Physical and Quantitative Biology, BME/CHE/PHY 558

Fall 2023 / MWF 11:00 – 11:53 AM,  in Laufer Center rootm 101.

Recitations: Mon, 12:00 pm – 13:00 pm, in Laufer Center Room 101.

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

Extra textbook: Physical Models of Living Systems. W. H. Freeman & Co., 2015

Prior years' course syllabi: 2022 2021, 2020, 2019, 2018, 2017, 2016, 2015, 2014

Please login to get the links to the videos

# Date Topic Reading Speaker
1 08/28 Introduction. Basic Biology. Probability, statistics MDF1, 2 Gabor Balazsi
2 08/30 Combinatorics. Distributions. Extremum principles MDF 2, 3 Gabor Balazsi
3 09/01 Energy and Multiplicity. Multivariate calculus MDF 4 Gabor Balazsi
  09/04 NO CLASS, Labor day    
4 09/6 Multivariate Optimization. Max Ent & Boltzmann principle MDF 5 Gabor Balazsi (TA: LV)
5 09/8 Energies vs. Entropy formulation, thermo states MDF 6 Gabor Balazsi
6 09/11 Driving forces. Path integrals MDF 6, 7 Gabor Balazsi
7 09/13 Ideal Gas. Carnot cycle MDF 7 Gabor Balazsi (TA: LV)
8 09/15 Free energies, chemical potentials MDF 8, 9 Gabor Balazsi
9 09/18 Susceptibilities. Boltzmann Law. MDF 9, 10 Gabor Balazsi (TA: LV)
10 09/20 Partition function. Simple gases, solids MDF 10,11 Gabor Balazsi
11 09/22 Chemical equilibria MDF 12, 13 Gabor Balazsi
12 09/25

Liquids, phase equilibria. Mixtures

 MDF 14, 15 Gabor Balazsi (TA: LV)
13 09/27

Solvation

 MDF 16 Gabor Balazsi
14 09/29

Diffusion, Fick's Law. Random walks. Time’s arrow

 MDF 17, 18 Gabor Balazsi
15 10/2

Chemical rates. Mass-action kinetics. Transition states

 MDF 19 Gabor Balazsi (TA: LV)
16 10/4

Coulomb & electrostatics: charges, potentials, fields

 MDF 20, 21 Gabor Balazsi
17 10/6

Electrochemical equilibria. Batteries

 MDF 22 Gabor Balazsi
  10/9

NO CLASS, Fall Break– Columbus Day.

    
18 10/11

Salts+charges. Poisson-Boltzmann. Intermolec. forces

  MDF 23, 24  Gabor Balazsi (TA: LV)
19 10/13

Real gas. Phase transitions. Adsorption & binding

 MDF 24,25 Gabor Balazsi
  10/16

MIDTERM EXAM 1

    
20 10/18

Michaelis-Menten. Catalysis. Cooperativity

 MDF 27, 28 Gabor Balazsi (TA: CK)
21 10/20

Bio-machine principles

 MDF 29 Jason Wagoner
22 10/23

Water: pure and as a solvent

 MDF 30, 31 Marivi Fernandez-Serra (TA: CH)
23 10/25 Polymers 1: conformations & random flights MDF 33, 34 Helmut Strey
24 10/27 Polymers 2: polymer solutions, Flory-Huggins MDF 32, 33 Helmut Strey
25 10/30

Protein structures

 PA1 Markus Seeliger (TA: CH)
26 11/1 Protein function & mechanisms PA2 Markus Seeliger

27

 11/3 Protein folding & stability PA3 Carlos Simmerling
28 11/6 Cooperativity in proteins PA5 Carlos Simmerling (TA: CK)
29 11/8 Protein Folding on Energy Landscapes, and Aggregation PA6 Rostam Razban
30 11/10 Protein evolution and sequence space PA7 Josh Rest
31 11/13 Gene expression and it's regulation   Gabor Balazsi (TA: CH)
32 11/15 Natural and synthetic gene networks   Gabor Balazsi
33 11/17 Drug discovery & methods   Dima Kozakov
34 11/20 Bioinformatics PA8 Dominik Kempa (TA: CH)
  11/22 NO CLASS, Thanksgiving break    
  11/24 NO CLASS, Thanksgiving break    
35 11/27 Drug discovery in industry   John H. Van Drie, Van Drie Research, LLC
36 11/29 Research Project Presentations    
  12/1 MIDTERM EXAM 2    

MDF = Molecular Driving Forces, chapter numbers.
PA = Protein Actions, chapter numbers.

TAs:  Lakshmanji Verma (LV), Chris Helenek (CH).

 

For videos, please go to Blackboard.

 

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