Simulation

Velocity Autocorrelation Function showing the signature negative region characteristic of liquid dynamics and the cage effect discovered by Rahman

Modernizing Rahman''s 1964 Argon Simulation

A digital restoration of Rahman’s seminal 1964 molecular dynamics paper using LAMMPS and a Python analysis pipeline featuring decorator-based caching, fully vectorized NumPy computations for O(N^2) operations, and modern tooling (uv, type hints, Makefile automation) transforming academic scripts into a reproducible research toolkit.

Scientific Computing

Velocity Autocorrelation Function showing the signature negative region characteristic of liquid dynamics

Modernizing Rahman's 1964 Argon Simulation

I replicated Rahman’s landmark 1964 liquid argon molecular dynamics simulation using modern tools, building a Python analysis pipeline with caching, vectorization, and type hints to bridge vintage science with modern software engineering.

Molecular Simulation

Embedding energy and effective charge functions for Ni and Pd from the original EAM paper

Embedded-Atom Method: Impurities and Defects in Metals

The foundational 1984 paper introducing EAM, a semi-empirical many-body interatomic potential that incorporates density functional theory concepts to accurately simulate metallic systems while maintaining computational efficiency comparable to pair potentials.

Molecular Simulation

Protein folding funnel diagram illustrating energy landscape

Umbrella Sampling: Monte Carlo Free-Energy Estimation

Torrie and Valleau’s 1977 paper introducing importance sampling with non-physical distributions to overcome the sampling gap problem in Monte Carlo free-energy calculations, particularly for phase transitions.

Molecular Simulation

Copper adatom trajectory on Cu(100) surface

Copper Adatom Diffusion on Cu(100): LAMMPS Simulation

Watch copper atoms move across a crystal surface in this molecular dynamics simulation. This video demonstrates surface diffusion mechanisms important for understanding catalysis and crystal growth processes.

Molecular Simulation

Adatom surface diffusion trajectory on FCC metal surface

Platinum Adatom Diffusion on Pt(100): LAMMPS Simulation

Visualize platinum atom diffusion on crystal surfaces in this LAMMPS molecular dynamics simulation. Understand surface mobility mechanisms crucial for catalysis and materials design.

Scientific Computing

Energy conservation plot showing kinetic, potential, and total energy oscillations for a copper adatom diffusion simulation

Automated Adatom Diffusion Workflow

An input-to-analysis workflow for simulating adatom diffusion on FCC metal surfaces using LAMMPS and EAM potentials, covering copper and platinum to compare how atomic mass and bonding strength affect surface dynamics, with a Python analysis layer that generates energy and trajectory diagnostic plots. The LAMMPS setup is adapted from Eric N. Hahn’s adatom tutorial.

Computational Biology

Molecular visualization of a methionine dipeptide structure from MD simulation

Generating Mini-Protein Trajectories with GROMACS

A practical guide to simulating mini-proteins using GROMACS; from alanine dipeptide to tryptophan systems for ML training data generation.

Computational Biology

Mini-Protein Trajectory Generation

An automated GROMACS pipeline for generating molecular dynamics datasets suitable for machine learning, simulating capped dipeptides across nine residue types with 0.1 ps force-output resolution and atomic force extraction for training Neural Network Potentials.

Creative Work

Rubik's Cube Player - Drexel Music Hackathon 2017

A project I built with Emmanuel Espino and Jason Zogheb at the 2017 Drexel Music Hackathon. It uses computer vision to read a Rubik’s cube and generates music based on how solved each face is.

Creative Work