Software

MesoHOPS is a Python library for running simulations with the Hierarchy of Pure States (HOPS), a formally exact trajectory-based approach for solving the time-evolution of open quantum systems coupled to non-Markovian thermal environments. The main feature of MesoHOPS is the implementation of adaptive HOPS (adHOPS), an extension of the HOPS formalism that leverages the dynamic localization of excitations to construct an adaptive basis, allowing for O(1) - i.e. size invariant - scaling with the number of molecules. 

pyLakoid is a Python library for running integrative biophysical simulations of photosynthetic light harvesting in the thylakoid membrane. The library contains modules for protein and membrane-scale structures, exciton transport, and spectroscopy. It also has a collection of exciton parameters for antennae proteins of photosystem II that can reproduce a variety of spectroscopic observables. A collection of pre-built protein models simplifies running spectroscopic simulations on both the protein and membrane length scales.