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msmdev committed Jul 28, 2022
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pyGPCCA - Generalized Perron Cluster Cluster Analysis
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Generalized Perron Cluster Cluster Analysis program to coarse-grain reversible and non-reversible Markov State Models.
Generalized Perron Cluster Cluster Analysis program to coarse-grain reversible and non-reversible Markov state models.

Markov State Models (MSM) enable the identification and analysis of metastable states and related kinetics in a
very instructive manner. They are widely used, e.g. to model molecular or cellular kinetics. |br|
Markov state models (MSM) enable the identification and analysis of metastable states and related kinetics in a
very instructive manner. They are widely used, e.g., to model molecular or cellular kinetics. |br|
Common state-of-the-art Markov state modeling methods and tools are very well suited to model reversible processes in
closed equilibrium systems. However, most are not well suited to deal with non-reversible or even non-autonomous
processes of non-equilibrium systems. |br|
To overcome this limitation, the Generalized Robust Perron Cluster Cluster Analysis (G-PCCA) was developed.
The G-PCCA method implemented in the *pyGPCCA* program readily handles equilibrium as well as non-equilibrium data by
To overcome this limitation, the Generalized Robust Perron Cluster Cluster Analysis (GPCCA or G-PCCA) was developed.
The GPCCA method implemented in the *pyGPCCA* program readily handles equilibrium as well as non-equilibrium data by
utilizing real Schur vectors instead of eigenvectors. |br|
*pyGPCCA* enables the semiautomatic coarse-graining of transition matrices representing the dynamics of the system
under study. Utilizing *pyGPCCA*, metastable states as well as cyclic kinetics can be identified and modeled.
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M. Weber, together with K. Fackeldey, had the original idea to employ Schur vectors instead of eigenvectors in the
coarse-graining of non-reversible transition matrices. |br|
Further, we would like to thank `Fabian Paul`_ for valuable discussions regarding the sorting of Schur vectors and his
effort to translate the original Sorting routine for real Schur forms `SRSchur`_ published by `Jan Brandts`_ from MATLAB
effort to translate the original sorting routine for real Schur forms, `SRSchur`_ published by `Jan Brandts`_, from MATLAB
into `Python code`_,
M. Weber and `Alexander Sikorski`_ for pointing us to `SLEPc`_ for sorted partial Schur decompositions,
and A. Sikorski for supplying us with an `code example`_ and guidance how to interface SLEPc in Python.
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