Physics&Chemistry Dissertation

A python package for the automated analysis and visualization of lipid-protein interactions.

a 2D classical molecular dynamics simulation written in python3.

Use PyConforMap to generate a simple scatter plot to map conformational landscapes of intrinsically disordered proteins, and quantify conformational diversity.

This is a small package, mainly intended for machine-learning researchers who want to take a look at potential-field estimation as is done in Molecular Dynamics (MD) or molecular simulations. The tool only generates a potential fields. None of the realistic geometric problems of molecular symmetry etc. are handled, just a 2D mountain landcape (nega

Restrained ensemble molecular dynamics method implementation for small angle scattering data.

Octane in a water box under CHARMM36 forcefield

Numerical Simulations course, Master Degree in Physics, University of Milan

Codes to reproduce the results of: Non-equilibrium molecular simulations of thin film rupture (J. Chem. Phys., 2023) by Rahman et al.

A repository for backing of simulation input files.

RAN-LifeTime is a package for RNA lifetime prediction task written in pytorch. https://arxiv.org/abs/2305.03925

NeuralMD for protein-ligand binding MD simulation

My notes site. About techniques, research notes and courses.

a VScode syntax highlight tool for molecular dynamics

A LAMMPS template for the molecular dynamics simulation of nanometric cutting of 3C-SiC using a diamond tool with a negative rake angle of 15° and a clearance angle of 10°

Molecular dynamics simulations of the rotational motion of nanoparticles in electric fields

Python implementation of Frenkel-Kontorova model in 1D. Open boundary conditions.

Esercizi da consegnare per il corso di Simulazione Numerica - prof. Davide Emilio Galli