Physical and Quantitative Biology, BME/CHE/PHY 558

Fall 2018 / MWF 10 – 10:53 AM in Laufer Center 101

Recitations: Mon, 11:00 am – 12:00 pm in Laufer Center 107.

Gabor Balazsi, Course PI

Course goals: The central idea of this course is the free energy, the quantitative way we understand thermodynamic forces driving the equilibria and transition rates in chemistry, physics and biology. We describe the components underpinning 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 cell biology and are the workhorse tools in computational drug discovery. We show how these basic ideas are applied: binding affinities form the basis for synthetic biology and drug discovery; coupled binding explains how biological machines convert energy and transduce signals or control gene activity; and polymer free energies form the basis for the folding of protein and RNA molecules; with implications for molecular and cellular evolution.

Textbook: Molecular Driving Forces by Dill & Bromberg. Garland Science, 2010

Extra textbook: Protein Actions by Bahar, Jernigan & Dill. Garland Science, 2017

Prior years' course syllabi: 2017, 2016, 2015, 2014

Please login to get the links to the videos

#	Date	Topic	Reading	Speaker
1	08/27	Introduction. Basic Biology. Probability, statistics	MDF1, 2	Gabor Balazsi
2	08/29	Combinatorics. Distributions. Extremum principles	MDF 2, 3	Gabor Balazsi
3	08/31	Energy and Multiplicity. Multivariate calculus	MDF 4	Gabor Balazsi
	09/03	NO CLASS, Labor day
4	09/05	Multivariate Optimization. Max Ent & Boltzmann principle	MDF 5	Gabor Balazsi
5	09/07	Energies vs. Entropy formulation, thermo states	MDF 6	Gabor Balazsi
6	09/10	Free energies, chemical potentials	MDF 8, 9	Gabor Balazsi
7	09/12	Microscopic modeling & Boltzmann Law	MDF 10	Gabor Balazsi
8	09/14	Equilibrium constants, binding affinities	MDF 13	Gabor Balazsi
9	09/17	Liquids, phase equilibria	MDF 14	Gabor Balazsi
10	09/19	Solvation, free energies of transfer	MDF 15,16	Gabor Balazsi
11	09/21	Diffusion, Fick's Law, Physical Dynamics	MDF 17, 18	Gabor Balazsi
12	09/24	Chemical rates. Mass-action kinetics	MDF 19	Gabor Balazsi
13	09/26	Transition states & activation processes	MDF 19	Gabor Balazsi
14	09/28	Coulomb & electrostatics: how charges interact	MDF 20	Gabor Balazsi
15	10/01	Electrostatic potentials	MDF 21	Gabor Balazsi
16	10/03	Electrochemical equilibria, batteries	MDF 22	Gabor Balazsi
17	10/05	Salts shield charges. Poisson-Boltzmann	MDF 23	Gabor Balazsi
18	10/08	NO CLASS, Fall Break/Columbus Day
19	10/10	Intermolecular interactions, Phase transitions	MDF 24,25	Gabor Balazsi
20	10/12	Adsorption & binding, Michaelis-Menten, catalysis	MDF 27	Gabor Balazsi
	10/15	MIDTERM EXAM
21	10/17	Binding cooperativity	MDF 28	Gabor Balazsi
22	10/19	Polymers 1: conformations & random flights	MDF 33, 34	Helmut Strey
23	10/22	Polymers 2: polymer solutions, Flory-Huggins	MDF 32, 33	Helmut Strey
24	10/24	Bio-machine principles	MDF 29	Jason Wagoner
25	10/26	Water: pure and as a solvent	MDF 30, 31	Emiliano Brini
26	10/29	Protein structures	PA1	Markus Seeliger
27	10/31	Protein function & mechanisms	PA2	Markus Seeliger
28	11/02	Protein folding & stability	PA3	James Robertson
29	11/05	Cooperativity in proteins	PA5	Emiliano Brini
30	11/07	Folding on Energy Landscapes, and Aggregation	PA6	Emiliano Brini
31	11/09	Protein evolution and sequence space	PA7	Max Shapino
32	11/12	Bioinformatics	PA8	Rob Patro
33	11/14	Gene expression and it's regulation		Gabor Balazsi
34	11/16	Natural and synthetic gene networks		Gabor Balazsi
35	11/19	Drug discovery & methods		Dima Kozakov
	11/22	NO CLASS, Thanksgiving break
	11/24	NO CLASS, Thanksgiving break
	11/26	Drug discovery in industry		John H. Van Drie, Van Drie Research, LLC
36	11/28	Research Project Presentations
	11/30	FINAL EXAM

MDF = Molecular Driving Forces, chapter numbers.
PA = Protein Actions, chapter numbers.

TAs: Luca Agozzino (#1 - #20), Roy Nassar (#21 - #36).

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