Physical and Quantitative Biology, BME/CHE/PHY 558
Fall 2019 / MWF 10 – 10:53 AM in Laufer Center 101
Recitations: Mon, 11:00 am – 12:00 pm in Laufer Center 107.
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 control gene activity; and polymer free energies form the basis for the folding of protein and RNA molecules; with implications for molecular and cellular evolution.
Textbook: Molecular Driving Forces by Dill & Bromberg. Garland Science, 2010
Extra textbook: Protein Actions by Bahar, Jernigan & Dill. Garland Science, 2017
Please login to get the links to the videos
|1||08/26||Introduction. Basic Biology. Probability, statistics||MDF1, 2||Gabor Balazsi|
|2||08/28||Combinatorics. Distributions. Extremum principles||MDF 2, 3||Gabor Balazsi|
|3||08/30||Energy and Multiplicity. Multivariate calculus||MDF 4||Gabor Balazsi|
|09/02||NO CLASS, Labor day|
|4||09/04||Multivariate Optimization. Max Ent & Boltzmann principle||MDF 5||Gabor Balazsi|
|5||09/06||Energies vs. Entropy formulation, thermo states||MDF 6||Gabor Balazsi|
|6||09/09||Driving forces. Path integrals||MDF 6, 7||Gabor Balazsi, TA Luca A.|
|7||09/11||Ideal Gas. Carnot cycle||MDF 7||Gabor Balazsi|
|8||09/13||Free energies, chemical potentials||MDF 8, 9||Gabor Balazsi|
|9||09/16||Susceptibilities. Boltzmann Law.||MDF 9, 10||Gabor Balazsi, TA: Xin Cao|
|10||09/18||Partition function. Simple gases, solids||MDF 10,11||Gabor Balazsi|
|11||09/20||Chemical equilibria||MDF 12, 13||Gabor Balazsi|
Liquids, phase equilibria. Mixtures
|MDF 14, 15||Gabor Balazsi. TA: Yiming Wan|
|MDF 16||Gabor Balazsi|
Diffusion, Fick's Law. Random walks. Time’s arrow
|MDF 17, 18||Gabor Balazsi|
Chemical rates. Mass-action kinetics. Transition states
|MDF 19||Gabor Balazsi, TA: Luca A.|
Coulomb & electrostatics: charges, potentials, fields
|MDF 20, 21||Gabor Balazsi|
Electrochemical equilibria. Batteries
|MDF 22||Gabor Balazsi|
Salts+charges. Poisson-Boltzmann. Intermolec. forces
|MDF 23, 24||Gabor Balazsi, TA: Zach F.|
Real gas. Phase transitions. Adsorption & binding
|MDF 24,25||Gabor Balazsi|
|10/14||NO CLASS, Fall Break/Columbus Day|
|20||10/16||Polymers 1: conformations & random flights||MDF 33, 34||Helmut Strey|
|21||10/18||Polymers 2: polymer solutions, Flory-Huggins||MDF 32, 33||Helmut Strey|
Michaelis-Menten. Catalysis. Cooperativity
|MDF 27, 28||Gabor Balazsi, TA: J. Pachter|
|MDF 29||Jason Wagoner|
Water: pure and as a solvent
|MDF 30, 31||Emiliano Brini|
|26||10/30||Protein function & mechanisms||PA2||Markus Seeliger|
|11/01||Protein folding & stability||PA3||Carlos Simmerling|
|28||11/04||Cooperativity in proteins||PA5||Carlos Simmerling, TA: Roy N.|
|29||11/06||Folding on Energy Landscapes, and Aggregation||PA6||Emiliano Brini|
|30||11/08||Protein evolution and sequence space||PA7||Max Shapino|
|31||11/11||Bioinformatics||PA8||Steve Skiena, TA: Cong Liu|
|32||11/13||Gene expression and it's regulation||Gabor Balazsi|
|33||11/15||Natural and synthetic gene networks||Gabor Balazsi|
|34||11/18||Drug discovery in industry||John H. Van Drie, Van Drie Research, LLC. TA: Luca Agozzino|
|11/20||Research Project Presentations|
|35||11/22||Drug discovery & methods||Dima Kozakov|
|11/25||MIDTERM EXAM 2|
|11/28||NO CLASS, Thanksgiving break|
|11/29||NO CLASS, Thanksgiving break|
MDF = Molecular Driving Forces, chapter numbers.
PA = Protein Actions, chapter numbers.
TAs: Luca Agozzino, Xin Cao, Yiming Wan, Zachary Fallon, Jonathan Pachter, Roy Nassar, Cong Liu, M. Tyler Guinn.
For videos, please go to Blackboard.
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