Biophysics II (BPHS 4090) - Christopher Bergevin

91��ɫ

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): (pdf)
Lab (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:
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 91��ɫU, you may be able to access the text online

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 for your lab books. Also, here are some 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 . 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
- Review problems/notes can be accessed . 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 91��ɫ MRI facility (1:30-3:30)
11.27.14 - Jclub: Hair cell transduction/synaptic ribbons
- The goal of this lecture is two-fold. On one hand, we will discuss some further topics related to cochlear biomechanics and physiology. On the other, we will operate as if we are having a 'journal club' session. The goal of such is to provide students with some exposure and experience as how to run a successful 'Jclub'. Since we learn much about the 'cutting edge' by reading current scientific literature, the notion of a productive Jclub is very important no matter what direction you ultimately pursue (i.e., this is not only relevant for those going to graduate school).
- We will focus our discussion on the following paper. Try to look it over (and preferably read) ahead of time. You will be expected to ask questions!
  - (Andor-Ardo et al. PNAS 2010)
- Here are some potentially helpful resources in the context of a Jclub:
  - (Swift, 2004)
  - (Phillips et al., 2004)
  - (Deenadayalan et al., 2008)
11.20, 11.25.14 - Cochlear mechanics II
- 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 ).
  - (Geography and Anthropology)
  - (I didn't watch this video to vet it!)
11.18.14 - Cochlear mechanics I
- Relevant H&R chapters: 11.15, 13.4-13.5
- Links to articles that may be of interest:
  - ('The nervous system', 1975)
  - (J. Acoustical Soc. Am., 1980)
  - (PNAS, 2001)
  - (J. Neurophysiol., 2001)
11.11.14 - NMR and MRI III
- Note: Lab 4 proposals due at start of class
- Relevant H&R chapters: 18.5
- Links to articles that may be of interest:
  - (Mori & Zhang, Neuron, 2006)
  - (Nature, 2013 article)
  - (Basser et al. 1994 Biophysical Journal)
  - on Medical Imaging (scroll to bottom)
11.06.14 - NMR and MRI II
- Recent from Nature of relevant interest
- Paper on 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)
- Additional (may be helpful)
- Relevant H&R chapters: 8.1-8.2, 8.6, 18.1
- Guidelines for Lab 4 can be found
10.28.14 - Spectroscopy II
- Links to the two papers discussed in class:
  - (Ribezzi-Crivellari & Ritort BJ, 2012)
  - (Zoldak et al. PNAS, 2013)
10.23.14 - Spectroscopy I
- Relevant H&R chapters: 14.1-14.3
- for helping prepare for 11/5 presentations.
10.21.14 - X-Ray Crystallography III
- This nice by Bill Bialek is quite useful/nice
10.16.14 - Error analysis
- Relevant H&R chapters: 11.1-11.2
- Imaging mentioned at start of class
- may also be of interest
- to article mentioned in class re scandal at RIKEN
10.14.14 - X-Ray Crystallography II
10.9.13 - X-Ray Crystallography I
- Additional (may be helpful)
- This may be of use
10.07.14 - Radiation Interactions w/ Biological Tissue
- Additional (may be helpful)
- Relevant H&R chapters: 15.10-15.12, 16.10-16.13
- Some with regard to Lab 3
- 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
- Relevant H&R chapters: 12.4-12.5, 16.4,16.9
- Relevant from a recent issue of Nature examining CT for lung cancer detection
09.25.14 - Photon Interactions w/ Matter
- Additional (may be helpful)
- Relevant H&R chapters: 15.1-15.6
09.23.14 - Radiation Interactions w/ Matter (Intro)
- Relevant H&R chapters: 14.1-14.4, 14.9
- Additional (may be helpful)
09.16,18.14 - Images: Sampling, Convolutions
- (9/16)
- (9/18)
- Relevant H&R chapters: 11.7-11.11, 11.14, 11.16, 12.1-12.2
- Additional (may be helpful)
- Zipped file containing several Matlab codes (chiefly specREP2.m) to visualize various aspects of (it is really worth your time to fiddle around with these and develop some intuition!) This (to build up a click, as demonstrated in class) might be useful.
09.11.14 - Images, Fourier transforms
- Relevant H&R chapters: 11.3-11.6, 11.9, 12.3
09.09.14 - Introduction, What is 'biophysics'?
- to William Bialek's text
- (according to the Biophysical Society; do you agree?)
- Note that HW1 has been assigned (see HW section at bottom of page)

HW Assignments

: Due 11/25/14
: Due 11/3/14
: Due 10/17/14
: Due 10/8/14 (the PNAS TOC can be found )
: Due 10/1/14
: Due 9/17/14
- Required readings can be accessed and

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.

→&�Բ��; to help get you started with plotting in Matlab.

→&�Բ��; to get Matlab running remotely (via 91��ɫ's internal server).

- Image processing II
- Nonlinearity and Fractals
- Error function (this one can count for two assignments given that there is a handful of questions to be answered)
- Riemann sums (good beginner place if you are uncomfortable with coding)
- Image processing
- Fourier transforms [you'll need , , , and ]
- Autocorrelation
- Solving ODEs