Teaching-Biophysics

"Teaching Biophysics" will host a collection of biophysics course syllabi, with the hope that this database of biophysics course syllabi can help standardization of learning outcomes and scope of biophysics courses at different levels. If you are planning to teach a biophysics course for the first time, it can help you finalize the list of topics you would like to cover in your course.

If you are interested in sharing your syllabus here, feel free to reach out to me via email, Twitter or Linkedin.

Tugba Ozturk, PhD

Computational Biophysicist

001. The Physics of Life

A course for non-science-major undergraduates

Syllabus: Shared by Dr. Raghuveer Parthasarathy named as 001.ThePhysicsOfLife_Parthasarathy_Winter2018.pdf

List of topics:

Introduction, Motivation, and Illustrations
Scale and Powers of 10 – In which we get a sense of the size of things
DNA mechanics – In which we examine the physical properties of life’s most important molecule, and why they matter
Proteins – In which we examine the shapes of proteins, and how their shapes are determined
Soap films, cell membranes – In which we examine similarities between the two, and also look more generally at materials that assemble themselves.
Randomness and diffusion – In which we explore the perpetual motion of small things, both its unavoidable causes and its far-reaching consequences
Life at Low Reynolds Number – In which we ask: Why don’t bacteria swim like whales?
Microscopy – In which we ask: How can we see small things?
Surfaces and surface tension – In which we explore the consequences of surface tension on the functioning of your lungs and ask: why can’t you walk on water
On size and shape– In which we ponder how size and shape of can affect an organism’s properties

Learning outcomes: Upon completing the course, students will have enhanced their abilities to:

understand how physical principles guide and constrain life;
assess and interpret graphs and quantitative data;
understand the process by which science generates knowledge.

Typical classroom size and background of students: About 50 students; non-science-major undergraduates

Prerequisites: None

Resources: None

Notes: Dr. Parthsarathy's new pop-science-biophysics book, So Simple a Beginning: How Four Physical Principles Shape Our Living World (2022), would be an appropriate resource for the course, supplemented with exercises. Dr. Parthsarathy mentioned that a few articles from Scientific American and other popular sources were assigned as readings in this course.

002. Introduction to Biophysics

A graduate course

Syllabus: Shared by Dr. Raghuveer Parthasarathy named as 002.IntroductionToBiophysics_Parthasarathy_Fall2020.pdf

List of topics:

INTRODUCTION; PHYSICS, STATISTICS, AND SIGHT: What are the fundamental limits on vision, and how close does biology come to reaching them? (A brief look)
COMPONENTS OF BIOLOGICAL SYSTEMS: What are the components of biological systems? What are the length, time, and energy scales that we’ll care about?
PROBABILITY AND HEREDITY: We’ll review concepts in probability and statistics. We’ll discuss a classic example of how a quantitative understanding of probability revealed how inheritance and mutation are related.
RANDOM WALKS: We can make sense of a remarkable array of biophysical processes, from the diffusion of molecules to the swimming strategies of bacteria to the conformations of biomolecules, by understanding the properties of random walks.
LIFE AT LOW REYNOLDS NUMBER: We’ll figure out why bacteria swim, and why they don’t swim like whales.
ENTROPY, ENERGY, AND ELECTROSTATICS: We’ll see how entropy governs electrostatics in water, the “melting” of DNA, phase transitions in membranes, and more.
MECHANICS IN THE CELL: We’ll look more at the mechanical properties of DNA, membranes, and other cellular components, and also learn how we can measure them.
CIRCUITS IN THE CELL: Cells sense their environment and perform computations using data they collect. How can cells build switches, memory elements, and oscillators? What physical principles govern these circuits?
COOL THINGS EVERYONE SHOULD BE AWARE OF: We live in an age in which we can shine a laser at neurons in a live animal to stimulate it, paste genes into any organism we wish, and read the genetic information in a single cell. It would be tragic to be ignorant of these almost magical things, and they contain nice physics as well!

Learning outcomes: Upon completing the course, students will have enhanced their abilities to:

understand the physical principles that govern the function of important biological phenomena such as DNA packaging, bacterial motion, membrane deformation, and gene regulation;
apply statistical and statistical-mechanical ideas to a wide variety of complex systems;
read contemporary papers in biophysics and follow the aims and approaches.

Typical classroom size and background of students: About 6-12 students; mostly physics graduate students; about 1 chemistry or biology student each time

Prerequisites: A good knowledge of undergraduate physics (especially statistical mechanics) and a corresponding adeptness with math. No prior knowledge of biology

Resources: No mandatory resource, excerpts from the following books:

Biological Physics by Philip Nelson
Physical Models of Living Systems by Philip Nelson,
Physical Biology of the Cell by Rob Phillips, Jane Kondev, Hernan Garcia & Julie Theriotand
Biophysics: Searching for Principles by William Bialek

Tugba thanks to Dr. Parthasarathy for sharing course syllabi and other resources.

003. Biological Physics

A graduate course

Syllabus: Shared by Dr. Diego Krapf named as 003.BiologicalPhysics_Krapf.pdf

List of topics:

Biosensors
Cell biophysics
Complex systems
Electrophysiology
Optical microscopy
Molecular biophysics
Nanotechnology
Neuroscience
Physical chemistry
Quantitative biology
Statistical physics
Soft condensed matter
Systems biology

Learning outcomes: Upon completing the course, students will have enhanced their abilities to:

model the motion of particles and molecules by diffusion
derive the dynamics of active particles and those of colloids in the presence of an electric field
describe the differences between the effects of an electric field in aqueous solutions vs. in vacuum
explain and estimate Debye lengths
discuss the freely jointed chain and the wormlike chain models of biopolymers
model molecular motors using differential equations
apply the formalism of Master equations to solve enzyme kinetics and two-state systems
discuss the physical mechanism of voltage gated ion channels
use the cable equation to compute the propagation of passive electrical signals
describe action potentials

Typical classroom size and background of students: About 15 students; mostly engineering graduate students

Prerequisites: Familiarity multivariate calculus and two semesters of physics

Resources: Biological Physics by Philip Nelson and handouts; The following books are suggested:

Physical Biology of the Cell by Phillips, Kondev, and Theriot (Garland Science, 2009)
Molecular Biology of the Cell, B. Alberts et. al (Garland Science, 2014)

Tugba thanks Dr. Krapf for sharing the course syllabus and other resources.

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