Molecular Dynamics First Principles Simulation of Chemical Systems

Solving the Newtonian equations of motion for biochemical molecules provides atomistic levels of visualizable insight of difficult-to-probe systems.

An image showing some molecular simulation and a graphical representation, with the integral of a generalized momentum at the bottom

Peptide Aggregation Investigating the Molecular Origins of Disease

The formation of abnormal plaques from natural cellular proteins is clinically associated with disease. Our methods let us investigate this phenomena in detail.

An image of simulated amyloid formation

Analysis of Biomolecules Statistical Mechanics & Machine Learning

With approaches ranging from traditional statistical mechanics to novel machine learning algorithms, we quantitatively characterize the properties of simulated biopolymers.

An image of free energy landscapes

Documentation Simulation and Computation

Centralized documentation and references critical to work in the Shea group. Includes tutorials and reference guides for molecular dynamics tools and general computational resources available to the Shea group.

A symbol of our documentation.