Physical and Quantitative Biology, BME/CHE/PHY 558

Fall 2017 / 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 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 regulate gene activity; and polymer free energies form the basis for the folding of protein and RNA molecules.

Prior years' course syllabi: 2016, 2015, 2014


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#DateTopicReadingSpeaker
1 08/28 Intro. Probability, statistics MDF1, 2 Gabor Balazsi
2 08/30 Entropy and energy as driving forces MDF 2, 3 Gabor Balazsi
3 09/01 Optimization methods, multivariate calculus MDF 4 Gabor Balazsi
09/04 NO CLASS, Labor day
4 09/06 Max Ent & the Boltzmann principle MDF 5 Gabor Balazsi
5 09/08 Energies vs. Entropy formulation, thermo states MDF 6 Gabor Balazsi
6 09/11 Free energies, chemical potentials MDF 8, 9 Gabor Balazsi
7 09/13 Microscopic modeling & Boltzmann Law MDF 10 Gabor Balazsi
8 09/15 Equilibrium constants, binding affinities MDF 13 Gabor Balazsi
9 09/18 Liquids, phase equilibria MDF 14 Gabor Balazsi
10 09/20 Solvation, free energies of transfer MDF 15,16 Gabor Balazsi
11 09/22 Diffusion, Fick's Law, Physical Dynamics MDF 17, 18 Gabor Balazsi
12 09/25

Chemical rates.  Mass-action kinetics

MDF 19 Gabor Balazsi
13 09/27

Transition states & activation processes

MDF 19 Gabor Balazsi
14 09/29

Coulomb & electrostatics: how charges interact

MDF 20 Gabor Balazsi
15 10/02

Electrostatic potentials

MDF 21 Gabor Balazsi
16 10/04

Electrochemical equilibria, batteries

MDF 22 Gabor Balazsi
17 10/06

Salts shield charges. Poisson-Boltzmann

MDF 23 Gabor Balazsi
18 10/09

Intermolecular interactions

MDF 24 Gabor Balazsi
19 10/11

Phase transitions

MDF 25 Gabor Balazsi
20 10/13

Adsorption & binding, Michaelis-Menten, catalysis

MDF 27 Gabor Balazsi
10/16

MIDTERM EXAM

21 10/18 Binding cooperativity  MDF 28  Gabor Balazsi
22 10/20 Polymers 1: conformations & random flights MDF 33, 34 Helmut Strey
23 10/23 Polymers 2: polymer solutions, Flory-Huggins MDF 32, 33 Helmut Strey
24 10/25

Bio-machine principles

MDF 29 Jason Wagoner
25 10/27

Water: pure and as a solvent

MDF 30, 31 Emiliano Brini
26 10/30

Protein structures

PA1 Emiliano Brini
27 11/01 Protein function & mechanisms PA2 James Robertson

28

11/03 Protein folding & stability PA3 James Robertson
29 11/06 Cooperativity in proteins PA5 James Robertson
30 11/08 Protein folding: kinetics, Landscapes, and Aggregation PA6 Jason Wagoner
31 11/10 Protein evolution and sequence space PA7 Alberto Perez
32 11/13 Bioinformatics PA8 Alberto Perez
33 11/15 Gene expression and it's regulation Gabor Balazsi
34 11/17 Natural and synthetic gene networks Gabor Balazsi
35 11/20 Drug discovery & methods Rob Rizzo
11/22 NO CLASS, Thanksgiving break
11/24 NO CLASS, Thanksgiving break
36 11/27 Drug discovery in industry John H. Van Drie, Van Drie Research, LLC
11/29 Research Project Presentations
37 12/01 Drug discovery in industry Wendy Cornell, Merck & Co.
12/04 FINAL EXAM

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

TAs: Michael Cortes (#1 - #20) and Cong Liu (#21 - #37).


 

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