Physical and Quantitative Biology, CHE/PHY 558

Fall 2016 / 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 thermodynamic forces driving, i.e., the equilibria and transition rates in chemistry, physics and biology. We describe the underpinning components of free energy, the entropy and internal energy. We explore the microscopic interactions - including hydrogen bonding, van der Waals interactions, 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 form the basis for drug discovery; coupled binding explains how biological machines convert energy and transduce signals or regulate gene activity; and polymer free energies form the basis for the folding of protein and RNA molecules.

(Click here to open the course webpage of 2015)

(Click here to open the course webpage of 2014)

Please login to get the links to the videos

08/29 Intro. Probability, statistics
[watch video: ] [Slides]
MDF1, 2 Gabor Balazsi
08/31 Entropy and energy as driving forces
[watch video: ] [Slides]
MDF 2, 3 Gabor Balazsi
09/02 Optimization methods
[watch video: ] [Slides]
MDF 4 Gabor Balazsi
09/05 NO CLASS, Labor day
09/07 Max Ent & the Boltzmann principle.
[watch video: ] [Slides]
MDF 5 Gabor Balazsi
09/09 Energies vs. Entropy formulation, thermo states
[watch video: ] [Slides]
MDF 6 Gabor Balazsi
09/12 Free energies, chemical potentials
[watch video: ] [Slides]
MDF 8, 9 Gabor Balazsi
09/14 Microscopic modeling & Boltzmann Law
[watch video: ] [Slides]
MDF 10 Gabor Balazsi
09/16 Equilibrium constants, binding affinities
[watch video: ] [Slides]
MDF 13 Gabor Balazsi
09/19 Liquids, phase equilibria
[watch video: ] [Slides]
MDF 14 Gabor Balazsi
09/21 Solvation, free energies of transfer
[watch video: ] [Slides]
MDF 15,16 Gabor Balazsi
09/23 Diffusion, Fick's Law, Physical Dynamics
[watch video: ] [Slides]
MDF 17, 18 Gabor Balazsi

Chemical rates.  Mass-action kinetics
[watch video: ] [Slides]

MDF 19 Gabor Balazsi

Transition states & activation processes
[watch video: ] [Slides]

MDF 19 Gabor Balazsi

Coulomb & electrostatics: how charges interact
[watch video: ] [Slides]

MDF 20 Gabor Balazsi

Electrostatic potentials
[watch video: ] [Slides]

MDF 21 Gabor Balazsi

Electrochemical equilibria, batteries
[watch video: ] [Slides]

MDF 22 Gabor Balazsi

Salts shield charges. Poisson-Boltzmann
[watch video: ] [Slides]

MDF 23 Gabor Balazsi

Intermolecular interactions
[watch video: ] [Slides]

MDF 24 Gabor Balazsi

Adsorption & binding, Michaelis-Menten, catalysis
[watch video: ] [Slides]

MDF 27 Gabor Balazsi

Binding cooperativity
[watch video: ] [Slides]

MDF 28 Gabor Balazsi
10/19 Polymers 1: conformations & random flights
[watch video: ] [Slides]
MDF 33, 34 Helmut Strey
10/21 Polymers 2: polymer solutions, Flory-Huggins
[watch video: ] [Slides]
MDF 32, 33 Helmut Strey

Bio-machine principles
[watch video: ] [Slides]

MDF 29 Jason Wagoner

Water: pure and as a solvent

MDF 30, 31 Emiliano Brini

Protein structures

PP1 Emiliano Brini
10/31 Protein function & mechanisms PP2 James Robertson
11/02 Protein folding & stability PP3 James Robertson
11/04 Cooperativity in proteins PP5 James Robertson
11/07 Protein folding & aggregation PP5 Jason Wagoner
11/09 Folding kinetics & energy landscapes PP6 Jason Wagoner
11/11 Protein evolution and sequence space PP7 Alberto Perez
11/14 Bioinformatics PP8 Alberto Perez
11/16 Gene regulation Gabor Balazsi
11/18 Natural and synthetic gene networks Gabor Balazsi
11/21 Drug discovery & methods Rob Rizzo
11/23 NO CLASS, Thanksgiving break
11/25 NO CLASS, Thanksgiving break
11/28 Drug discovery in industry John H. Van Drie, Van Drie Research, LLC
11/30 Biological laboratory visit Meet in front of LC 101 at 10 am.
12/02 Research Project Presentations
12/05 Drug discovery in industry Wendy Cornell, Merck & Co.

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: