1. Physics 414: Introduction to Biophysics Professor Henry Greenside www
Physics 414: Introduction to Biophysics Professor Henry Greenside August 29, 2017
First row, left to right:
Potassium channel, which is an extraordinary membrane molecule that only allows K+ ions to cross the lipid bilayer.
Kinesin motor molecule transporting vesicle along microtubule railway, crucial for moving proteins in soma to
Optical tweezer experiment that measures the location of a kinesin motor as a function of time. It takes discrete finite steps as it moves.
Second row, left to right:
Superresolution microscopic image of dividing cell, that can observe structure far below the diffraction limit of natural light.
The gene regulatory network for yeast.
An optogenetic experiment, in which light pulses are used to activate or inhibit virally infected neurons with ms precision

2. Today’s Class: The Big Picture and a Pep Talk
The structure and content of the course
Why study biophysics?
Some examples of biophysics.

3. This is required part of the course and counts towards 5% of your grade.
Goal is to encourage you to think actively and critically during each class, and to give me immediate feedback if something needs to be discussed further.
If I have time, I will try to answer some of your questions.

4. How to pronounce your names?
Anyone whose name I did not mention that plans to take the course?

5. Please: no cellphones or laptops during class
Tablets are ok provided that they lie flat on the desk and that you use them to take notes, not to surf the Internet.

6. Some details of the course
Webpage key source of information and files:
Intent is to teach this course as a friendly interactive seminar, with in-class discussions and occasional in-class group projects. I expect everyone to participate often.
Course grade based on
homeworks <=== most important part of course!!
class participation
end-of-class 1-minute questions
one 1.25 hr midterm
3-hour final exam.

7. What 414 will cover
About ten chapters of “Physical Biology of the Cell, 2nd Ed” with occasional supplementary reading. We start with Chapter 6.
Topics mainly at the molecular and cellular level, with emphasis on using physics to interpret biological experiments. In one semester of an intro course, will not be able to address some of the deeper, more interesting questions. (Physics 415!)
No experimental labs. :(

8. Please complete the assigned reading BEFORE class!
Will not be time in class to discuss most details
Class will be more rewarding, insightful if you come prepared to ask questions, participate in discussions.

9. Key physical ideas for 414
Simple harmonic oscillator (small perturbations about equilibrium)
Ideal gas and ideal gas solutions (osmosis)
Statistical physics of multi-level systems
Random walks, entropy, macromolecular structure
(Poisson-Boltzmann model of screening of charges by ions in solution)
Elasticity theory of 1d rods and 2d membranes
Newtonian fluid mechanics and Navier-Stokes equations
Diffusion and random walks
Nonlinear dynamics of chemical kinetics, pattern formation

10. Different physical models for DNA

11. Different physical models for a protein

12. Different physical models for water

13. Key biology ideas for 414
Theory of evolution: incredibly central to biophysics, key reason why understanding function is so hard.
Genetics and nature of inheritance
Cell theory
Unity of biochemistry (common molecular inventories, function)

14. Any Questions?

15. Example of biophysics through class discussion: Why do animals have heads?
Not all animals have heads, e.g., star fish, jelly fish, sea urchins
Biggest organisms are plants that don’t even have a nervous system but they don’t move, at least their center of mass does not. (Tips of roots and branches do move.)
One explanation: animals can react faster if major sensors are moved as close together as possible to reduce delays due to propagation time.
But raises new question: what determines the delay times, how fast can signals propagate in a biological system? If animals had metallic wires, could achieve speeds of order c, but no metal wires. Lord Kelvin’s cable theory applied to cable predicts that speed of pulses in leaky cable obey
V = (1/C)sqrt[D/(Ri Rm)]
So to get high speeds, want big diameter D or small capacitance C. Big D is bad, thick axons make brain bigger, more massive. Can make C small by using myelination, wrap axon with insulating tape (oligodendrocyte). But this is tricky, can’t cover entire axon since will suppress signal. One way to get higher speeds with smaller D is make neurons smaller so they travel distance is smaller, but thermal fluctuations establish lower bound on how small an axon can be and transmit reliably.
If one can’t use wires or light pipes, might try mechanical vibrations but these travel at most at speed of sound and indeed action potential speeds at fastest attain about v/4 for liquid medium. Can one do better by burning ATP molecules, active transport?

16. What are possible mechanisms and speeds that organisms could use to transmit information between internal components like neurons?
Speed of light: but organisms would require conducting wires or light tubes with light-to-chemical-to-light transducers.
Chemical diffusion is major method of communication within a cell for sizes up to about 5 microns, then is too slow. Takes a month for chemical to diffuse to end of 2-cm long axon.
Inside a cell, fastest possible passive signals would be speed of sound, about 1,000 m/s. Fastest action potentials are about 200 m/s, well below the peak mechanical speed.
Any other possibilities? If you could use energy of one or several chemical bonds (ATP), could you speed up transmission? Do animals even need faster transmission?

17. One-minute End-of-class Question