Physical and Quantitative Biology, BME/CHE/PHY 558
Fall 2018 / 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||08/27||Introduction. Basic Biology. Probability, statistics||MDF1, 2||Gabor Balazsi|
|2||08/29||Combinatorics. Distributions. Extremum principles||MDF 2, 3||Gabor Balazsi|
|3||08/31||Energy and Multiplicity. Multivariate calculus||MDF 4||Gabor Balazsi|
|09/03||NO CLASS, Labor day|
|4||09/05||Multivariate Optimization. Max Ent & Boltzmann principle||MDF 5||Gabor Balazsi|
|5||09/07||Energies vs. Entropy formulation, thermo states||MDF 6||Gabor Balazsi|
|6||09/10||Free energies, chemical potentials||MDF 8, 9||Gabor Balazsi|
|7||09/12||Microscopic modeling & Boltzmann Law||MDF 10||Gabor Balazsi|
|8||09/14||Equilibrium constants, binding affinities||MDF 13||Gabor Balazsi|
|9||09/17||Liquids, phase equilibria||MDF 14||Gabor Balazsi|
|10||09/19||Solvation, free energies of transfer||MDF 15,16||Gabor Balazsi|
|11||09/21||Diffusion, Fick's Law, Physical Dynamics||MDF 17, 18||Gabor Balazsi|
Chemical rates. Mass-action kinetics
|MDF 19||Gabor Balazsi|
Transition states & activation processes
|MDF 19||Gabor Balazsi|
Coulomb & electrostatics: how charges interact
|MDF 20||Gabor Balazsi|
|MDF 21||Gabor Balazsi|
Electrochemical equilibria, batteries
|MDF 22||Gabor Balazsi|
Salts shield charges. Poisson-Boltzmann
|MDF 23||Gabor Balazsi|
NO CLASS, Fall Break/Columbus Day
Intermolecular interactions, Phase transitions
|MDF 24,25||Gabor Balazsi|
Adsorption & binding, Michaelis-Menten, catalysis
|MDF 27||Gabor Balazsi|
|21||10/17||Binding cooperativity||MDF 28||Gabor Balazsi|
|22||10/19||Polymers 1: conformations & random flights||MDF 33, 34||Helmut Strey|
|23||10/22||Polymers 2: polymer solutions, Flory-Huggins||MDF 32, 33||Helmut Strey|
|MDF 29||Jason Wagoner|
Water: pure and as a solvent
|MDF 30, 31||Emiliano Brini|
|27||10/31||Protein function & mechanisms||PA2||Markus Seeliger|
|11/02||Protein folding & stability||PA3||James Robertson|
|29||11/05||Cooperativity in proteins||PA5||Emiliano Brini|
|30||11/07||Folding on Energy Landscapes, and Aggregation||PA6||Emiliano Brini|
|31||11/09||Protein evolution and sequence space||PA7||Max Shapino|
|33||11/14||Gene expression and it's regulation||Gabor Balazsi|
|34||11/16||Natural and synthetic gene networks||Gabor Balazsi|
|35||11/19||Drug discovery & methods||Dima Kozakov|
|11/22||NO CLASS, Thanksgiving break|
|11/24||NO CLASS, Thanksgiving break|
|11/26||Drug discovery in industry||John H. Van Drie, Van Drie Research, LLC|
|36||11/28||Research Project Presentations|
MDF = Molecular Driving Forces, chapter numbers.
PA = Protein Actions, chapter numbers.
TAs: Luca Agozzino (#1 - #20), Roy Nassar (#21 - #36).
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