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

Date Topic Reading Speaker
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
10/17 MIDTERM EXAM    
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
[watch video: ] [Slides]

MDF 30, 31 Emiliano Brini

Protein structures
[watch video: ] [Slides]

PP1 Emiliano Brini
10/31 Protein function & mechanisms
[watch video: ] [Slides]
PP2 James Robertson
11/02 Protein folding & stability
[watch video: ] [Slides]
PP3 James Robertson
11/04 Cooperativity in proteins
[watch video: ] [Slides]
PP5 James Robertson
11/07 No class    
11/09 Protein folding: kinetics, Landscapes, and Aggregation
[watch video: ] [Slides]
PP6 Jason Wagoner
11/11 Protein evolution and sequence space
[watch video: ] [Slides]
PP7 Alberto Perez
11/14 Bioinformatics
[watch video: ] [Slides]
PP8 Alberto Perez
11/16 Gene regulation
[watch video: ] [Slides]
  Gabor Balazsi
11/18 Natural and synthetic gene networks
[watch video: ] [Slides]
  Gabor Balazsi
11/21 Drug discovery & methods
[watch video: ] [Slides]
  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.
12/07 FINAL EXAM    

MDF = Molecular Driving Forces, chapter numbers.
PP = Protein Principles, draft textbook.


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