Dmitri Klimov, Professor
School of Systems Biology
           


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Courses
BINF690 Numerical Methods in Bioinformatics
BINF740 Introduction to Biophysics
BINF739/BIOL691 Molecular Modeling for Biologists
BINF741 Introduction to Computer Simulations of Biomolecules

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BINF740 Introduction to Biophysics


Course syllabus:

Lecture 1

Introduction to thermodynamics and statistical mechanics



Homework

  1. Read lecture notes
  2. Read sections 4.1-4.3 from Cotterill book
  3. Read sections 3.1.1-3.1.4 from Glazer book (both editions)
  4. Solve problems 4.2, C.1, and C.2 from Cotterill book

Lecture 2

Reaction kinetics and transport processes


Homework

  1. Read Chapters 4 and 5 from Cotterill book
  2. Read sections 2.3.5, 2.3.6, 3.1.5 from the Glazer book 1st edition or 2.1.5, 2.16, 3.1.6 from the 2nd edition
  3. Solve problems 5.1, 5.3 from Cotterill book

Lecture 3

Biomolecular energies, forces, and bonds


Homework

  1. Read Chapters 2 and 3 from Cotterill book
  2. Solve problems 3.2, 3.4 from Cotterill book

Lecture 4

Biomolecular structure



Homework

  1. Read lecture notes
  2. Read sections 7.1-7.4 from Cotterill book
  3. Read section 2.4.2 from the Glazer book 1st edition or 2.2.2 from the 2nd edition

Lecture 5

Biological energy


Homework

  1. Read chapter 9 from Cotterill book

Lecture 6

Membranes


Homework

  1. Read chapters 8 and 11 from Cotterill book
  2. Read section 2.5 from the Glazer book 1st edition or 2.3 from the 2nd edition
  3. Problem 11.1
  4. Problem on surface areas of droplets (optional, for extra credit)

Lecture 7

Propagation of nerve signals


Homework

  1. Read chapter 12 from Cotterill book

Lecture 8

Memory


Homework

  1. Read chapters 8 and 13 from Cotterill book
  2. Problems 8.1 and 13.1

Lecture 9

Biomechanics


Homework

  1. Read chapter 14 from Cotterill book
  2. Read sections 3.6 and 3.7 from Glaser book (both editions)

Lecture 10

Protein folding


Homework

  1. Read online notes
  2. Read the articles assigned in the class (see class notes)
  3. Derive the probability of native state fN for two-state folder using the definition of equilibrium constant
  4. Prepare conceptual question on protein folding (send via email by Monday)

Lecture 11

Molecular chaperones


Homework

  1. Read online notes
  2. Solve the problem on chaperone function in the lecture notes

Lecture 12

Protein Aggregation


Homework

  1. Read online notes
  2. Solve the problem on amyloid formation rates in the lecture notes

Lecture 13

Mechanical unfolding


Homework

  1. Read online notes
  2. Solve the problem on protein tandem unfolding in the lecture notes