Physical & Quantitative Biology, CHE/PHY 558

Spring 2013 / MWF 10 – 11 AM in Laufer Center 101

Ken Dill, Course PI

The central idea of this course is the free energy, the quantitative way we understand driving forces, i.e., the equilibria and rates in chemistry, physics and biology. We describe the underpinning components, the entropy and energy. We explore the microscopic interactions -- including hydrogen bonding, van der Waals, electrostatics and hydrophobic forces -- that explain physical and chemical mechanisms in biology and are the workhorse tools in computational drug discovery. We show how these basic ideas are applied: binding affinities are the basis for drug discovery; coupled binding is the basis for how biological machines convert energy and transduce signals; and polymer free energies are the basis for the folding of protein and RNA molecules.

Please login to get the links to the videos

1/28 Intro. Structural basis of biology. Time & space scales.   Dill
1/30 Probabilities. Counting states as a basis of entropy. MDF 1, 2 Dill
2/01 Entropy and Energy as driving forces. MDF 3 Dill
2/04 Partial derivatives. MDF4 de Graff
2/06 Max Ent and the Boltzmann distribution law. MDF 5 de Graff
2/08 Energies and enthalpies. Thermodynamic states. MDF 6 Dill
2/11 Free energies, chemical potentials. MDF 8, 9 Dill
2/15 Microscopic modeling and the Boltzmann law. MDF 10 Dill
2/18 Equilibrium constants. Binding affinities. MDF 13 Dill
2/20 Liquids & phase equilibria. MDF 14 Dill
2/22 Solvation. Free energies of transfer. MDF 16 Dill
2/22 Diffusion. Fick's Law. Physical dynamics. MDF 17, 18 Dill
2/25 Chemical rate models. Mass-action kinetics. MDF 19 Dill
2/27 Transition states. Activation barriers. MDF 19 Dill
3/01 Coulombic interactions. How charges interact. MDF 20 Dill
3/04 Electrostatic potentials. MDF 21 Wang
3/06 Electrochemical equilibria. MDF 22 Dill
3/08 How salts shield charges. The Poisson-Boltzmann model. MDF 23 Dill
3/11 Intermolecular forces: van der Waals, dipolar, hydrogen bonds. MDF 24 Dill
3/13 Properties of water. Hydrophobic solvation. MDF 30, 31 Dill
3/15 Polymers: random-flights, entropies & constraints. MDF 33, 34 Strey
3/18 Spring Break. No class.    
3/22 Spring Break. No class.    
3/25 Polymer solutions: Flory-Huggins theory. MDF 32, 33 Strey
3/27 Adsorption, binding polynomials. MDF 27 Dill
3/29 Binding cooperativity. MDF 28 Wang
4/01 Bio-machines. MDF 29 Wang
4/03 Protein structures. PP1 Seeliger
4/05 Protein function and mechanisms. PP2 Seeliger
4/08 Protein stability. PP3 Dill
4/10 Protein cooperativity: helix-coil transitions. PP4 Dill
4/12 Protein folding & aggregation. PP4 Dill
4/15 Protein folding kinetics. Markov models. Energy landscapes. PP5 Wang
4/17 Protein evolution and sequence space. PP6 Wang
4/19 Bioinformatics, sequence comparisons. PP7 Dill
4/22 Drug discovery 1: Lead identification: screening, informatics, DOCK.   Rizzo group
4/24 Drug discovery 2: computing binding affinities.   Rizzo group
4/26 Role of physical & computational modeling in biopharma.   Cornell
4/29 Student project presentations.    


Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person¹s work as your own is always wrong. Any suspected instance of academic dishonesty will be reported to the Academic Judiciary. For more comprehensive information on academic integrity, including categories of academic dishonesty, please refer to the academic judiciary website at

Email to your University email account is an important way of communicating with you for this course.  For most students the email address is This email address is being protected from spambots. You need JavaScript enabled to view it. ¹, and the account can be accessed here:  *It is your responsibility to read your email received at this account.*

For instructions about how to verify your University email address see this: You can set up email forwarding using instructions here: If you choose to forward your University email to another account, we are not responsible for any undeliverable messages.

See the policy statement regarding religious holidays at

Students are expected to notify the course professors by email of their intention to take time out for religious observance.  This should be done as soon as possible but definitely before the end of the add/drop¹ period.  At that time they can discuss with the instructor(s) how they will be able to make up the work covered.

If you have a physical, psychiatric/emotional, medical or learning disability that may impact on your ability to carry out assigned course work, you should contact the staff in the Disability Support Services office [DSS], 632-6748/9. DSS will review your concerns and determine, with you, what accommodations are necessary and appropriate. All information and documentation of disability is confidential. Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and Disability Support Services. For procedures and information go to the website:

Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the University Police and the Office of University Community Standards any serious disruptive behavior that interrupts teaching, compromises the safety of the learning environment, and/or inhibits students¹ ability to learn. See more here:

End of course evaluations have started for the courses listed below, please spend some time now to complete the surveys.