Physical & Quantitative Biology, CHE/PHY 558

Fall 2014 / MWF 10 – 11 AM in Laufer Center 101

Ken Dill, Course PI

Course goals: The central idea of this course is the free energy, the quantitative way we understand driving forces, i.e., the equilibria and rates in chemistry, physics and biology. We describe the underpinning components, the entropy and energy. We explore the microscopic interactions -- including hydrogen bonding, van der Waals, 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 are the basis for drug discovery; coupled binding is the basis for how biological machines convert energy and transduce signals; and polymer free energies are the basis for the folding of protein and RNA molecules.


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DateTopicReadingSpeaker
08/25 Intro. Structural basis of biology. Time & space scales.
[watch video: ]
Ken Dill
08/27 Probabilities. Counting states as a basis of entropy.
[watch video: ]
MDF 1, 2 Ken Dill
08/29 Entropy and Energy as driving forces.
[watch video: ]
MDF 3 Ken Dill
09/01 NO CLASS, Labor Day.
09/03 Partial derivatives.
[watch video: ]
MDF4 Ken Dill
09/05 Max Ent and the Boltzmann distribution law.
[watch video: ]
MDF 5 Ken Dill
09/08 Energies and enthalpies. Thermodynamic states.
[watch video: ]
MDF 6 Ken Dill
09/10 Free energies, chemical potentials.
[watch video: ]
MDF 8, 9

Darrin York, Taisung Lee

@Rutgers

09/12 Microscopic modeling and the Boltzmann law.
[watch video: ]
MDF 10

Darrin York, Taisung Lee

@Rutgers

09/15 Equilibrium constants. Binding affinities.
[watch video: ]
MDF 13 Ken Dill
09/17 Liquids & phase equilibria.
[watch video: ]
MDF 14 Ken Dill
09/19 Solvation. Free energies of transfer.
[watch video: ]
MDF 16 Ken Dill
09/22 Diffusion. Fick's Law. Physical dynamics.
[watch video: ]
MDF 17, 18 Ken Dill
09/24 Chemical rate models. Mass-action kinetics.
[watch video: ]
MDF 19 Gabor Balazsi
09/26 Transition states. Activation barriers.
[watch video: ]
MDF 19 Gabor Balazsi
09/29 Coulombic interactions. How charges interact.
[watch video: ]
MDF 20 Ken Dill
10/01 Electrostatic potentials.
[watch video: ]
MDF 21 Ken Dill
10/03 Electrochemical equilibria.
[watch video: ]
MDF 22 Ken Dill
10/06 Salts shield charges. The Poisson-Boltzmann model.
[watch video: ]
MDF 23 Ken Dill
10/08 Intermolecular forces: van der Waals, dipolar, hydrogen bonds.
[watch video: ]
MDF 24 Ken Dill
10/10 MIDTERM EXAM
10/13 Polymers: random-flights, entropies & constraints.
[watch video: ]
MDF 33, 34 Helmut Strey
10/15 Polymer solutions: Flory-Huggins theory.
[watch video: ]
MDF 32, 33 Helmut Strey
10/17 Properties of water. Hydrophobic solvation.
[watch video: ]
MDF 30, 31 Ken Dill
10/20 Adsorption, binding polynomials.
[watch video: ]
MDF 27 Ken Dill
10/22 Binding cooperativity.
[watch video: ]
MDF 28 Ken Dill
10/24 Bio-machines.
[watch video: ]
MDF 29 Ken Dill
10/27 Protein structures.
[watch video: ]
PP1 Markus Seeliger
10/29 Protein function and mechanisms.
[watch video: ]
PP2 Markus Seeliger
10/31 Protein stability.
[watch video: ]
PP3 Ken Dill
11/03 Protein cooperativity: helix-coil transitions.
[watch video: ]
PP4 Jin Wang
11/05 Protein folding & aggregation.
[watch video: ]
PP4 Ken Dill
11/07 Protein folding kinetics. Markov models. Energy landscapes.
[watch video: ]
PP5 Jin Wang
11/10 Protein evolution and sequence space.
[watch video: ]
PP6 Jason Wagoner
11/12 Bioinformatics, sequence comparisons.
[watch video: ]
PP7 Jason Wagoner
11/14 Drug discovery 1: Comp-aided design, dock, virtual screening
[watch video: ]
Joe Allen & Rob Rizzo
11/17 Drug discovery 2: Scoring, sampling, free-energy methods
[watch video: ]
Joe Allen & Rob Rizzo
11/19 MD, QM, docking and informatics in Biopharma
[watch video: ]
Wendy Cornell
11/21 Extra day, at the moment Review, for exam.
11/24 FINAL EXAM
11/26 NO CLASS, Thanksgiving break.
11/28 NO CLASS, Thanksgiving break.
12/01 Research Project Presentations.
12/03 Research Project Presentations.

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


 

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