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

Darrin York, Taisung Lee


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

Darrin York, Taisung Lee


09/15 Equilibrium constants. Binding affinities.
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MDF 13 Ken Dill
09/17 Liquids & phase equilibria.
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MDF 14 Ken Dill
09/19 Solvation. Free energies of transfer.
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MDF 16 Ken Dill
09/22 Diffusion. Fick's Law. Physical dynamics.
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MDF 17, 18 Ken Dill
09/24 Chemical rate models. Mass-action kinetics.
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MDF 19 Gabor Balazsi
09/26 Transition states. Activation barriers.
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MDF 19 Gabor Balazsi
09/29 Coulombic interactions. How charges interact.
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MDF 20 Ken Dill
10/01 Electrostatic potentials.
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MDF 21 Ken Dill
10/03 Electrochemical equilibria.
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MDF 22 Ken Dill
10/06 Salts shield charges. The Poisson-Boltzmann model.
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MDF 23 Ken Dill
10/08 Intermolecular forces: van der Waals, dipolar, hydrogen bonds.
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MDF 24 Ken Dill
10/13 Polymers: random-flights, entropies & constraints.
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MDF 33, 34 Helmut Strey
10/15 Polymer solutions: Flory-Huggins theory.
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MDF 32, 33 Helmut Strey
10/17 Properties of water. Hydrophobic solvation.
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MDF 30, 31 Ken Dill
10/20 Adsorption, binding polynomials.
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MDF 27 Ken Dill
10/22 Binding cooperativity.
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MDF 28 Ken Dill
10/24 Bio-machines.
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MDF 29 Ken Dill
10/27 Protein structures.
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PP1 Markus Seeliger
10/29 Protein function and mechanisms. PP2 Markus Seeliger
10/31 Protein stability. PP3 Ken Dill
11/03 Protein cooperativity: helix-coil transitions. PP4 Jin Wang
11/05 Protein folding & aggregation.
[watch video: ]
PP4 Ken Dill
11/07 Protein folding kinetics. Markov models. Energy landscapes. PP5 Jin Wang
11/10 Protein evolution and sequence space. PP6 Jason Wagoner
11/12 Bioinformatics, sequence comparisons. PP7 Jason Wagoner
11/14 Drug discovery 1: Comp-aided design, dock, virtual screening Joe Allen & Rob Rizzo
11/17 Drug discovery 2: Scoring, sampling, free-energy methods Joe Allen & Rob Rizzo
11/19 MD, QM, docking and informatics in Biopharma Wendy Cornell
11/21 Extra day, at the moment Review, for 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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