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


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


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).


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