Instructor: Prof. Keith Lidke

Room 1140, Physics and Astronomy
phone: (505)277-0302

Lab and Office Hours

Tentatively: Wednesday and Thursday at 13:30-16:30 in Physics (Lomas and Yale) room 118/120 (optics lab) and 173/175 (wet lab). The logistics and scheduling of lab experiments will depend on the number of students and the modules under study.


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.


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.

How to Register

If you are registering for the full three credits:
Undergrads: CRN: 59077, PHYC 480 001 ST: Biophysics
Grads: CRN 59079 PHYC 581 002 Adv T: Biophysics

If you are registering for one or two credits:
Undergrads: CRN 26132 PHYC 451 Problems, section 010.
Grads: CRN 16820 PHYC 551 Problems, section 010.


The modules listed below have attributes indicated by:
Appropriate for all undergraduates and graduate students
Appropriate for upper division physics majors and graduate students.
-X counts as X modules
(L) laboratory component
^Available as starting module in Fall 2017. Contact instructor if you had planned to start with other modules.
*May not be available in Fall 2017. Contact instructor if you plan to take this module.

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


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
*Optical Tweezers (L)

Biology and Wet Bench Methods

Chemical and Bio Safety / Buffers and pH (L)
^ Introduction to the Biology of the Cell
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)
*CAD / Adobe Inventor

Programming and Data/Image Analysis

^ Programming I: Basic Skills in MATLAB
^ Image Analysis
Image Analysis II
Estimation Theory I (Likelihood, Curve fitting)
Estimation Theory II (Bayesian Inference, MCMC)
CUDA Programming
Computer Control of Instruments 1: MATLAB
Computer Control of Instruments 2: C, C++, .NET SDK


*Microfluidics (L)
*Machine Shop (L)
Develop a New Module-3

Recommended Module Sequences

Undergraduate with Biophysics Concentration

Biophysics Grad I

Biophysics Grad II

Biomedical Sciences Grad

BioPhotonics Grad

General Reference Material

Installing MATLAB

Create an account at using your UNM email address.
Download and install MATLAB 2014b or later. We will not need or use most toolboxes. If you want to save download time and disk space, just install MATLAB and these toolboxes:
Symbolic Math Toolbox

Image Processing Toolbox
Optimization Toolbox
Parallel Computing Toolbox
Signal Processing Toolbox

At the point where it asks you to validate, you need to sign in with your mathworks account and provide an activation key. The key is given in the pdf linked to this page under the MATLAB section.


MATLAB documentation


Interview with Cleve Moler, creator of MATLAB

Numerical Recipes "