PHY542/NAN542/PHY498 — Topics in Biophysics I | Learning | Beckstein Lab

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PHY542/NAN542/PHY498 — Topics in Biophysics I

PHY542/NAN542/PHY498 — Topics in Biophysics I

This class serves as an introduction for physicists, chemists, and engineers to biophysics.

The biophysicist applies the ideas and tools of physics to living systems with the goal of quantitatively understanding biological systems. However, biology contains deep unifying concepts of its own and thus physicists coming into biology must have a well-rounded knowledge of not only the physical principles but also of the biological processes to be studied.

This course is an introduction to biophysics for graduate and senior undergraduate students from physics, chemistry, engineering or related fields. The goal of this lecture is to give you the basics to understand and critically analyze recent publications in the interdisciplinary field of biophysics and develop a sense for how to model biological processes using physical principles. We will have lectures and student presentations.

This course runs annually in the Fall semester.

Outline of topics

The topics of this class are:

  1. Molecular architecture of life
    • cells and their building blocks
    • chemical and physical basis of life
    • order-of-magnitude estimates
    • modelling biological processes with basic physical priniples
  2. Biophysical methods
    • probing structure and dynamics experimentally
    • computational methods
  3. Selected Topics: student presentations based on original literature

Recommended pre-requisites

This is a course for Physics undergraduate-seniors or Physics/Chemistry/Engineering graduates. You should know

  • calculus (including ordinary differential equations)
  • statistical mechanics/thermodynamics (at least UG level)

ASU class numbers



A few lectures were replaced by interactive practical sessions (using the students’ or provided laptops):

  1. Protein visualization and analysis with VMD
  2. Analysing MD Simulations with VMD
  3. Structural Bioinformatics


There’s not a single textbook assigned to the course. However, Part I draws particularly on Physical Biology of the Cell1. For background in cell biology and biochemistry most textbooks with “Cell” or “Biochemistry” respectively in the title will probably do, but my favorites are listed below3,4,5.

For a good background in statistical physics, thermodynamics, electrostatics, quantum mechanics as applied to macromolecules in solution I recommend Ken Dill’s Molecular Driving Forces2.

For tips and tricks for quickly calculating and estimating see Street Fighting Mathematics6.


1 Rob Phillips, Jane Kondev, Julie Therlot, Hernan G. Garcia. Physical Biology of the Cell. Second Edition. 2013, Garland Science, New York. Student & Instructor Resource Website

2 Ken A. Dill and Sarina Bromberg. Molecular Driving Forces. 2003, Garland Science, New York.

3 Thomas D. Pollard, William C. Earnshaw, Jennifer Lippincott-Schwartz. Cell Biology. Second Edition. 2008, Saunders/Elsevier, Philadelphia

4 Jeremy M Berg, John L Tymoczko, and Lubert Stryer. Biochemistry. 5th ed, 2002 WH Freeman, New York. Searchable online copy NCBI NBK21154.

5 Carl Branden and John Tooze. Introduction to Protein Structure. 1999. Garland Publishing/Taylor & Francis

6 Sanjoy Mahajan. Street Fighting Mathematics: The Art of Educated Guessing and Opportunistic Problem Solving. 2010, MIT Press, Cambridge. Freely available Creative Commons Edition from the book’s website. See also the MIT Open Courseware Course 18.098 / 6.099.

Discuss: “PHY542/NAN542/PHY498 — Topics in Biophysics I”

February 24, 2014 at 9:20 pm #

The final lectures on Biophysical methods were really helpful. Most of the papers I have come across in my other courses have used one or other of the methods, but they were never explained. It was nice to understand the methods used. I am using the format for critical review I learnt from this course in all similar assignments and it is paying dividends!

Posted by  Sneha Saikia
June 23, 2014 at 3:30 pm #

Topics in Biophysics-1 has been a wonderful experience that has equipped me with technical knowledge and skills. The course is well-organized and has helped me go a long way, right from learning the basics to reviewing a research paper. The assignments were challenging and fun. These were opportunities to learn in greater depth about relevant concepts.

Techniques on how to read and review research papers taught in this course, has made my life a lot easier. Also, the student seminar series has been a rewarding experience. It helped me understand the audience, and thus enriched the delivery of my presentation.

Posted by  Neeta
December 11, 2014 at 11:55 am #

I took PHY 542 as a quantitative elective for my graduate Biomedical Engineering program and it turned out being one of my favorite classes I’ve taken. Whether you have a background in physics, biology, or anything in between, I think this class has something new to offer everyone. The math involved isn’t really hard but it helps to have at least some understanding of thermodynamics and electromagnitism for that portion of the course. I would assume physics/engineering students would have some familiarity with those subjects.

I’d recommend this course to anyone because I loved its structure with the mini seminar-type presentations at the end, how it covers information in a way that will provide something new regardless of your background, and because Dr. Beckstein is a really enjoyable instructor.

Posted by  Derek

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