
    • Notes
    • Reading: Vol.2: ch.2.1-2.4.2 
  • 2018.03.02 – Core Conductor Model II 
  • 2018.03.05 – 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
  • 2018.03.07 – Cable Model II 
  • 2018.03.09 – Hodgkin-Huxley I 
  • 2018.03.12 – Hodgkin-Huxley II 
    • Notes
    • Reading: Vol.2: 4.2.3-4.2.3.1
  • 2018.03.14 – 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, 
  • 2018.03.16 – Hodgkin-Huxley IV 
    • Notes
    • Reading: Vol.2: 4.4.1, 4.4.2, 4.4.8
  • 2018.03.19 – Hodgkin-Huxley V 
    • Notes
    • 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
  • 2018.03.21 – Myelination & Saltatory conduction I
    • Notes
    • Draft code (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
    • Notes
    • Pre-Problem: Fonts
    • Reading: Vol.2: 5.1-5.2.4.4
  • 2018.03.26 – Student “Jclub” presentationsYou should come prepared to not only discuss your own paper, but the others as well (e.g., look them over carefully ahead of time and come prepared to discuss/ask questions!). Feel free to aim to use the monitor for your “presentation” too.
  • 2018.03.28 – Ion channels I
    • Notes
    • 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
    • Notes
    • 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
    • Notes
    • 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