Physical and Quantitative Biology, BME/CHE/PHY 558

Fall 2019 / 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: 2018, 2017, 2016, 2015, 2014

Please login to get the links to the videos

# Date Topic Reading Speaker
1 08/26 Introduction. Basic Biology. Probability, statistics MDF1, 2 Gabor Balazsi
2 08/28 Combinatorics. Distributions. Extremum principles MDF 2, 3 Gabor Balazsi
3 08/30 Energy and Multiplicity. Multivariate calculus MDF 4 Gabor Balazsi
  09/02 NO CLASS, Labor day    
4 09/04 Multivariate Optimization. Max Ent & Boltzmann principle MDF 5 Gabor Balazsi
5 09/06 Energies vs. Entropy formulation, thermo states MDF 6 Gabor Balazsi
6 09/09 Driving forces. Path integrals MDF 6, 7 Gabor Balazsi, TA Luca A.
7 09/11 Ideal Gas. Carnot cycle MDF 7 Gabor Balazsi
8 09/13 Free energies, chemical potentials MDF 8, 9 Gabor Balazsi
9 09/16 Susceptibilities. Boltzmann Law. MDF 9, 10 Gabor Balazsi, TA: Xin Cao
10 09/18 Partition function. Simple gases, solids MDF 10,11 Gabor Balazsi
11 09/20 Chemical equilibria MDF 12, 13 Gabor Balazsi
12 09/23

Liquids, phase equilibria. Mixtures

 MDF 14, 15 Gabor Balazsi. TA: Yiming Wan
13 09/25

Solvation

 MDF 16 Gabor Balazsi
14 09/27

Diffusion, Fick's Law. Random walks. Time’s arrow

 MDF 17, 18 Gabor Balazsi
15 09/30

Chemical rates. Mass-action kinetics. Transition states

 MDF 19 Gabor Balazsi, TA: Luca A.
16 10/02

Coulomb & electrostatics: charges, potentials, fields

 MDF 20, 21 Gabor Balazsi
17 10/04

Electrochemical equilibria. Batteries

 MDF 22 Gabor Balazsi
18 10/07

Salts+charges. Poisson-Boltzmann. Intermolec. forces

  MDF 23, 24  Gabor Balazsi, TA: Zach F.
19 10/09

Real gas. Phase transitions. Adsorption & binding

 MDF 24,25 Gabor Balazsi
  10/11

MIDTERM EXAM

    
  10/14 NO CLASS, Fall Break/Columbus Day    
20 10/16 Polymers 1: conformations & random flights MDF 33, 34 Helmut Strey
21 10/18 Polymers 2: polymer solutions, Flory-Huggins MDF 32, 33 Helmut Strey
22 10/21

Michaelis-Menten. Catalysis. Cooperativity

 MDF 27, 28 Gabor Balazsi, TA: J. Pachter
23 10/23

Bio-machine principles

 MDF 29 Jason Wagoner
24 10/25

Water: pure and as a solvent

 MDF 30, 31 Emiliano Brini
25 10/28

Protein structures

 PA1 Markus Seeliger
26 10/30 Protein function & mechanisms PA2 Markus Seeliger

27

 11/01 Protein folding & stability PA3 Carlos Simmerling
28 11/04 Cooperativity in proteins PA5 Carlos Simmerling, TA: Roy N.
29 11/06 Folding on Energy Landscapes, and Aggregation PA6 Emiliano Brini
30 11/08 Protein evolution and sequence space PA7 Max Shapino
31 11/11 Bioinformatics PA8 Steve Skiena, TA: Cong Liu
32 11/13 Gene expression and it's regulation   Gabor Balazsi
33 11/15 Natural and synthetic gene networks   Gabor Balazsi
34 11/18 Drug discovery in industry   John H. Van Drie, Van Drie Research, LLC. TA: Luca Agozzino
  11/20 Research Project Presentations    
35 11/22 Drug discovery & methods   Dima Kozakov
  11/25 MIDTERM EXAM 2    
  11/28 NO CLASS, Thanksgiving break    
  11/29 NO CLASS, Thanksgiving break    

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

TAs:  Luca Agozzino, Xin Cao, Yiming Wan, Zachary Fallon, Jonathan Pachter, Roy Nassar, Cong Liu, M. Tyler Guinn.

 

For videos, please go to Blackboard.

 

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
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: http://www.stonybrook.edu/mycloud.  *It is your responsibility to read your email received at this account.*

For instructions about how to verify your University email address see this: http://it.stonybrook.edu/help/kb/checking-or-changing-your-mail-forwarding-address-in-the-epo. You can set up email forwarding using instructions here: http://it.stonybrook.edu/help/kb/setting-up-mail-forwarding-in-google-mail. If you choose to forward your University email to another account, we are not responsible for any undeliverable messages.

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