Biophysics II (BPHS 4090) - Christopher Bergevin

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Fall 2012 - 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: MWF 10:30-11:30 (Norman Bethune College BC 228) AND M 2:30-5:30 (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: MWF 11:30-12:30
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

→ The last exam for the class will take place on Friday 12/7/12 (time/location TBD). The exam will only cover material since the last exam. This includes the following topics: x-ray crystallography, spectroscopy, surface plasmon resonance, NMR/MRI, and cochlear mechanics. In addition to the course notes (which should serve as your chief reference), some relevant Hobbie & Roth (4th ed.) chapters include: 18.1-18.5, 18.7-18.9, 18.12. Also for reference, posting some sample from 4090 Fall 2011 and their . Note that for this test, you will be allowed to bring a single(-sided) sheet of paper containing any formulae and whatnot you believe will be of practical use. You'll be expected to turn this in with your exam.
: Due 12/3/12
Last day of class is 12/3/12.
: Due 11/23/12
Relevant Hobbie chapters for exam I: 12.1-5, 14.1-2, 14.4, 15.1-7, 15.9-12, 16.9-16.10 (and don't forget topics on anomalous diffusion)
: Due 10/22/12
First exam has been postponed to Monday 10/22 (from 10/19). Study guide/notes will be posted soon...
First lab report due Wednesday 10/17 (rather than 10/12)
: Due 10/10/12
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?

In-Class Notes

12.3.12 - Course summary
- Problem: Some call him
- Problem:
- Returning to our initial theme of
- This is also of relevant interest (albeit in a somewhat unsatisfying fashion)
11.30.12 - Cochlear mechanics, transmission lines, and WKB approximations....
11.28.12 - MRI V
- Problem:
11.26.12 - MRI IV
- Problem:
- Some useful from Franklin et al.
11.23.12 - MRI III
- Problem:
- Some of NMR (courtesy of Serdyuk et al., 2007)
- A helpful on getting a talk together (Mermin, 1992)
11.19-21.12 - Student-Led Paper Discussions
- 11/19 - Imaging brain electric signals with genetically targeted voltage-sensitive fluorescent proteins
- 11/21 - An analytical method for computing voxel S values for electrons and photons
- Criteria for grading (i.e., grading):
  - leading a clear/coherent overview
  - discuss relevant theory
  - clearly discuss figures and data
  - comment critically on paper substance
  - comment critically on narrative
  - address audience questions raised
  - put forth questions to engage audience
- A useful reference to think about here is pgs.2-3 of this from a different
11.14.12 - MRI II
- Problem:
11.14.12 - MRI I
- Problem:
11.12.12 - Surface Plasmon Resonance
- Problem:
- of Prof. Jennifer Chen (Chemistry) who works on the development of SPR applications here at 91��ɫ
11.09.12 - Spectroscopy III
- Problem:
- A recent in Nature on x-ray crystallography
- Some recent papers from Nature Methods:
11.07.12 - Spectroscopy II
- Problem:
- A recent from the Biophysical Journal entitled 'Force Spectroscopy with Dual-Trap Optical Tweezers: Molecular Stiffness Measurements and Coupled Fluctuations Analysis'
11.05.12 - Spectroscopy I
- Problem:
- An interesting (re spectroscopy data collected using a CD and a cereal box)
11.02.12 - No Class (co-curricular days)
10.31.12 - No Class (co-curricular days)
- Some papers of relevant interest from a recent issue of PNAS (this is just a sampling!):
  - [Chemical physics of protein folding]
  - [Microfluidics separation reveals the stem-cell-like deformability of tumor-initiating cells]
  - [Optical tweezers reveal relationship between microstructure and nanoparticle penetration of pulmonary mucus]
  - [Bottom-up construction of in vitro switchable memories]
  - [Crystal structure of the Leishmania major peroxidase-cytochrome c complex ]
  - [Force measurements on cargoes in living cells reveal collective dynamics of microtubule motors]
10.29.12 - X-Ray Crystallography III
- Some useful links:
  - Drenth's 2007 (Springer)
  - U. of Florida (see the BCH 6747 notes in particular)
  - Structural Medicine group (University of Cambridge)
  - Wikipedia page on
10.26.12 - X-Ray Crystallography II
- Problem:
10.24.12 - X-Ray Crystallography I
- Problem A:
- Problem B:
- Supporting images: , ,
10.19.12 - Review problems
- Problem (a la Polya):
  A bear, starting from the point P, walked one mile due south.
  Then he changed direction and walked one mile due east.
  Then he turned again to the left and walked one mile due north,
  and arrived exactly at the point P he started from.
  → What was the color of the bear?
10.17.12 - Radiation Therapy II
- Problem:
- Case study: light scattering in the retina (ref. here are two chapters from a text by Villars and Benedek; and
- to a recent PNAS paper on the energetic costs of cellular computation (worthwhile topic to consider for the discussion project)
- Potentially useful ('Radiation Physics for Medical Physicists' by Podgorsak; Springer, 2010) for some of the current class topics related to radiation/biomaterial interactions (link should allow you to explore other chapters in the book too)
10.15.12 - Radiation Therapy I
- Re Edward Tufte and his book The Visual Display of Quantitative Information (see this for that Paris-Lyon train map image)
10.12.12 - Biological effects due to radiation - Models of energy transfer
10.10.12 - Biological effects due to radiation - Overview
- Problem:
10.05.12 - Tomography II
- Problem:
10.03.12 - Tomography I
- Problem:
- Several links to articles in the most recent issue of the Biophysical Journal whose titles explicitly state their (cool-sounding?) methodology: ,
10.01.12 - Interactions between high-energy photons and matter
- Problem:
- on the discussion re 'active diffusion'
- Article on by means of charge transport and atomic force microscopy
09.28.12 - Interaction of electromagnetic radiation and matter
- Problem:
- A recent issue of Nature Methods had some articles that may be of relevant interest given some current topics in class: , , and
- First HW assignment is posted (see HW section below)
09.26.12 - Anomalous diffusion (cont.)
- Problem:
- to the manual for Softcell, a Matlab code that is very useful for visually getting a feel for diffusion/random walks, Hodgkin-Huxley dynamics, etc.... A zipped file containing the code can be downloaded
09.24.12 - Case study: Intracellular single molecule kinetics and 'anomalous' diffusion
- to be discussed in class (Barkai et al. Physics Today 2012)
09.21.12 - Case study: Two-photon excitation microscopy & the biophysics of hair cells
- Problem:
- re fluorescence (from the University of Basel)
- Here are links for several of the papers discussed in class: , , ,
09.19.12 - (very basic) Review of atomic physics and quantum mechanics
- Problem:
09.17.12 - Convolutions (revisted)
- Problem:
- mentioned in class (re 'how to buy a daughter')
- from recent PNAS (within the context as to how much of what is there can be considered 'bio' and/or 'biophysics')
09.14.12 - Fourier (revisted)
- Problem:
09.12.12 - Convolutions
- Problem:
- Link to a showing micrographs (w/ fluorescent labels, via confocal microscopy) geared towards understanding water-permeable channels in cell membranes
- Link to the MIT OCW page for (their Signals and Systems course)
09.10.12 - Images & Fourier Analysis
- Matlab to help visualize a 'square wave'
09.07.12 - What is 'biophysics'?
- to a useful reference text by William Bialek (Princeton)

HW Assignments

: Due 12/3/12
: Due 11/23/12
: Due 10/22/12
: Due 10/10/12