Physical & 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

DateTopicReadingSpeaker
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 MDF 17, 18 Gabor Balazsi
09/26

Chemical rates.  Mass-action kinetics

MDF 19 Gabor Balazsi
09/28

Transition states & activation processes

MDF 19 Gabor Balazsi
09/30

Coulomb & electrostatics: how charges interact

MDF 20 Gabor Balazsi
10/03

Electrostatic potentials

MDF 21 Gabor Balazsi
10/05

Electrochemical equilibria, batteries

MDF 22 Gabor Balazsi
10/07

Salts shield charges. Poisson-Boltzmann

MDF 23 Gabor Balazsi
10/10

Intermolecular interactions

MDF 24 Gabor Balazsi
10/12

Adsorption & binding, Michaelis-Menten, catalysis

MDF 27 Gabor Balazsi
10/14

Binding cooperativity

MDF 28 Gabor Balazsi
10/17 MIDTERM EXAM
10/19 Polymers 1: conformations & random flights MDF 33, 34 Helmut Strey
10/21 Polymers 2: polymer solutions, Flory-Huggins MDF 32, 33 Helmut Strey
10/24

Bio-machine principles

MDF 29 Jason Wagoner
10/26

Water: pure and as a solvent

MDF 30, 31 Emiliano Brini
10/28

Protein structures

PP1 Emiliano Brini
10/31 Protein function & mechanisms PP2 James Robinson
11/02 Protein folding & stability. PP3 James Robinson
11/04 Cooperativity in proteins PP4 James Robinson
11/07 Protein folding & aggregation PP4 Jason Wagoner
11/09 Folding kinetics & energy landscapes PP5 Jason Wagoner
11/11 Protein evolution and sequence space PP6 Alberto Perez
11/14 Bioinformatics PP7 Alberto Perez
11/16 Gene regulation Gabor Balazsi
11/18 Natural and synthetic gene networks Gabor Balazsi
11/21 Drug discovery & methods PP6 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 Research Project Presentations.
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.


 

ACADEMIC INTEGRITY
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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.


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CRITICAL INCIDENT MANAGEMENT
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