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.

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: 2016, 2015, 2014

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# Date Topic Reading Speaker
1 08/28 Introduction. Basic Biology. Probability, statistics
[watch video: ] [Slides]
MDF1, 2 Gabor Balazsi
2 08/30 Combinatorics. Distributions. Extremum principles
[watch video: ] [Slides]
MDF 2, 3 Gabor Balazsi
3 09/01 Energy and Multiplicity. Multivariate calculus
[watch video: ] [Slides]
MDF 4 Gabor Balazsi
  09/04 NO CLASS, Labor day    
4 09/06 Multivariate Optimization. Max Ent & Boltzmann principle
[watch video: ] [Slides]
MDF 5 Gabor Balazsi
5 09/08 Energies vs. Entropy formulation, thermo states
[watch video: ] [Slides]
MDF 6 Gabor Balazsi
6 09/11 Free energies, chemical potentials
[watch video: ] [Slides]
MDF 8, 9 Gabor Balazsi
7 09/13 Microscopic modeling & Boltzmann Law
[watch video: ] [Slides]
MDF 10 Gabor Balazsi
8 09/15 Equilibrium constants, binding affinities
[watch video: ] [Slides]
MDF 13 Gabor Balazsi
9 09/18 Liquids, phase equilibria
[watch video: ] [Slides]
MDF 14 Gabor Balazsi
10 09/20 Solvation, free energies of transfer
[watch video: ] [Slides]
MDF 15,16 Gabor Balazsi
11 09/22 Diffusion, Fick's Law, Physical Dynamics
[watch video: ] [Slides]
MDF 17, 18 Gabor Balazsi
12 09/25

Chemical rates.  Mass-action kinetics
[watch video: ] [Slides]

MDF 19 Gabor Balazsi
13 09/27

Transition states & activation processes
[watch video: ] [Slides]

MDF 19 Gabor Balazsi
14 09/29

Coulomb & electrostatics: how charges interact
[watch video: ] [Slides]

MDF 20 Gabor Balazsi
15 10/02

Electrostatic potentials
[watch video: ] [Slides]

MDF 21 Gabor Balazsi
16 10/04

Electrochemical equilibria, batteries
[watch video: ] [Slides]

MDF 22 Gabor Balazsi
17 10/06

Salts shield charges. Poisson-Boltzmann
[watch video: ] [Slides]

MDF 23 Gabor Balazsi
18 10/09

Intermolecular interactions
[watch video: ] [Slides]

MDF 24 Gabor Balazsi
19 10/11

Phase transitions
[watch video: ] [Slides]

MDF 25 Gabor Balazsi
20 10/13

Adsorption & binding, Michaelis-Menten, catalysis
[watch video: ] [Slides]

MDF 27 Gabor Balazsi


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

Bio-machine principles
[watch video: ] [Slides]

MDF 29 Adam de Graff
25 10/27

Water: pure and as a solvent
[watch video: ] [Slides]

MDF 30, 31 Emiliano Brini
26 10/30

Protein structures
[watch video: ] [Slides]

PA1 Markus Seeliger
27 11/01 Protein function & mechanisms
[watch video: ] [Slides]
PA2 Markus Seeliger


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

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

TAs: Michael Cortes (#1 - #20). Chuan Tian, Bihua Yu and Cong Liu (#21 - #36).


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