Generalized Markov State Modeling Method for Nonequilibrium Biomolecular Dynamics: Exemplified on Amyloid β Conformational Dynamics Driven by an Oscillating Electric Field

• DOI: 10.1021/acs.jctc.8b00079
• Publication Date: 2018-05-29T20:54:56Z
• Authors: Bernhard Reuter; Marcus Weber; Konstantin Fackeldey; Susanna Röblitz; Martin E. Garcia
• Keywords: Metastability

Markov state models (MSMs) have received an unabated increase in popularity recent years, as they are very well suited for the identification and analysis of metastable states related kinetics. However, state-of-the-art modeling methods tools enforce fulfillment a detailed balance condition, restricting their applicability to equilibrium MSMs. To date, unsuitable deal with general dominant data structures including cyclic processes, which essentially associated nonequilibrium systems. overcome this limitation, we developed generalization common robust Perron Cluster Analysis (PCCA+) method, termed generalized PCCA (G-PCCA). This method handles simulation data, utilizing Schur vectors instead eigenvectors. G-PCCA is not limited detection but enables sense, unraveling processes. exemplified by application on molecular dynamics Amyloid β (1–40) peptide, periodically driven oscillating electric field.