Current Topics in Biophysics (BPHS 2090)

York University

Fall 2015 - Course Website

Basic Information

• This course is primarily taught by Prof. Stan Jerzak. See York’s corresponding moodle page for additional info.
  
• Prof. Chris Bergevin will be covering the F15 lectures for 11/10-12/3.

Class Notes

• 12.03.15 - Sensory biophysics
  • Slides
• 12.01.15 - Midterm
  • The exam will cover material from the lectures notes of 11/10-26. Anything on the slides (and discussed in class) is fair game. The questions will be a mix of conceptual and quantitative problems (thus bringing a calculator may be helpful, though it’s not necessary). Math-wise, you will not need to solve differential equations per se, but there will be a reasonable degree of “math”. Lastly, feel free to bring a single two-sided sheet if you want, upon which you can put anything (e.g., formulae, graphs, notes, , smiley faces, etc…).
• 11.26.15 - Neurons: Spikes, Ion channels, and Synapses (cont.)
  • Slides
• 11.24.15 - Neurons: Spikes, Ion channels, and Synapses
  • Slides
• 11.19.15 - Low Reynolds # (cont.)
  • Slides
• 11.17.15 - Motility (cont.), (basic) Fluid mechanics
  • Slides
  • Matlab codes from class: EXrandomWalk1D.m and EXwalker2D.m
• 11.12.15 - Diffusion (cont.), Motility
  • Slides
• 11.10.15 - What is 'biophysics’?, Diffusion
  • Slides

References

• Berg, HC (1993) Random walks in biology
• Berg, HC (2000) Motile behavior of bacteria
• Bialek, W. (2012) Searching for principles
• Chow & Skolnick (2015) Effects of confinement on models of intracellular macromolecular dynamics (PNAS)
• Clarke et al (2015) Contrast coding in the electrosensory system: parallels with visual computation (Nature Neurosci. Rev.)
• Delgutte, B (1997) Auditory Neural Processing of Speech
• Douarche et al. (2015) Bacillus subtilis Bacteria Generate an Internal Mechanical Force within a Biofilm (Biophys. J.)
• Duchesne et al. (2015) Bacterial Motility Reveals Unknown Molecular Organization (Biophys. J.)
• Harman et al. (2013) Viscous Dynamics of Lyme Disease and Syphilis Spirochetes Reveal Flagellar Torque and Drag (Biophys. J.)
• Kasdorf et al. (2015) Diffusion Regulation in the Vitreous Humor (Biophys. J.)
• Mainen & Sejnowski (1995) Reliability of spike timing in neocortical neurons (Science)
• Marx (2014) A deep look at synaptic dynamics (Nature)
• Nelson, P (2004) Biological physics : energy, information, life
• Rieke et al (1996) Spikes: Exploring the Neural Code
• Stevens, KN (1998) Acoustic phonetics
• Weiss, TF (1996) Cellular biophysics
• Zhang & Peskin (2015) Improved signaling as a result of randomness in synaptic vesicle release (PNAS)

Miscellaneous/Resources

• What is biophysics? (according to the Biophysical Society)