Introduzione | Lorenzo Rovigatti

# Computational Biophysics

## A.A. 2025/2026

### Prof. Lorenzo Rovigatti (lorenzo.rovigatti@uniroma1.it)

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# My research

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

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# Some examples

## Polymer networks & objects

## All-DNA materials

## DNA nanotechnology

## Self-assembly of a viral genome

## Coarse-grained proteins

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# Schedule

* Monday 12-14, Aula I (CU032)
* Tuesday 16-18, Aula 8
* Friday 12-13, Aula 8

# 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!

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# 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

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# 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.

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# How to write an e-mail

<table>
<tr>
<th>Da</th>
        <td>pincopallo.42839183@studenti.uniroma1.it</td>
    </tr>
<tr>
<th>A</th>
        <td>lorenzo.rovigatti@uniroma1.it</td>
    </tr>
<tr>
<th>Object</th>
        <td class="highlight-red fragment">COMPBIO: richiesta ricevimento / meeting request</td>
    </tr>
<tr>
<th>Testo</th>
        <td>
            <p>Dear [Caro] professore,</p>
            <p>Would it be possible to meet this week to discuss [...]? I'm available [...]</p>
            <p>best [cordiali saluti],</p>
            <p>Pinco Pallo</p>
        </td>
    </tr>
</table>

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# 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

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# 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
  
<div class="focus">
I will suggest papers to read during the lectures. Check the <a href="https://lorenzo-rovigatti.github.io/comp_bio_notes/">notes</a> to find more references!
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# 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

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# My notes

I have prepared a large *corpus* of notes ([link](https://lorenzo-rovigatti.github.io/comp_bio_notes)) that I use as basis for the lectures. However, these are

1. Incomplete (but we're getting there!)
2. Possibly ripe with typos and errors (but better than the previous year!)
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.