Biophysics II (BPHS 4090) - Christopher Bergevin

York University

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): 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: 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 YorkU, you may be able to access the text online here

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 problems from 4090 Fall 2011 and their solutions. 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.
HW4: Due 12/3/12
Last day of class is 12/3/12.
HW3: 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)
HW2: 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)
HW1: Due 10/10/12
A few random useful links:
- Article with some useful bits on being a graduate student (Snieder et al. 2012)
- A helpful paper on getting a talk together (Mermin, 1992)
- Another helpful paper on getting a talk together (Benka, 2008), though less humorous…
- Numerical Recipes in C
- Wolfram’s ‘Integral calculator’
- Some history of NMR (courtesy of Serdyuk et al., 2007)
- A potentially useful reference text (Methods in Modern Biophysics, by Nolting) can be found/downloaded here
- Polya’s problem-solving guide
- A course of practical mathematical interest?

In-Class Notes

12.3.12 – Course summary
- Problem: Some call him chuck
- Problem: Only one?
- Returning to our initial theme of What is biophysics?
- This link is also of relevant interest (albeit in a somewhat unsatisfying fashion)
11.30.12 – Cochlear mechanics, transmission lines, and WKB approximations….
- Notes
11.28.12 – MRI V
- Problem: i^i
- Notes
11.26.12 – MRI IV
- Problem: Falsity….
- Notes
- Some useful supporting pics from Franklin et al.
11.23.12 – MRI III
- Problem: c and t (but why?)
- Notes
- Some history of NMR (courtesy of Serdyuk et al., 2007)
- A helpful paper on getting a talk together (Mermin, 1992)
11.19-21.12 – Student-Led Paper Discussions
- 11/19 paper – Imaging brain electric signals with genetically targeted voltage-sensitive fluorescent proteins
- 11/21 paper – 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 syllabus from a different course
11.14.12 – MRI II
- Problem: Bucket types
- Notes
11.14.12 – MRI I
- Problem: Match cubes
- Notes
11.12.12 – Surface Plasmon Resonance
- Problem: Embedded
- Notes
- Lab homepage of Prof. Jennifer Chen (Chemistry) who works on the development of SPR applications here at York
11.09.12 – Spectroscopy III
- Problem: Rotations & reflections
- Notes
- A recent historical perspective in Nature on x-ray crystallography
- Some recent papers from Nature Methods:
11.07.12 – Spectroscopy II
- Problem: Which one is it….
- Notes
- A recent paper 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: A long river & Galileo dropping things
- Notes
- An interesting link (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)
- Halloween…
- Some papers of relevant interest from a recent issue of PNAS (this is just a sampling!):
  - Wolynes et al. [Chemical physics of protein folding]
  - Zhang et al. [Microfluidics separation reveals the stem-cell-like deformability of tumor-initiating cells]
  - Kirch et al. [Optical tweezers reveal relationship between microstructure and nanoparticle penetration of pulmonary mucus]
  - Padirac et al. [Bottom-up construction of in vitro switchable memories]
  - Jasion et al. [Crystal structure of the Leishmania major peroxidase-cytochrome c complex ]
  - Hendricks et al. [Force measurements on cargoes in living cells reveal collective dynamics of microtubule motors]
10.29.12 – X-Ray Crystallography III
- Notes
- Some useful links:
  - Drenth’s 2007 text (Springer)
  - U. of Florida Macromolecular Structure Group (see the BCH 6747 notes in particular)
  - Structural Medicine group Protein Crystallography Course (University of Cambridge)
  - Wikipedia page on reciprocal latticies
10.26.12 – X-Ray Crystallography II
- Problem: A jumble…
- Notes
10.24.12 – X-Ray Crystallography I
- Problem A: A cultural divide
- Problem B: P is to uzzle
- Notes
- Supporting images: image 1, image 2, image 3
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?
- Problems (from 2011 4090)
- Solutions (subset)
10.17.12 – Radiation Therapy II
- Problem: Overlap
- Notes
- Case study: light scattering in the retina (ref. here are two chapters from a text by Villars and Benedek; ch.3.1 and ch.3.2
- Link to a recent PNAS paper on the energetic costs of cellular computation (worthwhile topic to consider for the discussion project)
- Potentially useful reference (‘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 link for that Paris-Lyon train map image)
- Notes
10.12.12 – Biological effects due to radiation – Models of energy transfer
- Notes
10.10.12 – Biological effects due to radiation – Overview
- Problem: FontS….
- Notes
10.05.12 – Tomography II
- Problem: Pointillism
- Notes
10.03.12 – Tomography I
- Problem: Politically incorrect?
- Notes
- Several links to articles in the most recent issue of the Biophysical Journal whose titles explicitly state their (cool-sounding?) methodology: Ram et al., PernÃ„Â±a-Andrade et al.
10.01.12 – Interactions between high-energy photons and matter
- Problem: Hole in a sphere
- Notes
- Follow-up on the discussion re ‘active diffusion’
- Article on DNA repair by means of charge transport and atomic force microscopy
09.28.12 – Interaction of electromagnetic radiation and matter
- Problem: Playing with matches
- Notes
- A recent issue of Nature Methods had some articles that may be of relevant interest given some current topics in class: Marco Capitanio , Single-molecule imaging, and Fluorescence dynamic range
- First HW assignment is posted (see HW section below)
09.26.12 – Anomalous diffusion (cont.)
- Problem: I-Spy
- Link 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 here
09.24.12 – Case study: Intracellular single molecule kinetics and ‘anomalous’ diffusion
- Notes
- Article 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: Yellow Paint
- Notes
- Reference re fluorescence (from the University of Basel)
- Here are links for several of the papers discussed in class: Denk et al. (PNAS, 1989), Denk et al. (Neuron, 1995), Denk and Svoboda (Neuron, 1997), Knopfel (Nature Neuroscience Reviews, 2012)
09.19.12 – (very basic) Review of atomic physics and quantum mechanics
- Problem: Symbols & An Equation
- Notes
09.17.12 – Convolutions (revisted)
- Problem: Pachinko
- Notes
- Slate article mentioned in class (re ‘how to buy a daughter’)
- Table of contents 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: Orthogonality?
- Notes
09.12.12 – Convolutions
- Problem: Twiddled Bolts
- Notes
- Link to a paper showing micrographs (w/ fluorescent labels, via confocal microscopy) geared towards understanding water-permeable channels in cell membranes
- Link to the MIT OCW page for 6.003 (their Signals and Systems course)
09.10.12 – Images & Fourier Analysis
- Notes
- Matlab code to help visualize a ‘square wave’
09.07.12 – What is ‘biophysics’?
- Notes
- Link to a useful reference text by William Bialek (Princeton)

HW Assignments

HW4: Due 12/3/12
HW3: Due 11/23/12
HW2: Due 10/22/12
HW1: Due 10/10/12