# Computational Biophysics ## A.A. 2024/2025 ### Prof. Lorenzo Rovigatti (lorenzo.rovigatti@uniroma1.it) --- # My research * Soft matter (including biophysics) * Self-assembly (colloids, proteins, nucleic acids) * DNA nanotechnology * Polymeric assemblies (star polymers, microgels) --- # Some pictures <div class="r-stack"> <div class="fragment fade-out" data-fragment-index="0"> ## Polymer networks <img src="../../images/talks/fs_2023/polymer_network.png" height="500"> </div> <div class="fragment current-visible" data-fragment-index="0"> ## Polymeric objects (microgels) <img src="../../images/talks/fs_2023/microgels.png" height="500"> </div> <div class="fragment current-visible" data-fragment-index="1"> ## All-DNA materials <img src="../../images/talks/fs_2023/DNA_gel.png" height="500"> </div> <div class="fragment current-visible" data-fragment-index="2"> ## DNA nanotechnology <img src="../../images/talks/fs_2023/tetrahedron.png" height="500"> </div> <div class="fragment" data-fragment-index="3"> ## Coarse-grained proteins <img src="../../images/compbio/cg_strategy.png" height="500"> </div> </div> --- # 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 <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> --- # Program <div class="warning"> This program is preliminary as the course is going to be different from previous years. Let's see what we can do! </div> * 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 <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! </div> --- # 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](https://lorenzo-rovigatti.github.io/comp_bio_notes)) 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.