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Christopher Bergevin
Home » Biophysics II (BPHS 4090)

Biophysics II (BPHS 4090)

York University

Fall 2014 – Course Website

Basic Information 

  • Course Description: This course will focus on applications of quantum physics in biology and medicine. Three lectures hours per week and three laboratory hours every other week. One term. Three credits. Prerequisites: SC/BPHS 3090 3.00; SC/PHYS 3040 6.00. 
  • Location & Time: T,Th 1:00-2:30 (CB 120) AND W 1:30-4:30 (Petrie 108) 
  • Course Syllabus (includes course logistics):  here (pdf) 
  • Lab wiki (note that some of the dates on the wii may be incorrect; refer to the course syllabus of this webpage for the most up to date info) 
  • Instructor:  Christopher Bergevin
    Office: Petrie 240 
    Email: cberge [AT] yorku.ca 
    Office Hours: TBD (or by appt.) 
    Phone: 416-736-2100 ext.33730 
  • Text  Intermediate Physics for Medicine and Biology Fourth Edition, by R. Hobbie & B. Roth (Springer) 
    → Via YorkU, you may be able to access the text online here

Updates and useful bits 

  • [10/7/14] As discussed in class, Lab 2 reports can be handed in on Monday 10/13.
  • [10/1/14] Here are some guidelines for your lab books. Also, here are some guidelines for your Lab 2 report (due 10/10; note that this is a few days later than specified in the syllabus given HW3 is also due in the same week).
  • Each HW will likely contain (at least) one Fermi problem. These are designed to give you an open-ended problem where you can creatively flex your quantitative muscle. Take advantage of such and have some fun!

Class Notes 

  • 12.04.14 – Course summary
    • Notes
    • Review problems/notes can be accessed here. Remember that the final exam will take place on Tuesday Dec.16 from 10 AM until 1 PM (location TBD).
  • 12.02.14 – No class (university ‘study day’) 
  • 12.01.14 – Visit to York MRI facility (1:30-3:30) 
  • 11.27.14 – Jclub: Hair cell transduction/synaptic ribbons 
  • 11.20, 11.25.14 – Cochlear mechanics II
    • Notes
    • Relevant H&R chapters: 13.1-13.3 
    • Rough Google search turned up some links for tips on making ‘posters’. Since your Lab 4 project culminates in the construction/presentation of a poster consistent with the style of what would be presented at an academic conference, there are some useful tips contained via these links. You are however encouraged to also look at other (more general) resources to (e.g., Tufte’s excellent book).
  • 11.18.14 – Cochlear mechanics I
    • Notes
    • Relevant H&R chapters: 11.15, 13.4-13.5 
    • Links to articles that may be of interest: 
      • Kiang (‘The nervous system’, 1975)
      • Kiang (J. Acoustical Soc. Am., 1980)
      • Manley (PNAS, 2001)
      • Manley (J. Neurophysiol., 2001)
  • 11.11.14 – NMR and MRI III
  • 11.06.14 – NMR and MRI II
    • Notes
    • Recent news item from Nature of relevant interest
    • Paper on chemotaxis alluded to in lecture (Levine & Rappel, Physics Today 2013)
    • Relevant H&R chapters: 18.2-18.4 (ch.3.4-3.7 provide some useful background too) 
  • 11.04.14 – NMR and MRI I (the very basics)
    • Notes
    • Additional notes (may be helpful)
    • Relevant H&R chapters: 8.1-8.2, 8.6, 18.1 
    • Guidelines for Lab 4 can be found here
  • 10.28.14 – Spectroscopy II
  • 10.23.14 – Spectroscopy I
    • Notes
    • Relevant H&R chapters: 14.1-14.3 
    • Guide for helping prepare for 11/5 presentations.
  • 10.21.14 – X-Ray Crystallography III
    • Notes
    • This nice summary by Bill Bialek is quite useful/nice
  • 10.16.14 – Error analysis
    • Notes
    • Relevant H&R chapters: 11.1-11.2 
    • Imaging article mentioned at start of class
    • This may also be of interest 
    • Link to article mentioned in class re scandal at RIKEN
  • 10.14.14 – X-Ray Crystallography II
  • 10.9.13 – X-Ray Crystallography I
  • 10.07.14 – Radiation Interactions w/ Biological Tissue
    • Notes
    • Additional notes (may be helpful)
    • Relevant H&R chapters: 15.10-15.12, 16.10-16.13 
    • Some guidelines/suggestion with regard to Lab 3
    • Link to a paper on the Linear-Quadratic Model (to get a flavor for how oncologists deal with the physical/mathematical side of things…)
  • 10.02.14 – No lecture
  • 09.30.14 – Tomography
    • Notes
    • Relevant H&R chapters: 12.4-12.5, 16.4,16.9 
    • Relevant article from a recent issue of Nature examining CT for lung cancer detection
  • 09.25.14 – Photon Interactions w/ Matter
  • 09.23.14 – Radiation Interactions w/ Matter (Intro) 
  • 09.16,18.14 – Images: Sampling, Convolutions
    • Pre-Problem (9/16)
    • Pre-Problem (9/18)
    • Notes
    • Relevant H&R chapters: 11.7-11.11, 11.14, 11.16, 12.1-12.2
    • Additional notes (may be helpful)
    • Zipped file containing several Matlab codes (chiefly specREP2.m) to visualize various aspects of Fourier transforms (it is really worth your time to fiddle around with these and develop some intuition!) This code (to build up a click, as demonstrated in class) might be useful. 
  • 09.11.14 – Images, Fourier transforms
  • 09.09.14 – Introduction, What is ‘biophysics’?
    • Slides
    • Link to William Bialek’s text
    • What is biophysics? (according to the Biophysical Society; do you agree?)
    • Note that HW1 has been assigned (see HW section at bottom of page) 

HW Assignments 

  • HW6: Due 11/25/14
  • HW5: Due 11/3/14
  • HW4: Due 10/17/14
  • HW3: Due 10/8/14 (the PNAS TOC can be found here)
  • HW2: Due 10/1/14
  • HW1: Due 9/17/14
    • Required readings can be accessed here and here

Course Computing 

→ Below are several assignments from previous iterations of BPHS 4090. While you are not required to do these, they are posted here for useful reference. Put another way, any attempts to work these assignments through will likely be time well spent. 

→ Guide to help get you started with plotting in Matlab. 

→ Guide to get Matlab running remotely (via York’s internal server).