Complete tarball of the software used

This course is an introduction to biophysics examining many topics in this broad area. This will be the first biophysics course taught by the Physics department. However the participation of upper division students from other majors is encouraged. The course will cover a wide range of topics, applying physical principles and techniques to different problems in biology. There will be a number of projects for students to collaborate on. Varied backgrounds in a team, such as biology, and physics, will enhance the learning experience.

These are a preliminary list of topics to be covered. The exact list will depend on the interest and backgrounds of the students taking the course.

**3D Diffusion**

### Diffusion and Brownian motion

Physical and mathematical underpinnings:

- Langevin eqn, diffusion eqn, Einstein Relation.

### Biological applications

- Sedimentation, bacterial metabolism, pattern formation

### Electrostatic interactions

Physical and mathematical underpinnings:

- Poisson-Boltzmann eqn and its solution,

**Electrophoresis in nanopillars**

### Chemical Forces

- Chemical Potential and Chemical reactions
- Electrophoresis
- Self-assembly, micelles, cell membranes

### Cooperative transitions

- Helix coil transition
- Stretching of macromolecules
- Protein folding
- Unzipping of DNA

### Machines in membranes

- Electro-osmotic effects
- Ion pumping

### Nerve Impulses

- Action Potentials
- Ion Channels

### Physical Techniques and related biology

- X-ray diffraction, light and neutron scattering
- Nuclear magnetic Resonance
- Fluorescence
- DNA Microarrays
- Manipulation of bio-molecules using optical tweezers.
- Tomography
- Patch clamps

These are some simulation projects using "scipy" to illustrate and explore many of the biophysics problems above.

### Two dimensional diffusion

### Three dimensional Brownian motion

- Absorption of a diffusion particle to a site on a surface

### Brownian motion of a tethered molecule in an optical trap

**Formation of Spots**

### Pattern formation and diffusion

- How nonlinear partial differential equations produce patterns
- Why a cheetah has stripes on their tails but spots on their body.
- How instabilities produce patterns

### Tomography

- You are given 1d projections of an object at different angles
- and will be guided through how to construct the original object

**2D X-ray diffraction**

### X-ray crystallography

- 2D structure reconstruction using heavy atom substitution

### De-noising images

- Filtering, and deconvolution

### Stretching DNA

## Reference Material

A lot of material can be found on the web. See the useful links page. However there is also an excellent hardcopy book by Philip Nelson "Biological Physics" available at the Bay Tree Bookstore that will has a clear exposition and good problems in many areas of biophysics. In assignments, I will give reference to web material as well.

## Grading and Evaluations

Since this is an interdisciplinary topic, the way students participate in the course will vary. Therefore evaluation of student performance will depend on this. The instructor will try hard to gauge how much has been learned and this will be based on several factors.

### Homework

This is divided up into book problems and projects. Most of the projects are designed to be collaborative and collaboration is strongly encouraged.

### Quizzes

I will give 3 half hour quizzes during the quarter on Tuesday: April 19, May 3, and May 17, largely based on the homework.

### Final

A final exam Monday June 6, 8:00AM-11:00AM

## Acknowledgements

This work was funded by National Science Foundation CCLI Grant DUE-0942207.