Biological Physics

Overview

The course is not lecture-based. It is built from guided study modules covering cellular biophysics, diffusion, fluorescence spectroscopy and microscopy, single-molecule and super-resolution imaging, and computational image analysis. Half of the fourteen currently available modules include a laboratory component, carried out on the research instruments in the Lidke lab.

Module selection depends on degree program and prior background. A physics undergraduate and a biomedical sciences graduate student enrolled in the same semester will take different modules, and will work different problems within the modules they share.

There is no required text. Each module lists its own readings, drawn largely from Alberts, Molecular Biology of the Cell; Phillips et al., Physical Biology of the Cell; Nelson, Biological Physics; Lakowicz, Principles of Fluorescence Spectroscopy; and Pawley, Handbook of Biological Confocal Microscopy, together with primary literature. Copies of the main reference texts can be borrowed from the instructor.

Course format

Credits and units

Modules are valued in units according to scope and workload: most are worth one unit, and modules with extensive laboratory or advanced content are worth two. Each credit of enrollment is three module units, so a three-credit semester is nine units.

Selection and pace

Modules are chosen in consultation with the instructor and finalized in the first two weeks. Students then work through them individually — reading, problem sets, and laboratory work — meeting with the instructor regularly to review progress. Laboratory sessions are scheduled one at a time, both for instrument access and for direct instruction. Some students run two modules in parallel; others work strictly in sequence.

Structure of a module

Each module supplies curated readings, a problem set matched to the student’s background, a laboratory or computational component where applicable, and a short exam at the end. Laboratory modules end in a written report: the concentration of an unknown determined by absorbance, a measured point spread function, a fiber-coupling efficiency, a reconstructed super-resolution image.

Differentiation by program

Physics and engineering students work the theoretical derivations and computational implementations; biomedical sciences students work the experimental data analysis and biological interpretation. Graduate students are held to a higher standard on laboratory work and add a short literature review to each module.

Software and accounts

Computational work may be done in MATLAB (UNM site license), Python, or Julia. A few analysis tools are MATLAB-specific — the lab’s smite single-molecule package, for instance — and a lab workstation is available for that work. Students need a computer able to run scientific computing software and a GitHub account.

Modules

Fourteen modules are available in Fall 2026, grouped below by area. Further topics from the broader curriculum can be developed on request — see available by request.

• lab includes a laboratory component
• 2 units counts as two module units
• advanced for upper-division physics majors and graduate students; untagged modules suit all students

Available by request

The full curriculum runs to roughly forty modules. The topics below are planned but not yet built out as complete modules; any of them can be developed for a student with a specific research need, given notice early in the semester.

• Membranes and Lipids L
• Muscle and Motor Proteins
• Polymer Models
• Free Energy and Entropic Forces
• Ion Channels
• Molecular Dynamics
• X-ray Crystallography
• AFM and SNOM
• Optical Tweezers L
• Gel Electrophoresis L
• Bio-conjugation Techniques L
• DNA: PCR, Sequencing, Origami L
• Correlation Methods (FCS, ICS, RICS)
• Optical Design in OSLO/Zemax
• CAD and Mechanical Design
• Programming I in Python or Julia
• Image Analysis II
• Estimation Theory I: likelihood and curve fitting
• Estimation Theory II: Bayesian inference and MCMC
• GPU/CUDA Programming
• Computer Control of Instruments
• Microfluidics L
• 3D Printing L
• Develop a New Module 3 units

Recommended sequences

Suggested orderings for common degree programs, each totaling nine module units — a full three-credit enrollment. These are starting points rather than requirements; students enrolling for one or two credits take the first three or six units.

• Biology
• Theory
• Optics & microscopy
• Computation

Starting points

Safety modules come before the work they cover: Lasers and Laser Safety before any microscope use, Chemical and Bio Safety before any wet-bench work.

Enrolling

Course materials live in private repositories in the class GitHub organization, UNMBiophysicsFall2026 — one repository per module, holding the readings, problem sets, laboratory protocols, sample data, and analysis code. Enrolled students are added to the organization during the first week and receive the full syllabus — grading, policies, and schedule — along with the module repositories for their selected sequence and GitHub Classroom repositories for submitting work.

Registration is through LoboWeb: PHYS 480 for undergraduates, PHYS 581 for graduate students. A GitHub account is needed in the first week; accounts are free.

Questions about module selection, whether a by-request module can be developed around a particular research problem, or how the course fits a degree program: klidke@unm.edu, or PAIS 2218 during office hours.