Dmitri Klimov, Professor

School of Systems Biology

School of Systems Biology

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BINF740 Introduction to Biophysics

BINF741 Introduction to Computer Simulations of Biomolecules

**Course syllabus:**

**Introduction to thermodynamics and statistical mechanics **

Homework

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

** Reaction kinetics and transport processes**

Homework

- Read Chapters 4 and 5 from Cotterill book
- 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
- Solve problems 5.1, 5.3 from Cotterill book

** Biomolecular energies, forces, and bonds**

Homework

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

**Biomolecular structure **

Homework

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

**Biological energy **

Homework

- Read chapter 9 from Cotterill book

**Membranes **

Homework

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

**Propagation of nerve signals **

Homework

- Read chapter 12 from Cotterill book

**Memory **

Homework

- Read chapters 8 and 13 from Cotterill book
- Problems 8.1 and 13.1

**Biomechanics **

Homework

- Read chapter 14 from Cotterill book
- Read sections 3.6 and 3.7 from Glaser book (both editions)

** Protein folding **

Homework

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

** Molecular chaperones **

Homework

- Read online notes
- Solve the problem on chaperone function in the lecture notes

** Protein Aggregation **

Homework

- Read online notes
- Solve the problem on amyloid formation rates in the lecture notes

** Mechanical unfolding **

Homework

- Read online notes
- Solve the problem on protein tandem unfolding in the lecture notes