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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Date | Topic | Reading | Speaker |
---|---|---|---|
08/25 | Intro. Structural basis of biology. Time & space scales. [watch video: {access !public}here{/access}] |
Ken Dill | |
08/27 | Probabilities. Counting states as a basis of entropy. [watch video: {access !public}here{/access}] |
MDF 1, 2 | Ken Dill |
08/29 | Entropy and Energy as driving forces. [watch video: {access !public}here{/access}] |
MDF 3 | Ken Dill |
09/01 | NO CLASS, Labor Day. | ||
09/03 | Partial derivatives. [watch video: {access !public}here{/access}] |
MDF4 | Ken Dill |
09/05 | Max Ent and the Boltzmann distribution law. [watch video: {access !public}here{/access}] |
MDF 5 | Ken Dill |
09/08 | Energies and enthalpies. Thermodynamic states. [watch video: {access !public}here{/access}] |
MDF 6 | Ken Dill |
09/10 | Free energies, chemical potentials. [watch video: {access !public}here{/access}] |
MDF 8, 9 |
Darrin York, Taisung Lee @Rutgers |
09/12 | Microscopic modeling and the Boltzmann law. [watch video: {access !public}here{/access}] |
MDF 10 |
Darrin York, Taisung Lee @Rutgers |
09/15 | Equilibrium constants. Binding affinities. [watch video: {access !public}here{/access}] |
MDF 13 | Ken Dill |
09/17 | Liquids & phase equilibria. [watch video: {access !public}here{/access}] |
MDF 14 | Ken Dill |
09/19 | Solvation. Free energies of transfer. [watch video: {access !public}here{/access}] |
MDF 16 | Ken Dill |
09/22 | Diffusion. Fick's Law. Physical dynamics. [watch video: {access !public}here{/access}] |
MDF 17, 18 | Ken Dill |
09/24 | Chemical rate models. Mass-action kinetics. [watch video: {access !public}here{/access}] |
MDF 19 | Gabor Balazsi |
09/26 | Transition states. Activation barriers. [watch video: {access !public}here{/access}] |
MDF 19 | Gabor Balazsi |
09/29 | Coulombic interactions. How charges interact. [watch video: {access !public}here{/access}] |
MDF 20 | Ken Dill |
10/01 | Electrostatic potentials. [watch video: {access !public}here{/access}] |
MDF 21 | Ken Dill |
10/03 | Electrochemical equilibria. [watch video: {access !public}here{/access}] |
MDF 22 | Ken Dill |
10/06 | Salts shield charges. The Poisson-Boltzmann model. [watch video: {access !public}here{/access}] |
MDF 23 | Ken Dill |
10/08 | Intermolecular forces: van der Waals, dipolar, hydrogen bonds. [watch video: {access !public}here{/access}] |
MDF 24 | Ken Dill |
10/10 | MIDTERM EXAM | ||
10/13 | Polymers: random-flights, entropies & constraints. [watch video: {access !public}here{/access}] |
MDF 33, 34 | Helmut Strey |
10/15 | Polymer solutions: Flory-Huggins theory. [watch video: {access !public}here{/access}] |
MDF 32, 33 | Helmut Strey |
10/17 | Properties of water. Hydrophobic solvation. [watch video: {access !public}here{/access}] |
MDF 30, 31 | Ken Dill |
10/20 | Adsorption, binding polynomials. [watch video: {access !public}here{/access}] |
MDF 27 | Ken Dill |
10/22 | Binding cooperativity. [watch video: {access !public}here{/access}] |
MDF 28 | Ken Dill |
10/24 | Bio-machines. [watch video: {access !public}here{/access}] |
MDF 29 | Ken Dill |
10/27 | Protein structures. [watch video: {access !public}here{/access}] |
PP1 | Markus Seeliger |
10/29 | Protein function and mechanisms. [watch video: {access !public}here{/access}] |
PP2 | Markus Seeliger |
10/31 | Protein stability. [watch video: {access !public}here{/access}] |
PP3 | Ken Dill |
11/03 | Protein cooperativity: helix-coil transitions. [watch video: {access !public}here{/access}] |
PP4 | Jin Wang |
11/05 | Protein folding & aggregation. [watch video: {access !public}here{/access}] |
PP4 | Ken Dill |
11/07 | Protein folding kinetics. Markov models. Energy landscapes. [watch video: {access !public}here{/access}] |
PP5 | Jin Wang |
11/10 | Protein evolution and sequence space. [watch video: {access !public}here{/access}] |
PP6 | Jason Wagoner |
11/12 | Bioinformatics, sequence comparisons. [watch video: {access !public}here{/access}] |
PP7 | Jason Wagoner |
11/14 | Drug discovery 1: Comp-aided design, dock, virtual screening [watch video: {access !public}here{/access}] |
Joe Allen & Rob Rizzo | |
11/17 | Drug discovery 2: Scoring, sampling, free-energy methods [watch video: {access !public}here{/access}] |
Joe Allen & Rob Rizzo | |
11/19 | MD, QM, docking and informatics in Biopharma [watch video: {access !public}here{/access}] |
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.
ACADEMIC INTEGRITY
Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person¹s work as your own is always wrong. Any suspected instance of academic dishonesty will be reported to the Academic Judiciary. For more comprehensive information on academic integrity, including categories of academic dishonesty, please refer to the academic judiciary website at http://www.stonybrook.edu/uaa/academicjudiciary/
ELECTRONIC COMMUNICATION
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RELIGIOUS OBSERVANCES
See the policy statement regarding religious holidays at http://www.stonybrook.edu/registrar/forms/RelHolPol%20081612%20cr.pdf.
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.
DISABILITIES
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CRITICAL INCIDENT MANAGEMENT
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