581 Biophysics

UNM Physics 480/581: Biological Physics

Instructor: Prof. Keith Lidke

Room 2218 PAIS
e-mail: klidke@unm.edu

Lab and Office Hours

Monday and Wednesday at 15:30-16:45 in PAIS 1140, 2410, 2409 The logistics and scheduling of lab experiments will depend on the number of students and the modules under study.

Overview

This course is designed to provide a flexible biophysics curriculum for undergraduate and graduate students from a range of majors and degree programs including Physics and Astronomy, Optics, Engineering and Biomedical Science. This is not a lecture-based course, it is instead organized around a selection of guided study modules that cover a wide range of topics in biophysics, microscopy and spectroscopy. Many modules have a significant laboratory component. The course can be taken for 1 to 3 credits where each credit requires three modules (9 modules required for 3 credits). The class may be taken twice for up to a total of 6 credits.

There is no required text for the class. Many reference resources will be listed or linked in each module.

Grading

Letter grades correspond with numerical scores as given by this scale: Grade Scale. Grades will be assigned based on the following:

Homework and Lab (70%)

Homework assignments and lab experiments will be specific to each module.

Module Exams (30%)

Each module has a corresponding final exam. Exam proctoring will be offered once per week a time and place TBD.

Modules

The modules listed below have attributes indicated by: Appropriate for all undergraduates and graduate students
Appropriate for upper division physics majors and all graduate students
-X counts as X modules
(L) laboratory component
^ Available in Fall 2024. Contact instructor if you had planned to start with other modules.
* May not be available in Fall 2024. Contact instructor if you plan to take this module.

This section will be periodically updated to provide more details about the modules.

Biophysics

Diffusion
Membranes and Lipids (L)
Muscle and Motor Proteins
Polymer Models
Free Energy and Entropic Forces
* Theory of FRET
* Ion Channels
* Molecular Dynamics
* X-ray crystallography
* AFM and SNOM
* Optical Tweezers (L)

Biology and Wet Bench Methods

Chemical and Bio Safety / Buffers and pH (L)
^ Introduction to the Biology of the Cell
BioChemistry
Gel Electrophoresis (L)
Bio-conjugation Techniques (L)
Immunofluorescence (L)
DNA: PCR, Sequencing, Origami (L)

Microscopy, Spectroscopy and Optics

^ Lasers and Laser Safety (L)
Fluorescence Spectroscopy and Imaging-2 (L)
Super-resolution-2 (L)
Single Particle Tracking (L)
Forster Resonant Energy Transfer (FRET)
Point Spread Functions
Correlation Methods (FCS, ICS, RICS, etc)
* Oslo/Zeemax
* CAD / Adobe Inventor

Programming and Data/Image Analysis

^ Programming I: Basic Skills in MATLAB
^ Programming I: Basic Skills in Python
^ Programming I: Basic Skills in Julia
^ Image Analysis
Image Analysis II
Estimation Theory I (Likelihood, Curve fitting)
Estimation Theory II (Bayesian Inference, MCMC)
CUDA Programming
Computer Control of Instruments

Other

* Microfluidics (L)
* 3D Printing (L)
Develop a New Module-3

Recommended Module Sequences

General Reference Material

Installing MATLAB

Create an account at mathworks.com using your UNM email address.
Download and install the latest version of MATLAB (e.g. R2024b). We will not need or use most toolboxes. If you want to save download time and disk space, just install MATLAB and these toolboxes:
- Statistics
- Symbolic Math Toolbox
- Image Processing Toolbox
- Optimization Toolbox
- Parallel Computing Toolbox
- Signal Processing Toolbox
Follow instructions for validating your access with your UNM account.

Keith A. Lidke