"Atomic democracy" for site analysis of surfaces and bulks with known lattice structure(s).

A package for multiple-scale simulations on the dynamical and kinetic processes in materials

Building and analyzing residue interaction networks with cofactors (includes tutorial).

A Python module for performing data analysis of atomistic trajectories relevant for glasses and supercooled liquids.

Molecular Dynamics Trajectory Analysis Tools

Repository for my senior design project/thesis code

Machine Learning Transition State Analysis (MLTSA) suite with Analytical models to create data on demand and test the approach on different types of data and ML models.

A user-friendly Python package to manipulate input and output files of LAMMPS molecular dynamics code. One Python class per LAMMPS file type. Include conversion into pandas DataFrame.

A Jekyll website for the research guides--UNIX, AMBER, Analysis, and R.

A python molecular dynamics data analysis tool.

A library for the Analysis of Molecular Dynamics Simulations of Self Assembling Peptides. Started during an internship at CNTE, Niguarda Hospital, Milan

A package to find collective variables of dynamical systems by training neural networks

Reactive molecular dynamics trajectory analysis

This repository contains Jupyter notebooks used to perform computational analysis of LAT1 (SLC7A5) cholesterol binding sites, as published in JCTC

Efficiently compute off-resonance Raman spectra from first principles calculations (e.g. VASP) using polynomial models and ML/AI.

Order parameter calculations from Desmond Maestro .csv out files