My research

• Soft matter (including biophysics)
• Self-assembly (colloids, proteins, nucleic acids)
• DNA nanotechnology
• Polymeric assemblies (star polymers, microgels)

Some pictures

Polymer networks

Polymeric objects (microgels)

All-DNA materials

DNA nanotechnology

Coarse-grained proteins

Schedule

• Monday 13-15, Aula 3
• Tuesday 12-14, Aula 7
• Thursday 16-18, Aula 8

Why six hours per week? I may have to put the course on hold for one-two weeks…

Etiquette

• English? Italian? It depends on the audience…
• Ask questions and interrupt me if something is not clear!
• Feel free to pose questions either in English or Italian, don’t be shy!

Organisation

• The course will feature frontal lectures only
• There will be some hands-on lectures where I’ll ask you to bring your own laptop
• Office hours (= ricevimento): write to me and we will set up a meeting!
• Your grade will be based on
  • A final project (optional)
  • Homework assignments (optional)
  • An oral exam on the project and homeworks (if done), or on the lectures’ content

Homeworks?

• I will present codes that implement some of the algorithms discussed during lectures
• At the end of some sections I will present possible exercises that are related to the codes and methods presented.
• If you like a topic, you can try to tackle an exercise at home.
• If the task is carried out successfully, you will be assigned a grade and will be exempt from studying that topic for the oral exam.
• The final project can be chosen out of the possible extensions I foresaw for the homeworks, or you can suggest something yourself.

How to write an e-mail

Program

• Introduction to biophysics and Python programming
• Introduction to proteins
• Introduction to nucleic acids
• Folding, design and structure prediction of proteins and nucleic acids
• Notions of quantum molecular mechanics
• Molecular dynamics
• Coarse-grained models
• Enhanced sampling techniques

Books & papers

• A. L. Lehninger, Principles of biochemistry
  • A bible of biochemistry
• A.V. Finkelstein, O. Ptitsyn, Protein physics: a course of lectures
  • Protein physics in a nutshell
• T. Schlick, Molecular modeling and simulations: an interdisciplinary guide
  • Very useful as a crash course to DNA, RNA, and proteins, as well as to the way the are modelled with a computer
• J. N. Israelachvili, Intermolecular and surface forces
  • An excellent (and comprehensive) book on intermolecular forces
• D. Frenkel, B. Smit, Understanding molecular simulation: from algorithms to applications
  • The bible of molecular simulations

Prerequisites

• Interest in biology/biochemistry (!)
• Willingness to (and possibly some experience with) writing and reading codes
• Working knowledge of thermodynamics and basic statistical mechanics
• Recommended: a laptop/computer with a working installation of Python and Jupyter

My notes

I’m preparing a large corpus of notes (link) that I want to use for the lectures. However, these are

1. Incomplete
2. Possibly full of typos and errors
3. Half-stolen, half-copied from books and papers

However, they also contain the codes and the homeworks I plan to assign. Use them responsably, and point out problems/issues.