Berlin 2018 – scientific programme
Parts | Days | Selection | Search | Updates | Downloads | Help
BP: Fachverband Biologische Physik
BP 9: Postersession I
BP 9.5: Poster
Monday, March 12, 2018, 17:30–19:30, Poster A
Unraveling the effects of an oscillating electric field on Amyloid-beta (1-40) conformational dynamics using G-PCCA, a generalized Markov state modeling method — •Bernhard Reuter1, Marcus Weber2, and Martin E. Garcia1 — 1Theoretical Physics II, Institute of Physics, University of Kassel, Kassel, Germany — 2Zuse Institute Berlin (ZIB), Berlin, Germany
We have studied the influence of a strong oscillating electric field on the Amyloid-beta (1-40) peptide, associated with Alzheimer disease. To this end we conducted extensive molecular dynamics (MD) simulations utilizing the GROMACS v5.1.2 program package. Typically Markov state models (MSMs) are very well suited for the identification and analysis of metastabilities and related kinetics. However, the state-of-the-art methods and tools require the fulfillment of a detailed balance condition, violated in the non-equilibrium case. To date, they are unsuitable to deal with more general dominant data structures including cyclic processes, which are essentially associated with the effects of an oscillating electric field. Instead, for this purpose we utilized a generalization of the common robust Perron cluster cluster analysis (PCCA+) method, termed generalized Perron cluster cluster analysis (G-PCCA). Applying G-PCCA we identified and analyzed, by comparison to equilibrium simulations in the absence of an external electric field, significant non-thermal effects on the conformational dynamics of Amyloid-beta, imposed by the oscillating electric field.