Biophysics: The physics of life

Learning objectives

By the end of the course, the student will be able to:

• Recognize the basic physical principles behind cellular processes (how things happen to just what things happen)
• Explore and explain life processes (and other physical processes) using the concept of free energy
• Recognize and understand the interplay between heat and work in the processes of life
• Have an intuitive understanding of the role of entropy, especially in life processes
• Understand the relationship between free energy and entropy and how the former takes into account the latter and mimics physical intuition

Syllabus

click here

Schedule

kBT = 3;
DeltaE = 4;
state = Table[
 If[RandomReal[] < 1/(1 + Exp[DeltaE/kBT]), 1, 2], {i, 1, 
 100}];
ListPlot[state, PlotRange -> {.7, 2.1}]

Project Ideas

• Simulate protein folding with a toy model
• Do a literature search and propose modeling and experiments to understand why cryophiles and thermophiles can get away with using the same proteins in vastly different temperature regimes.
• Simulate a simple biomolecular machine
• Propose an idea from here
• Something about Boltzmann distributions like this
• A project based on Statistical thermodynamics of helix–coil transitions in biopolymers
• Build a real circuit that models how signals move on along the axon.
• Build a computational model for tethered Brownian motion
• Model self-assembly by some simple computational model, or another (there are probably lots of other models too. You could even make one up perhaps.)
• Do chapter 9 from our text
• Do chapter 12 from our text
• Borrow one of my many books on biophysics. Do a chapter or section from one of them.
• Study "ratchets." Make a simulation. (useful article here) Also check out: D. Astumian, Science 276, 917 (1997), D. Astumian: Making Molecular Motors. Scientific American, July 2002.
• Understand entropy and chemical potential better.
• Computational modeling based on Wang-Landau Algorithm