Course Syllabus

Useful Links

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Lecture Material

How to turn in assignments

Complete zipfile of the software used

 

This course is an introduction to biophysics examining many topics in this broad area. This is the first biophysics course taught by the Physics department. Participation of upper division students from other majors is strongly 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.

 

Diffusion and Brownian motion Physical and mathematical underpinnings: Langevin eqn, diffusion eqn, Einstein Relation.

3D Diffusion

Biological applications

• Sedimentation, bacterial metabolism, pattern formation

Electrostatic interactions

Physical and mathematical underpinnings:

• Poisson-Boltzmann eqn and its solution

                    

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

Electrophoresis in nanopillars

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

• Approach to steady state

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

• Correlation analysis

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

Formation of spots

Tomography

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

 

X-ray crystallography 2D structure reconstruction using heavy atom substitution

2D X-ray diffraction

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" covering 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

• The homework will be mostly in the form of projects that take a week to complete. Most of the projects are designed to be collaborative and are done in teams with normally three students, each with different backgrounds. There will also be the option of longer projects that take two weeks, that will be more challenging and require more initiative. Follow the instructions in How to turn in assignments carefully.
• Weight: 50%

 

Quizzes

• 3 half hour quizzes during the quarter on Thursday: April 18, May 2, and May 23, largely based on the homework. 
• Weight: 30%

Test accommodation is available to DRC students. Please let the instructor know immediately if this is requested so proctoring can be arranged.

Final Presentations

The last week of class will be devoted to given presentations on more challenging projects that the team has developed.

• Weight: 20%

Acknowledgements

 

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

 

Title IX reporting

Please be aware that under the UC Policy on Sexual Violence and Sexual Harassment, faculty and student employees (including Teaching Assistants, Readers, Tutors, etc.) are “responsible employees” and are required to notify the Title IX Officer of any reports of incidents of sexual harassment and sexual violence (sexual assault, domestic and dating violence, stalking, etc.) involving students. Academic freedom exceptions exist for disclosures made within a class discussion or assignment related to course content; under those conditions only, a report to the Title IX Officer is not required. 

You might also not be aware, but if you discriminate against a student based on gender, for example,  show a pattern of ignoring a teammate based on gender, this can get reported to faculty who will then be obligated to report this behavior to the Title IX Officer.