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Selected Topics in Biophysics

Instructor: Gasper Tkacik

Teaching Assistant: Sarah Cepeda, Roshan Prizak

Description

 

This course will highlight a number of problems in biology where the interaction with physics has proven to be crucial to understanding the phenomena involved. The focus is on physical thinking about biological systems, rather than about accumulating biological detail, and stresses the role of quantitative analysis. For physicists, the course should be easy on the formal level, but will introduce new phenomenology; known physical concepts will appear in contexts usually not covered by standard physics curricula. The course will be mostly blackboard based. It will center around the idea that important processes of life happen at room temperatures at the level of individual microscopic objects, e.g., single molecules, single photons, yet can nevertheless generate remarkable precision and reproducibility. The primary reference is Bialek W: “Biophysics: Searching for principles”, but we will use a variety of other sources.

We will cover three topics, each lasting for approximately two weeks:

1) The role of noise in living systems,
2) Applications of statistical physics in biology,
3) Optimality and efficient representation.

 


Requirements/Exams

Target audience: Students with quantitative backgrounds (Physics, Engineering, CS/Math) or Biology students with a strong background in physics or math, wanting to get acquainted with the concepts and problems of biophysics.

Prerequisites: Linear algebra, basic calculus, basics of statistical physics, some experience with data analysis / work in Matlab or Mathematica is a plus but not required.

 


Credits

3 ECTS


Final Grade

The final grade will be composed of a final written exam (60%) and regular small homework problems (40%).

 

Schedule (subject to change)

Date Topic Location Other
Oct 6 Noise in biology: Introduction, Counting single photons Mondi 2  
Oct 8 Noise in biology: Counting single photons, Mutations Mondi 1  
Oct 13 Noise in biology: Mutations, Counting single molecules Mondi 2  
Oct 15 Noise in biology: Counting single molecules, noise and chemotaxis Mondi 2  
Oct 20 Statistical mechanics: Molecular recognition, chemical potential Mondi 2  
Oct 22 --- NO LECTURE ---    
Oct 27 Statistical mechanics: Michaelis-Menten kinetics, kinetic proofreading Mondi 2  
Oct 29 Statistical mechanics: TBA    
Nov 3 Statistical mechanics: Inverse statistical mechanics    
Nov 5 Statistical mechanics: Inverse statistical mechanics    
Nov 10 Optimization and efficient coding    
Nov 12 Optimization and efficient coding    
Nov 17 Optimization and efficient coding    

Homework

File | Due Date

PS_1.pdf | Recitation Tue Oct 13, Due before recitation, Tue Oct 20.

PS_2.pdf | Recitation Tue Oct 19, Due before recitation, Tue Oct 27.

PS_3.pdf | Recitation Tue Nov 3, Due before recitation, Tue Nov 10.

PS_4.pdf | Recitation Tue Nov 17, Due Tue Nov 24.

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