Physical and Quantitative Biology, BME/CHE/PHY 558

Fall 2020 / MWF 10:30 – 11:25 AM  online via Zoom

Recitations: Mon, 11:30 am – 12:30 pm online via Zoom.

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

Extra textbook: Physical Models of Living Systems. W. H. Freeman & Co., 2015

Prior years' course syllabi: 2019, 2018, 2017, 2016, 2015, 2014

Please login to get the links to the videos

# Date Topic Reading Speaker
1 08/24 Introduction. Basic Biology. Probability, statistics MDF1, 2 Gabor Balazsi
2 08/26 Combinatorics. Distributions. Extremum principles MDF 2, 3 Gabor Balazsi
3 08/28 Energy and Multiplicity. Multivariate calculus MDF 4 Gabor Balazsi
4 08/31 Multivariate Optimization. Max Ent & Boltzmann principle MDF 5 Gabor Balazsi
5 09/02 Energies vs. Entropy formulation, thermo states MDF 6 Gabor Balazsi
6 09/04 Driving forces. Path integrals MDF 6, 7 Gabor Balazsi
  09/07 NO CLASS, Labor day    
7 09/09 Ideal Gas. Carnot cycle MDF 7 Gabor Balazsi
8 09/11 Free energies, chemical potentials MDF 8, 9 Gabor Balazsi
9 09/14 Susceptibilities. Boltzmann Law. MDF 9, 10 Gabor Balazsi
10 09/16 Partition function. Simple gases, solids MDF 10,11 Gabor Balazsi
11 09/18 Chemical equilibria MDF 12, 13 Gabor Balazsi
12 09/21

Liquids, phase equilibria. Mixtures

MDF 14, 15 Gabor Balazsi
13 09/23


MDF 16 Gabor Balazsi
14 09/25

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

MDF 17, 18 Gabor Balazsi
15 09/28

Chemical rates. Mass-action kinetics. Transition states

MDF 19 Gabor Balazsi
16 09/30

Coulomb & electrostatics: charges, potentials, fields

MDF 20, 21 Gabor Balazsi
17 10/02

Electrochemical equilibria. Batteries

MDF 22 Gabor Balazsi
18 10/05

Salts+charges. Poisson-Boltzmann. Intermolec. forces

 MDF 23, 24  Gabor Balazsi
19 10/07

Real gas. Phase transitions. Adsorption & binding

MDF 24,25 Gabor Balazsi


20 10/12

Michaelis-Menten. Catalysis. Cooperativity

MDF 27, 28 Gabor Balazsi
21 10/14

Bio-machine principles

MDF 29 Jason Wagoner
22 10/16

Water: pure and as a solvent

MDF 30, 31 Emiliano Brini
23 10/19 Polymers 1: conformations & random flights MDF 33, 34 Helmut Strey
24 10/21 Polymers 2: polymer solutions, Flory-Huggins MDF 32, 33 Helmut Strey
25 10/23

Protein structures

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


10/28 Protein folding & stability PA3 Carlos Simmerling
28 10/30 Cooperativity in proteins PA5 Carlos Simmerling
29 11/02 Protein Folding on Energy Landscapes, and Aggregation PA6 Emiliano Brini
30 11/04 Protein evolution and sequence space PA7 Max Shapino
31 11/06 Bioinformatics PA8 Steve Skiena
32 11/09 Gene expression and it's regulation   Gabor Balazsi
33 11/12 Natural and synthetic gene networks   Gabor Balazsi
34 11/13 Drug discovery & methods   Dima Kozakov
35 11/16 Drug discovery in industry   John H. Van Drie, Van Drie Research, LLC
36 11/18 Research Project Presentations    
  11/20 MIDTERM EXAM 2    
  11/23 NO CLASS, Thanksgiving break    
  11/25 NO CLASS, Thanksgiving break    
  11/27 NO CLASS, Thanksgiving break    

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

TAs:  TAs: Jonathan Pachter, Yuzhang Wang, Darya Stepanenko.


For videos, please go to Blackboard.


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