Biophysics II (BPHS 4090) - Christopher Bergevin

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Fall 2013 - 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 10:00-11:30 (CC 335) 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: T 11:30-1, W 12:30-1:30 (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

[12/5/13] Some info/problems regarding the final exam can be found . Remember that the final exam will take place on Friday Dec.13 from 7-10 PM in ACE 006.
[11/27/13] In case they may be of use, here is a and a (e.g., modifiable using a vector-based graphics program such as Adobe Illustrator). No need to use these, they are only provided to help in case you'd like to use them. Will also repeat here the blurb from 11/21 below: "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!)
[11/21/13] Here are some potentially helpful resources in the context of a Jclub:
- (Swift, 2004)
- (Phillips et al., 2004)
- (Deenadayalan et al., 2008)
[11/1/13] Guidelines for Lab 4 can be found
[10/8/13] Some with regard to Lab 3
[9/24/13 Update] A few general announcements, including some minor course tweaks (to make your lives easier):
- Max May (maxmay9 AT gmail.com) has graciously agreed to be our class rep
- There was some degree of confusion about what is due with regard to the first lab assignment (sorry about that). Was only expecting you to hand in your lab books, not type up a lab report. So let's clarify this:
  - If you handed in a lab report for Lab 1, you do not need to do such again for Lab 2 (only hand in your lab notebook).
  - If you did not hand in a report for Lab 1, make sure your lab book is handed in ASAP. For Lab 2, you will need to hand in both your lab book and a report. We'll discuss what the report should contain on 9/25 (most basically: an intro/overview, discussion in details of the methods used, your key results presented graphically, discussion/limitations, and a summary that includes a brief description of what you've learned).
  - Regardless, for Lab 2, you will be expected to provide some sort of substantial quantitative component (e.g., quantify uncertainty, statistical analysis) based upon the data you collect. Your approach to towards such should be laid out and explained clearly, whether it be in your lab book or report.
  - Lab 3 will be a bit more open-ended, in that you need to pick some setup or apparatus and really delve into its capabilities in detail. For Lab 3, you will be expected to give a short oral presentation on 10/29, in addition to handing in your lab book.
  - Lab 4 will be the hardest, as you essentially need to construct your own question/hypothesis and rigorously examine it (preferably via your methodology developed in Lab 3). You should strive to get as much input and feedback from your peers and instructors: having a well-crafted question to tackle will be crucial to doing well. You'll not only need to submit a proposal (on 11/12) which we'll discuss together in class, but also prepare a poster on your project (details to follow on how to construct such).
  →&�Բ��;Note: Keeping a good lab book is an important skill (and contributes towards your grade). Some various online references can help towards this end. Make sure to look over these various links: , , (not too hard to search out many others too!)
- Am relaxing the Latex requirement. While you are still highly encouraged to learn/use Latex (as it is very powerful), you can use whatever typesetting program you choose for your lab report.
- The 'Computer Assignments' will be slowed down a bit, as I realize that some of you have not had much exposure to coding yet. As such, here is what we'll do: Given that it is important to get exposure to programmable coding, the computer assignments will still get regularly assigned (and will contribute towards your HW grade). However, the due date for all 'computer assignments' will be the last day of class (Dec.5, 2013; i.e., there is no penalty for turning them in late up until 12/5) and you need only complete 4 of them total. You are free to choose which ones, and any extra you do can count towards extra credit. Also note that you are free to use any programming language you want (unless the assignment is in fact Matlab-specific, as it may be sometimes). Note that there are a *lot* of online references for general programming guidance in Matlab (like ) if you have not covered the various basics such as loops and conditional statements. Also, feel free to ask for help!
- 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!
For those interested in future studies/careers in neuroscience... () [courtesy of Science]
A few random useful links:
- with some useful bits on being a graduate student (Snieder et al. 2012)
- A helpful on getting a talk together (Mermin, 1992)
- Another helpful on getting a talk together (Benka, 2008), though less humorous...
- Wolfram's
- Some of NMR (courtesy of Serdyuk et al., 2007)
- A potentially useful reference text (Methods in Modern Biophysics, by Nolting) can be found/downloaded
- Polya's problem-solving
- A of practical mathematical interest?

Class Notes

12.05.13 - Course summary
- Review problems/notes can be accessed . Remember that the final exam will take place on Friday Dec.13 from 7-10 PM in ACE 006.
- Note that the computer assignments are due by 5 PM today. Each student is required to turn in (any) 4 of the 8 assignments posted below. Submissions should either be a brief report (e.g., answering the questions posed, showing any relevant figures generated) along with the associated code with comments (to clearly demonstrate you understand the code). Preferably, when done in Matlab, these codes can be run directly to generate any relevant numbers/figures.
12.03.13 - No class (university 'study day')
- Though we will not discuss in class, here is what we would have covered today: Similar in spirit to 11/28, 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!
  - (Dierkes et al., Eur. J. Phys. E 2012)
11.28.13 - Jclub I: 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 papers. 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)
11.26.13 - Cochlear mechanics III
- Notes (Lec.22) are continued from
- Useful (but not strictly correct) youtube shown in class on 11/21
- Relating back to MRI, this paper hot off the virtual press might be of interest: (Inglis et al., PNAS 2013)
11.21.13 - 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!)
11.19.13 - 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)
11.14.13 - NMR and MRI IV
- Note: Lab 4 proposal critiques due by 8 PM on 11/13
- Notes (Lec.19) are continued from
- Relevant H&R chapters: 18.7-18.9 (and read over 18.11-18.13)
11.12.13 - NMR and MRI III
- Note: Lab 4 proposals due before 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)
11.07.13 - NMR and MRI II
- 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)
11.05.13 - 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
- Links to the two (non-NMR) papers that may be of interest:
  - (Smith et al. PNAS, 2013)
  - (Sinha et al. PNAS, 2013)
10.29.13 - Student Presentations
- As per the course syllabus: "Third lab has students independently identifying an experimental approach and get together the setup they need to explore such. The focus here is to develop a deep understanding of the methodology and capabilities. Students must use the methodology in some context to quantitatively assess the chosen methodology. This lab will require an oral presentation that details the methodology and subsequent analysis approach (in addition to detailed lab book notes)."
- You will have 9 minutes and time will be strictly adhered to (i.e., you may be penalized for going over time). Also expect to address questions from the audience at the end of the talk.
- Note the quantitative descriptor: you will be expected to clearly demonstrate some degree of rigorous data analysis stemming from your chosen project. This can take many forms (consult course instructors if you unclear on how to proceed).
- for helping prepare for 10/29 presentations. (Note that you will have 9 minutes, not 11).
- Also remember that your lab notebook will be due/graded.
10.24.13 - Spectroscopy II
- Links to the two papers discussed in class:
  - (Ribezzi-Crivellari & Ritort BJ, 2012)
  - (Zoldak et al. PNAS, 2013)
10.22.13 - Spectroscopy I
- for helping prepare for 10/29 presentations. (Note that you will have 9 minutes, not 11).
10.17.13 - Error analysis
- Relevant H&R chapters: 11.1-11.2
10.15.13 - X-Ray Crystallography II
- Additional (may be helpful)
- This may be of use
- Additional (may be helpful; from Dobrovolny)
10.10.13 - X-Ray Crystallography I
- Additional (may be helpful)
- This may be of use
10.08.13 - 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...)
10.03.13 - Tomography
- Relevant H&R chapters: 12.4-12.5, 16.4,16.9
10.01.13 - Photon Interactions w/ Matter (cont), Two-Photon Microscopy
- Pre-Problem (we further discussed )
- Notes (see 9/26 slides)
- to journal article discussed in class (Denk et al. 1995, Neuron)
09.26.13 - Photon Interactions w/ Matter
- Additional (may be helpful)
- Relevant H&R chapters: 15.1-15.6
09.24.13 - Radiation Interactions w/ Matter (Intro)
- Relevant H&R chapters: 14.1-14.4, 14.9
- Additional (may be helpful)
- providing a (very!) basic overview on how the 'ChemCam' on Curiosity works
- to recent article in Nature re quantum mechanics (further food for thought)
09.17.13, 09.19.13 - Images: Sampling, Convolutions
- (9/17), (9/19)
- 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!)
- to article by Barkai et al. mentioned in class
09.12.13 - Images: Spectral (i.e., Fourier) analysis
- Relevant H&R chapters: 11.3-11.6, 11.9, 12.3
- Additional (may be helpful)
- Matlab code to visualize/generate a from a summation of sinusoids
- Matlab code to demonstrate how a (you'll also need )
09.10.13 - 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

No HW for the week of 11/19 [focus on Lab 4 project and computer assignments (remember the 12/5 due date!)]
No HW for the week of 10/29 (given the Lab 3 presentations)
: Due 10/23/13
: Due 10/16/13
: Due 10/9/13
: Due 10/2/13 (the PNAS TOC can be found )
: Due 9/25/13 (additional relevant )
: Due 9/18/13
- Required readings can be accessed and

Computer Assignments

→ As per 9/24 updates noted above, you only need to do 4 of the assignments over the course of the semester. The absolute due date for such is the final day of class (12/5/13), though you are encouraged to get such done earlier, as the computing skills will certainly come in very handy for understanding course material, the HW, and the labs/project.

- 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