Course Syllabus

Useful Links

Software Help

Lecture Material

How to turn in assignments

Complete zipfile of the software used

 

Online update:

Given the uncertainty of how well internet connectivity will continue to work, I've been advised to have lectures up on Canvas, that is, online, as much as is practically possible. This will allow students to view the lectures even if their connectivity is not optimal for real time interaction. 

Students can therefore watch these prerecorded lectures instead of attempting to watch them live as this, might not be practical. The instructor is happy to answer questions through Zoom or email at times that work with students in the class. 

Part of the class grade has been final presentations, which in previous years, were carried out in class. As this is not possible, we can see if there is a practical way of doing this live in Zoom. However this may not be possible, in which case we will have to figure out some alternative, such as prerecording videos and having them uploaded to Canvas. Or if even that is not possible, having write-ups submitted. But we'll have to see how the situation evolves to determine if and how final presentations can be accomplished.

Homework teams, normally of size 3, will be assigned close to the beginning of the quarter. Please let the instructor know if you have any teammates that you wish to work with. If you wish to drop the course, let the instructor know as soon as possible, so that viable teams can be assigned. 

Like most classes at UCSC, this class was not designed to be delivered online, and it will be challenging to get this to work well for everyone. To make it more viable, students are asked to use Piazza (link on the left) to ask questions. This will allow other students to take advantage of the answers already posted, and also is another way of promoting communication between students. Students are encouraged to attempt to answer each other's questions, even if they're not completely sure about the answer. This was the original intention of Piazza, and this will promote a more positive atmosphere. Also you should search to see if a question was asked before asking a similar question, for obvious reasons.

Students sometimes change their settings so as not to be bothered so much by class announcements in Canvas. However given the lack of a real classroom, and the possibility of rapid changes,  it's very important that announcements are received and acted on quickly. Therefore you should  change your Canvas settings for immediate email receipt of announcements.

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 a couple of 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. If you have a biology background, you won't need to know how to program, or much physics, and if you're a physics major, you won't need to know any biology. It's fine if you do, but the idea of this course is that projects are collaborative. 
• Weight: 80%

 

Final Presentations

The last week of class will be devoted to given presentations on more challenging projects that the team has developed. The time for these presentation should be set to the final exam time: 

Wednesday, June 9        4:00–7:00 p.m.

• 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.