Physical & Quantitative Biology, CHE/PHY 558

Fall 2015 / MWF 10 – 10:50 AM in Laufer Center 101

Gabor Balazsi, Course PI

Course goals: 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.

(Click here to open the course page of 2014)

Please login to get the links to the videos

08/24 Intro. Probability, statistics.
[watch video: ] [Slides]
MDF1, 2 Gabor Balazsi
08/26 Entropy and energy as driving forces.
[watch video: ] [Slides]
MDF 2, 3 Gabor Balazsi
08/28 Optimization methods.
[watch video: ] [Slides]
MDF 4 Gabor Balazsi
08/31 Max Ent & the Boltzmann principle.
[watch video: ] [Slides]
MDF 5 Gabor Balazsi
09/02 Energies, enthalpies, thermo states.
[watch video: ] [Slides]
MDF 6 Gabor Balazsi
09/04 Free energies, chemical potentials.
[watch video: ] [Slides]
MDF 8, 9 Gabor Balazsi
09/07 NO CLASS, Labor day
09/09 Microscopic modeling & Boltzmann Law.
[watch video: ] [Slides]
MDF 10 Ken Dill
09/11 Equilibrium constants, binding affinities.
[watch video: ] [Slides]
MDF 13 Gabor Balazsi
09/14 Liquids, phase equilibria.
[watch video: ] [Slides]
MDF 14 Gabor Balazsi
09/16 Solvation, free energies of transfer.
[watch video: ] [Slides]
MDF 15,16 Gabor Balazsi
09/18 Coulomb & electrostatics: how charges interact.
[watch video: ] [Slides]
MDF 20 Gabor Balazsi
09/21 Electrostatic potentials.
[watch video: ] [Slides]
MDF 21 Gabor Balazsi
09/23 Electrochemical equilibria, batteries.
[watch video: ] [Slides]
MDF 22 Gabor Balazsi
09/25 Salts shield charges. Poisson-Boltzmann
[watch video: ] [Slides]
MDF 23 Gabor Balazsi
09/28 Intermolecular interactions.
[watch video: ] [Slides]
MDF 24 Gabor Balazsi
09/30 Adsorption & binding, Michaelis-Menten, catalysis.
[watch video: ] [Slides]
MDF 27 Gabor Balazsi
10/02 Protein structures.
[watch video: ] [Slides]
PP1 Emiliano Brini
10/05 Protein function & mechanisms.
[watch video: ] [Slides]
PP2 Markus Seeliger
10/07 Binding cooperativity.
[watch video: ] [Slides]
MDF 28 Jason Wagoner
10/09 Bio-machine principles.
[watch video: ] [Slides]
MDF 29 Jason Wagoner
10/14 Polymers 1: conformations & random flights.
[watch video: ] [Slides]
MDF 33, 34 Helmut Strey
10/16 Polymers 2: polymer solutions, Flory-Huggins.
[watch video: ] [Slides]
MDF 32, 33 Helmut Strey
10/19 Water: pure and as a solvent.
[watch video: ] [Slides]
MDF 30, 31 Jin Wang
10/21 Diffusion, Fick's Law, Physical Dynamics.
[watch video: ] [Slides]
MDF 17, 18 Jin Wang
10/23 Chemical rates.  Mass-action kinetics
[watch video: ] [Slides]
MDF 19 Gabor Balazsi
10/26 Transition states & activation processes.
[watch video: ][Slides]
MDF 19 Gabor Balazsi
10/28 Protein folding & stability. PP3 Jin Wang
10/30 Cooperativity in proteins.
[watch video: ][Slides]
PP4 Markus Seeliger
11/02 Protein folding & aggregation.
[watch video: ][Slides]
PP4 Emiliano Brini
11/04 Folding kinetics & energy landscapes.
[watch video: ][Slides]
PP5 Jin Wang
11/06 Protein evolution and sequence space.
[watch video: ][Slides]
PP6 Alberto Perez
11/09 Bioinformatics.[watch video: ][Slides] PP7 Alberto Perez
11/11 Gene regulation.[watch video: ][Slides] Gabor Balazsi
11/13 Natural and synthetic gene networks.[watch video: ][Slides] Gabor Balazsi
11/16 Drug discovery in industry: Wendy Cornell from Merck [watch video: ][Slides] Wendy Cornell
11/18 Drug discovery & methods.[watch video: ][Slides] Rob Rizzo
11/20 Extra day Review for final exam.
11/25 NO CLASS, Thanksgiving break.
11/27 NO CLASS, Thanksgiving break.
11/30 Research Project Presentations.
12/02 Research Project Presentations.

MDF = Molecular Driving Forces, chapter numbers.
PP = Protein Principles, draft textbook.


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: