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

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

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

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.

Molecular Dynamics Trajectory Analysis Tools

Gromacs Analysis Library for Rust

Library for Reading Gromacs TPR Files

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

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

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

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

Repository for my senior design project/thesis code

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

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

Two Phase Thermodynamic (2PT) Method to compute adsorption isotherms

Calculate lipid order parameters from Gromacs simulations

Degrees of freedom calculator for rigid and semi-rigid molecules

Center Any Group in a Gromacs Trajectory