Provide a list of additional objects and functionality to Mathematica to alleviate the construction and analysis of Markov State Models. Especially in the context of Molecular Dynamics Simulations.
The project is a Mathematica library that will register a series of additional objects that refer to the mathematical objects used in Markov State Theory (e.g. transitionmatrix, timeseries, clusterings, etc.) Commands for generation and manipulation and analysis of these object are provided allowing a simple and fast way to construct markov state models from trajectories and employ various tasks such as timescale estimation, clustering, etc.
Apr 24, 2012