Physical & Quantitative Biology, CHE/PHY 558

Fall 2015 / MWF 10 – 11 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)


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DateTopicReadingSpeaker
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. MDF 4 Gabor Balazsi
08/31 Max Ent & the Boltzmann principle. MDF 5 Gabor Balazsi
09/03 Energies, enthalpies, thermo states. MDF 6 Gabor Balazsi
09/05 Free energies, chemical potentials. MDF 8, 9 Gabor Balazsi
09/09 Microscopic modeling & Boltzmann Law. MDF 10 Ken Dill
09/11 Equilibrium constants, binding affinities. MDF 13 Gabor Balazsi
09/14 Liquids, phase equilibria. MDF 14 Gabor Balazsi
09/16 Solvation, free energies of transfer. MDF 16 Gabor Balazsi
09/18 Coulomb & electrostatics: how charges interact. MDF 20 Gabor Balazsi
09/21 Electrostatic potentials. MDF 21 Gabor Balazsi
09/23 Electrochemical equilibria, batteries. MDF 22 Gabor Balazsi
09/25 Salts shield charges. Poisson-Boltzmann MDF 23 Gabor Balazsi
09/28 Intermolecular interactions. MDF 24 Gabor Balazsi
09/30 Adsorption & binding, Michaelis-Menten, catalysis. MDF 27 Gabor Balazsi
10/02 Protein structures. PP1 Markus Seeliger
10/05 Protein function & mechanisms. PP2 Markus Seeliger
10/07 Binding cooperativity. MDF 28 Jason Wagoner
10/09 Bio-machine principles. MDF 29 Jason Wagoner
10/12 MIDTERM EXAM
10/14 Polymers 1: conformations & random flights. MDF 33, 34 Helmut Strey
10/16 Polymers 2: polymer solutions, Flory-Huggins. MDF 32, 33 Helmut Strey
10/19 Water: pure and as a solvent. MDF 30, 31 Jin Wang
10/21 Diffusion, Fick's Law, Physical Dynamics. MDF 17, 18 Jin Wang
10/23 Chemical rates.  Mass-action kinetics. MDF 19 Gabor Balazsi
10/26 Transition states & activation processes. MDF 19 Gabor Balazsi
10/28 Protein folding & stability. PP3 Markus Seeliger
10/30 Cooperativity in proteins. PP4 Markus Seeliger
11/02 Protein folding & aggregation. PP4 Markus Seeliger
11/04 Folding kinetics & energy landscapes. PP5 Jin Wang
11/06 Protein evolution and sequence space. PP6 Alberto Perez
11/09 Bioinformatics. PP7 Alberto Perez
11/11 Gene regulation. Gabor Balazsi
11/13 Natural and synthetic gene networks. Gabor Balazsi
11/16 Drug discovery & methods. Rob Rizzo
11/18 Drug discovery in industry: Wendy Cornell from Merck Wendy Cornell
11/20 Extra day Review for final exam.
11/23 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.


 

ACADEMIC INTEGRITY
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 http://www.stonybrook.edu/uaa/academicjudiciary/

ELECTRONIC COMMUNICATION
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RELIGIOUS OBSERVANCES
See the policy statement regarding religious holidays at http://www.stonybrook.edu/registrar/forms/RelHolPol%20081612%20cr.pdf

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.


DISABILITIES
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: http://www.sunysb.edu/ehs/fire/disabilities.shtml.

CRITICAL INCIDENT MANAGEMENT
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: http://www.stonybrook.edu/sb/behavior.shtml