Biophysics II (BPHS 4090/PHYS 5800)

York University

Fall 2015 - 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 (MC 111) 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
  
  
• Required Texts
  • Principles of Magnetic Resonance Imaging (D.G. Nishimura)
  • What is life? (E. Schrodinger)
  • 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

• [12/7/15] See info below regarding the final exam.
• [11/3/15] Added some new papers to the suggested list for the Jclub below (see 10/20 entry right below). You should let the course instructor know by Friday at the latest what paper you aim to discuss. Also, don't forget that the lab 3 proposal is due tomorrow (11/4).
• [10/23/15] Heading into the midterm, here are several strategies to best prepare:
  • The topics/themes to be covered on the exam: Fourier analysis, sampling/convolutions, radiation interaction with matter, tomography, and error analysis
  • Any topic covered in class lectures is fair game
  • Reviewing past HW problems will likely be helpful
  • For the H&R chapters listed for each lecture, the associated problems for that section will likely be useful to study/practice
• [10/20/15] Two-fold reminder. First the midterm is coming up soon (Tuesday 10/27). Anything covered in the course so far is fair game. More details will be posted soon to help prepare/study. Also remember that you are allowed a single double-sided sheet to bring with you. On it you can put anything you want. Second is that the Lab 2 report is due this Friday (10/16).
• [10/20/15] As discussed in class today, each student will be hosting a mini-Jclub in mid-November. More details will follow soon, but in a nutshell you will lead a 35 discussion that critically assesses your chosen paper. You will also be expected to engage/participate in other student's presentation. Here is a list of some suggested papers (in no particular order), mostly review papers (which have pluses and minuses re leading a discussion on). You are not required to pick from this list per se, but you do need the instructor's approval for whatever paper you pick (even if form this list):
  • Use of the Linear-Quadratic Radiobiological Model for Quantifying Kidney Response in Targeted Radiotherapy [Dale, 2004; Can. Biotherp. Radiopharm.] (link)
  • Coupling Mechanism and Significance of the BOLD Signal: A Status Report [Hillman, 2014; Ann. Rev. Neurosci.] (link)
  • The new nanophysiology: regulation of ionic flow in neuronal subcompartments [Holcman & Yuste, 2015; Nature Rev. Neurosci.] (link)
  • Correlated light and electron microscopy: ultrastructure lights up! [de Boer et al, 2015; Nature Meth.] (link)
  • Electron Transfer Between Biological Molecules by Thermally Activated Tunneling [Hopfield, 1974; PNAS] (link)
  • The cells that flock together [2015; PNAS] (link; this paper itself is not okay, but the papers it cites might be)
  • Mechanobiological oscillators control lymph flow [Kunert et al, 2015; PNAS] (link)
  • Hydrodynamic collective effects of active protein machines in solution and lipid bilayers [Mikhailov et al, 2015; PNAS] (link)
  • Protein misfolding occurs by slow diffusion across multiple barriers in a rough energy landscape [Yu et al, 2015; PNAS] (link)
  • Mixing Crowded Biological Solutions in Milliseconds [Liau et al, 2005; Analyt. Chem.] (link)
  • Super-Resolution Fluorescence Microscopy [Huang et al, 2014; Ann. Rev. Neurosci.] (link)
  • Scanning X-Ray Nanodiffraction on Dictyostelium discoideum [Priebe et al, 2014; Biophys. J.] (link)
  • Cryoelectron tomography reveals the sequential assembly of bacterial flagella in Borrelia burgdorferi [Zhao et al, 2013; PNAS] (link)
  • Biophysical implications of lipid bilayer rheometry for mechanosensitive channels [Bavi et al, 2014; PNAS] (link)
  • In vivo X-ray cine-tomography for tracking morphological dynamics [Rolo et al, 2014; PNAS] (link)
  • Voltage-sensitive dye imaging of transcranial magnetic stimulation-induced intracortical dynamics [Kozyrev et al, 2014; PNAS] (link)
  • Cortical entrainment to music and its modulation by expertise [Doelling & Poeppel, 2015; PNAS] (link)
  • Robustness of sensory-evoked excitation is increased by inhibitory inputs to distal apical tuft dendrites [Egger et al, 2015; PNAS] (link)
  • Determining hydrodynamic forces in bursting bubbles using DNA nanotube mechanics [Hariadi et al, 2015; PNAS] (link)
  • Interrogating the activities of conformational deformed enzyme by single-molecule fluorescence-magnetic tweezers microscopy [Guo et al, 2015; PNAS] (link)
  • Bursts of beta oscillation differentiate postperformance activity in the striatum and motor cortex of monkeys performing movement tasks [Feingold et al, 2015; PNAS] (link)
  • Clique topology reveals intrinsic geometric structure in neural correlations [Giusti et al, 2015; PNAS] (link)
  • Resting state of the human proton channel dimer in a lipid bilayer [Li et al, 2015; PNAS] (link)
• Lab 1 notebooks will be due on Monday 10/5 (so they can be graded and handed back by 10/9). As per the lab syllabus, what we want to see is clear/detailed notes of actions taken in lab, along with some (reasonable) degree of analysis and interpretation.
• 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).
• Some HWs will contain a 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

• 12.10.15 - FINAL EXAM
  • Will take place in Accolade East (ACE) room 006 at 2 PM on Thursday 12/10.
  • Exam will be comprehensive (i.e., any topic covered in class over the course of the semester is fair game), including topics relevant to the student "Jclub" presentations (within reason) and cochlear mechanics. As before, you will be allowed a single double-sided sheet with anything you want on it.
  • As per the course syllabus, there will be no make ups. Please do not miss the exam!
  • Some tips/resources to best prepare:
  • Look carefully over material and problems covered on the midterm exam.
  • Read the papers covered for the student Jclub presentations.
  • You might be wise to examine these 2014 study problems (except the problems on pgs.7 and 8)
  • Hobbie and Roth have some good problems in ch.18 dealing with NMR/MRI. In particular, problems: 18.8, 18.9, 18.10, 18.13, 18.14, 18.15, 18.20, 18.23, 18.29, 18.32, 18.38 (Note: To help facilitate studying on this front, a hard copy of solutions to ch.18 problems will be placed in the department's main office (Petrie rm.128). Ask Janaki to "sign them out". You may look over, take notes, and even take a picture if you are so inclined. But you cannot take the solutions, nor photocopy them.
  • Hobbie and Roth also have some useful problems dealing with 2-D Fourier transforms. Specifically ch.12.
• 12.04.15 - Student presentations
  • Will take place in Farq 103 from 4-7.
• 12.03.15 - Cochlear mechanics (cont.) -- LAST DAY OF CLASS
  • Notes
• 12.01.15 - Cochlear mechanics
  • Notes
• 11.26.15 - NMR and MRI V
  • Notes
  • Links to articles that may be of interest:
    • Principles of Diffusion Tensor Imaging and Its Applications to Basic Neuroscience Research (Mori & Zhang, Neuron, 2006)
    • Reading Minds (Nature, 2013 article)
    • MR Diffusion Tensor Spectroscopy and Imaging (Basser et al. 1994 Biophysical Journal)
    • Nature Outlook section on Medical Imaging (scroll to bottom)
• 11.24.15 - Student Jclub IV
  • Sparse MRI: The Application of Compressed Sensing for Rapid MR Imaging, Lustig et al. (Mag. Res. Med., 2007)
• 11.19.15 - Student Jclub III
  • In vivo X-ray cine-tomography for tracking morphological dynamics, Rolo et al. (PNAS, 2014)
  • pH-Taxis of Biohybrid Microsystems, Zhuang et al. (Sci. Rep., 2015)
• 11.17.15 - Student Jclub II
  • Determining hydrodynamic forces in bursting bubbles using DNA nanotube mechanics, Hariadi et al. (PNAS, 2015)
  • Mixing Crowded Biological Solutions in Milliseconds, Liau et al. (Anal. Chem., 2005)
• 11.12.15 - Student Jclub I
  • A simple microviscometric approach based on Brownian motion tracking, Hnyluchova et al. (Rev. Sci. Instr., 2015)
  • Binaural Beat Technology in Humans: A Pilot Study to Assess Neuropsychologic, Physiologic, and Electroencephalographic Effects, Wahbeh et al. (J. Alt. & Comp. Med., 2007)
• 11.10.15 - NMR and MRI IV
  • Notes
• 11.05.15 - NMR and MRI III
  • Notes
  • Relevant H&R chapters: 18.5
• 11.03.15 - NMR and MRI II
  • Notes
  • 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)
• 10.27.15 - MIDTERM
• 10.22.15 - 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
  • Article from Nature on Richard R. Ernst discussed in class
  • Guidelines for Lab 3 proposal can be found here
• 10.20.15 - Jclub: Optical coherence tomography and cochlear mechanics
  • The goal of this lecture is two-fold. On one hand, we will discuss some topics related to cochlear biomechanics and physiology. On the other, we will operate as if we are having a 'journal club' (or "Jclub) session. The goal of such is to provide students with some exposure and experience as how to run a 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). Furthermore, as per the course syllabus , students will be leading a Jclub themselves in class in mid-November.
  • We will focus our discussion on the following paper. Look it over (and preferably read) ahead of time. You will be expected to ask questions!
    • Noninvasive in vivo imaging reveals differences between tectorial membrane and basilar membrane traveling waves in the mouse cochlea (Lee et al. PNAS 2015)
  • Notes
  • Here are some potentially helpful resources in the context of a Jclub:
    • How to make journal clubs interesting (Swift, 2004)
    • What makes evidence-based journal clubs succeed? (Phillips et al., 2004)
    • How to run an effective journal club: a systematic review (Deenadayalan et al., 2008)
  • See "Updates and useful bits" section above for some suggested papers.
• 10.15.15 - Error analysis
  • Notes
  • Relevant H&R chapters: 11.1-11.2
  • Notes/code from the F14 offering of PHYS 2030 might be helpful regarding some more detail on topics touched upon here (e.g., nonlinear regression, DAQ). Specifically, see notes from: 10/7, 10/9, 10/14, 11/11, 11/18, 11/20, 11/25, and 11/27
• 10.13.15 - Radiation Interactions w/ Biological Tissue
  • Notes
  • Additional notes (may be helpful)
  • Relevant H&R chapters: 15.10-15.12, 16.10-16.13
  • Here are some potentially links dealing with the lecture's core theme:
    • Link to a paper on the Linear-Quadratic Model to get a flavor for how oncologists deal with the physical/mathematical side of things [Use of the Linear-Quadratic Radiobiological Model for Quantifying Kidney Response in Targeted Radiotherapy; Dale 2004]
    • Link to another one... [The Linear-Quadratic Model Is an Appropriate Methodology for Determining Isoeffective Doses at Large Doses Per Fraction; Brenner 2008]
    • Link to an article entitled "Antimatter, gamma rays help steer giant cancer-killing machines"
    • Article in The Economist entitled "Beam me up: It may be possible to destroy tumours using beams of antimatter"
    • Article from New Scientist entitled "Making antimatter and putting it to use"
• 10.08.15 - 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
• 10.06.15 - Radiation Interactions w/ Matter II (cont.)
  • Notes (same as 10/1)
  • Overview of recent Nature article mentioned in class (which did in fact use two-photon imaging in-vivo; see the extended Methods online)
• 10.01.15 - Radiation Interactions w/ Matter II
  • Notes
  • Additional notes (may be helpful)
  • Relevant H&R chapters: 15.1-15.6
  • This eBook (Radiation Physics for Medical Physicists, Podgorsak 2010) may be helpful
• 09.29.15 - Radiation Interactions w/ Matter I
  • Notes
  • Relevant H&R chapters: 14.1-14.4, 14.9
  • Additional notes (may be helpful)
• 09.22.15 - Sampling, Convolutions (cont.)
  • Notes (same as 9/17)
  • Relevant H&R chapters: 11.7-11.11, 11.14, 11.16, 12.1-12.2
  • Useful link (tied to the U. of Rhode Island) re 1-D FFTs and the connection to sinc
  • For those interested in learning more about ‘signals and systems’, this link to the MIT 6.003 OpenCourseware is likely to be of great interest
• 09.17.15 - Sampling, Convolutions
  • Notes
  • Relevant H&R chapters: 11.7-11.11, 11.14, 11.16, 12.1-12.2
  • Additional notes (may be helpful)
  • Example codes: EXconvolution1.m (demonstrates how two simple waveforms are convolved; you’ll also need this), EXconvolution2.m (demonstrates convolving a sampled sinusoid with an impulse), EXsharpenImage.m (simple code to demonstrate 2-D convolution in spatial domain within context of image processing)
• 09.15.15 - Fourier analysis (1-D and 2-D)
  • Slides
  • Relevant Nishimura chapters: 2.1-2.2
  • Relevant H&R chapters: 11.3-11.6, 11.9, 12.3
  • 1-D Example codes (Matlab): EXbuildImpulse (zipped folder containing relevant pieces to build up an impulse from the Fourier components) and EXspecREP3 (zipped folder containing relevant pieces to to fiddle with a variety of 1-D discrete Fourier transform properties)
  • 2-D Example codes (Matlab): 2D FFT (zipped folder, incl. some images; fourier2D.m is likely the easiest starting point, followed by gratingFourier.m)
• 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

• HW4: Due 10/21/15 (Solutions)
• HW3: Due 10/9/15 (Solutions)
• HW2: Due 9/30/15 (Solutions)
• HW1: Due 9/18/15 (Solutions)

Course Computing

• Computing Exercise 8 - Image processing II
• Computing Exercise 7 - Nonlinearity and Fractals
• Computing Exercise 6 - Error function (this one can count for two assignments given that there is a handful of questions to be answered)
• Computing Exercise 5 - Riemann sums (good beginner place if you are uncomfortable with coding)
• Computing Exercise 4 - Image processing
• Computing Exercise 3 - Fourier transforms [you'll need this, this, this, and this]
• Computing Exercise 2 - Autocorrelation
• Computing Exercise 1 - Solving ODEs