Biophysical Techniques (BPHS 4090/PHYS 5800)

Biophysical Techniques (BPHS 4090/PHYS 5800) Instructors: Prof. Christopher Bergevin (cberge@yorku.ca) Schedule: MWF 1:30-2:30 (CB 122) Website: http://www.yorku.ca/cberge/4090w2017.html York University Winter 2017 Lec.1

What is biophysics? Rene Magritte

Question How do we make a 3-D image of inside the body? http://neurosciencenews.com/files/2014/03/mri-scan-normal-brain-sagital-view.jpg http://sciencenordic.com/sites/default/files/imagecache/620x/mr-uio_none.jpg

Wikipedia

https://nanomri.files.wordpress.com/2011/09/mri.jpg

Question How might we see brain function?

Question How do we make a 3-D image of really small things (e.g., molecular structure)?

Question How do we make a 3-D image of really small things (e.g., molecular structure)? Franklin & Gosling (1953) à How did Watson and Crick actually figure out a double helix for DNA? (we ll come back to this in a bit) Watson & Crick (1953)

Hoppe et al (1983)

Question How do we make a 3-D image of really small things (e.g., molecular structure)?

Hoppe et al (1983)

Some approaches are somewhat straightforward (connection to BPHS 4080) Others are more abstract... (and potentially covered in BPHS 4090) Hoppe et al (1983)

Question How do we make a 3-D image of inside the body? Question How might we see brain function? MRI/NMR CT Ultrasound PET lasers & microscopes etc... How do these things work? à Exploring the answer to this question gets to the heart of 4090 Question How do we make a 3-D image of really small things (e.g., molecular structure of DNA)? Diffraction (e.g. X-ray crystallography) Spectroscopy NMR Electron microscopy Spectrometry Diffusion etc... All of these use a variety of different physical approaches, such as: MRI = quantum nature of spin states CT = absorption of radiation Ultrasound = acoustic transmission/reflection PET = emission of decaying radioactive isotopes X-ray diffraction = scattering stemming from very ordered structures, etc.

ex. MRI imaging Bloch equations MRI nicely illustrates how a wide variety of topics in physics come together, such as: quantum mechanics statistical mechanics spectral analysis (e.g., Fourier) harmonic oscillator Hoppe

ex. X-ray Crystallography Redux How did Watson and Crick actually figure out a double helix? Crystallography nicely illustrates how a wide variety of topics such as: Matter-EM interaction Bragg scattering spectral analysis (e.g., Fourier) etc... Nolting

Aside: DNA Structure à How did Watson and Crick actually figure out a double helix? Mathematically, it is a bit gnarly... http://www.princeton.edu/~wbialek/phy562.html

http://www.princeton.edu/~wbialek/phy562.html

Aside: DNA Structure à How did Watson and Crick actually figure out a double helix? Extracting some of the bits... Note the basics bits you already know: scatters diffraction frequency/wavelength energy of a photon cross-section (wave)vector momentum transfer Ultimately this boils down to: http://www.princeton.edu/~wbialek/phy562.html

Aside: DNA Structure à Based upon theoretical considerations, they knew what to expect... Note: This level of analysis/detail is outside the scope of 4090 (but not 5800?) http://www.princeton.edu/~wbialek/phy562.html

Franklin & Gosling (1953) Watson & Crick Watson & Crick (1953)

Rosalind Franklin (1920-1958) After this period and other periods of hospitalization, Franklin spent time convalescing with various friends and family members. These included Anne Sayre, Francis Crick, his wife Odile, with whom Franklin had formed a strong friendship [...] Even while undergoing cancer treatment, Franklin continued to work, and her group continued to produce results seven papers in 1956 and six more in 1957. [...] She returned to work in January 1958, and she was given a promotion to Research Associate in Biophysics on 25 February. She fell ill again on 30 March, and she died on 16 April 1958 https://en.wikipedia.org/wiki/rosalind_franklin#illness_and_death

Deisenhofer et al. (1984) à With these tools (i.e., x-ray crystallography) in hand, researchers extended the method much more broadly...

Note (re stereo images ): Try crossing your eyes. Once you get it, the 3-D effect is striking Deisenhofer et al. (1984)

Hoppe

This is only tentative, but at least provides some idea of the direction we will be heading in... Course website: http://www.yorku.ca/cberge/4090w2017.html

Some general themes 4090/5800 will touch upon and/or delve into: Ø Ø What is an image? How does one analyze such? How does light and/or radiation interact w/ matter? Biological tissue? Ø Ø Notion of invasiveness (i.e., potentially doing a small bit of harm to do a greater immediate good) Elements of signal processing and computing Ø Ø Fourier analysis (backbone to MRI, CT, ultrasound,.) Interplay re stat. mech. between individual ( microscopic ) and collective ( macroscopic )

Course text (which we will only loosely follow; the bulk of the content will be contained in the course notes/codes) à You can (legitimately!) get a soft copy of the book

What is biophysics? Rene Magritte

I believe that much has been lost in the emergence of the conventional views about the nature of the interaction between physics and biology. By focusing on methods, we miss the fact that, faced with the same phenomena, physicists and biologists will ask different questions. In speaking of biological importance, we ignore the fact that physicists and biologists have different definitions of understanding. By organizing ourselves around structures that come from the history of biology, we lose contact with the dreams of our intellectual ancestors that the dramatic qualitative phenomena of life should be clues to deep theoretical insights, that there should be a physics of life and not just the physics of this or that particular process Bialek (2012)