Fall 2023 MW 12:30-1:45 PM
Howey S104

Instructor: JC Gumbart
Office: Howey W202
Phone: 404-385-0797
Email: gumbart at physics.gatech.edu
Office Hours (by appointment or whenever you catch me!)

TA: Gvantsa Gutishvili
Office: Howey W210
Email: ggutishvili3 at gatech.edu
Office Hours TBD or by appointment

Full Syllabus

Overview

This course will introduce how physical concepts can be used to gain insight into the working of biological systems at a molecular level.  The material will pull from all areas of physics, but particularly classical and statistical mechanics, with a bit of EM and QM thrown in.  While the mathematics is not onerous, students should feel comfortable with simple matrix and differential equations as well as plotting and manipulating data.  Finally, no prior knowledge of biology is required – just a desire to learn a different way of thinking about complex systems!

Learning Goals

After completion of this course, students will be able to (1) read and understand molecular biophysics papers, (2) analyze data from experiments and simulations, (3) design a testable model of a biophysical phenomenon or system, including writing code for modeling and/or analysis, and (4) communicate their results, both orally and in writing.

Textbooks

Physical Biology of the Cell by Phillips, Kondev & Theriot, 2^nd edition (recommended)
Biological Physics, Philip Nelson, student edition (suggested – as low as $10 for digital version!)
Physical Models of Living Systems, Philip Nelson, 1^st edition (suggested)

Grading

• Class Participation (20%): Students are to be expected to attend all classes and actively participate. A significant amount of learning will come from the discussions in class. This will be graded on the “honor system”, i.e., attendance will not be explicitly taken. However, this is subject to change with advance notice later in the semester at the instructor’s discretion if attendance is generally low or if an individual student is observed to attend infrequently or not at all. 
• Homework (40%; 30% for graduate students): Approximately 6-8 homework sets with problems involving visualization and analysis of biological structures with the program VMD, pencil-and-paper calculations using equations derived in class, and analyzing simple models using Python. Homework will be turned at the beginning of class on the due date. Late homework will be accepted with a 10% penalty for one extra day, 25% penalty for two extra days. Extensions may be granted under specific extenuating circumstances, negotiated in advance.
• Papers + reading questions (15%): The ability to critically read and digest the scientific literature is a skill that has to be learned. Therefore, we will read a few biophysics papers and devote part of a class day to discussing each. Before we discuss them in class, you will write a one-page critique of the paper and turn it in at the beginning of class. The critiques will be scored as 1, 0.5 or 0. If your critique clearly demonstrates that you have read the paper, you will get a 1. If you copy abstract/summary or other parts of the paper, you will get a zero. If you have read the paper but completely missed the point, you will get a 0.5. Missing critique will be scored as zeros. Additionally, you may also be asked to read some material before coming to class and answer a few questions ahead of time, which will be scored in a similar fashion. No late critiques nor answers to reading questions will be accepted.
• Project (25%; 35% for graduate students): In the second half of the term, you will have to carry out a project in which you model a chosen biophysical phenomenon or system. The basis for this project will either be a well-known phenomenon (e.g., propagation of neural excitations) or an experimental paper on a particular protein. In the former case, you will have to design and implement a mathematical model in code, with which you can produce and analyze output for comparison with real data. In the latter case, you will determine a pertinent question about the protein and design a set of molecular dynamics simulations to answer it, including coding your own analysis scripts using VMD. You will have to present the project to the class as well as in a paper to be turned in during finals week. This paper will need to be in a form suitable for publication, with specific formatting provided in class.

Needed programs (we will help you get these installed and running if you have any problems!)

• VMD: This is a molecular visualization program. We will use it to look at and analyze protein structures and simulation data. Please download it for your computer here: VMD Download page (yes, the Windows version is horribly out of date but should still work for most purposes)
• Python has rapidly become one of the most common programming languages used in scientific computing. Therefore, we will use it (Python 3 specifically) occasionally to run pre-written programs and plot data.
  No prior experience is needed! You are welcome to use the interpreter of your choice, but I recommend using Jupyter notebooks. You will first need to install Anaconda; for more details see here. You also need to install vpython and ivisual with the commands
  conda install -c vpython vpython and
  pip install ivisual at the command line.

Schedule (approximate!)

Note: Expect this schedule to change on the fly. The topics will be covered as time permits, but we may move things around or change the format of delivery as needed.

• Week 1, 8/21, 8/23: introduction to biology: messy, hot, and crowded visualization with VMD, stat mech.
• 2, 8/28, 8/30: stat mech, randomness, and distributions; four classes of biomolecules
• 3, 9/6: discuss Gunawardena 2014
• 4, 9/11, 9/13: polymer theory; FJC/WLC models
• 5, 9/18, 9/20: DNA/RNA structure; bending/packing; electrostatics
• 6, 9/25, 9/27: discuss Wang 1997; electrostatics (cont.)
• 7, 10/2, 10/4: amino acid properties, pKa; protein folding
• 8, 10/11: protein synthesis
• 9, 10/16, 10/18: diffusion; discuss Dill 2012, class projects
• 10, 10/23, 10/25: diffusion (cont.); crowding
• 11, 10/30, 11/1: chemical equilibrium, rate equations; cytoskeleton
• 12, 11/6, 11/8: molecular motors (e.g, ATP synthase, kinesin/myosin)
• 13, 11/13, 11/15: discuss Yildiz 2003; genetics, central dogma; gene structure, mutation
• 14, 11/20: genetics (cont.)
• 15, 11/27, 11/29: bioelectricity (ion channels, Nerst potential, Hodgkin-Huxley model, etc.)
• 16, 12/4: QM in biology (photosynthesis, excitation transfer, etc.)
• FINAL EXAM PERIOD (TBD): poster presentations