Modern Biophysics

Steven Plotkin (University of British Columbia)

Sep 3, 2025 — Dec 3, 2025

About the course

This graduate course is designed to provide graduate students with key concepts and practical applications in Biophysics, with an emphasis on the quantitative tools as they are used in current research. Biophysics is a highly interdisciplinary field—the researchers who attend the annual Biophysical Society meeting, for example, come from departments spanning all of the STEM disciplines. Nevertheless, they share a common interest to establish a quantitative understanding of living matter. Despite growing interest however, a gap remains in graduate training to prepare students to contribute effectively to this broad and rapidly evolving field. This course aims to address this gap by covering both foundational and advanced concepts and applications that are commonly used by practicing biophysicists today. The structure of the course will follow selected advanced material from Physical Biology of the Cell by Rob Phillips, Jane Kondev, Julie Theriot, and Hernan G. Garcia. Each topic will be introduced conceptually, developed mathematically, and explored through real biological case studies using both textbook material and current literature. Given student interest, the course may include interviews with leading biophysicists on their recent published work. Topics will include:

Diffusion problems in biology
Enzymatic reactions including ODEs, diffusion-limited reactions, and Michaelis-Menton reactions
Statistical mechanics as it applies to Biology, including Gibbs free energy of biochemical reactions
Liquid-liquid phase separation, and its role in the cell and in transcription
Polymer physics; DNA looping, persistence length, polymer entropy
Heterogeneous mixtures and osmotic pressure
Quantitative analysis of genetic networks
Expression distributions of transcription and translation
Phase portrait analysis and stability/metastability of cellular states
Genetics of enhancers – from a biophysical perspective
Pattern formation including Turing patterns, symmetry breaking in an embryo
Quantitative genomics (time permitting)

Registration

This course is available for registration under the Western Dean's Agreement. To register, you must obtain the approval of the course instructor and you must complete the Western Dean's agreement form , using the details below. The completed form should be signed by your home institution department and school of graduate studies, then returned to the host institution of the course.

Enrollment Details

Course Name: Directed Studies in Physics (A)
Date: Sep 3, 2025 — Dec 3, 2025
Course Number: PHYS_V 555A
Section Number: Section 104
Section Code

Instructor(s)

Steven Plotkin
steven.plotkin@ubc.ca
University of British Columbia

For help with completing the Western Dean’s agreement form, please contact the graduate student program coordinator at your institution. For more information about the agreement, please see the Western Dean's Agreement website

Other Course Details

Class Schedule

Wed, Fri 10am-11:30am (classes will begin Sept. 10)

Remote Access

Remote participation will be via zoom. Lectures will also be recorded and shared via UBC’s media capture system Panopto. Annotated notes on pre-distributed PDF slides are made during class using an iPad, recorded in real time, and uploaded to UBC’s Canvas server after class, along with links to the lecture recording.

Availability

This course may be open to students at universities outside of the PIMS network.

Grading

There will be no Final exam, instead there will be a final project. I’ve tentatively planned for an in-class midterm, but as a directed studies class, this may become a “take-home” midterm. For percentages, here is a tentative breakdown:

Homework (45%)

Homework due each Sunday at 11:59 pm.

Homework is assigned a week prior to the due date. I will allow late homework, however a 10% penalty per day after the due date is applied to late HW. There will be ~11 homework assignments. Assignments are roughly the same length; The points for each assignment will be weighted proportional to the number of problems in it.

Midterm (20%)

The midterm will take place on evening of Nov 13 or Nov 14 at 6 pm.

The content cut-off for the material will be up and including the Friday before midterm break (Nov 7) and the format will be discussed in class in advance. Email me by Friday Sept 12 if you have a conflict (steve@phas.ubc.ca). The in-class midterm may be replaced with a take-home midterm. |

Final Project (20%)

Date and time the final project is due will be announced, but it will be some time during the Dec exam period. We will discuss how to best design these projects to be most beneficial to everyone.

Guest speaker interviews and Lab Tutorial (15%)

I am thinking of including interviews of postdocs or professors, as I have done in the past. If we do this, we will read an assigned publication by a guest scientist or their lead first-author student/PDF, and we will then interview that scientist/student on the paper. Both general and specific questions may be asked during each interview. However, technical questions specific to the paper are essential for credit. The number of interviews we have is TBD.

One of your planned assignments will also be to complete a lab tutorial involving some more open-ended questions about experimental observations, which will be described further in Module 7 of the course.

Textbook

The textbook for Physics 305 is Physical Biology of the Cell (2nd edition), by Rob Phillips, Jane Kondev, Julie Theriot, and Hernan Garcia. It is available from multiple resources including Amazon as either a paperback or eTextbook. Downloadable resources for the text are here. We will also use material from select journal sources.