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A7: Dynamical coarse-graining for non-equilibrium steady states with stochastic dynamics

The aim of this project is to develop a novel approach to the coarse-graining of driven systems based on Markov State Modelling, building on recent developments in stochastic thermodynamics. In the first funding period, we have developed the basic formalism based on a cycle decomposition algorithm that allows to cluster cycles based on “similarity” and to replace clusters of cycles by a single cycle, thus drastically reducing the number of states while preserving the entropy production and dynamical features. In the second funding period, we plan to further develop the work and apply it to mechanical unfolding of biomolecules and to molecular machines (F1-ATPase).


Unfolding dynamics of small peptides biased by constant mechanical forces
Fabian Knoch, Thomas Speck
Molecular Systems Design & Engineering, (2018);
doi:10.1039/c7me00080d

Nonequilibrium Markov state modeling of the globule-stretch transition
Fabian Knoch, Thomas Speck
Physical Review E 95 (1), (2017);
doi:10.1103/physreve.95.012503

Thermodynamic formalism for transport coefficients with an application to the shear modulus and shear viscosity
Thomas Palmer, Thomas Speck
The Journal of Chemical Physics 146 (12), 124130 (2017);
doi:10.1063/1.4979124

Polydisperse hard spheres: crystallization kinetics in small systems and role of local structure
Matteo Campo, Thomas Speck
J. Stat. Mech. 2016 (8), 084007 (2016);
doi:10.1088/1742-5468/2016/8/084007

Nucleation pathway and kinetics of phase-separating active Brownian particles
David Richard, Hartmut Löwen, Thomas Speck
Soft Matter 12 (24), 5257-5264 (2016);
doi:10.1039/c6sm00485g

Cycle representatives for the coarse-graining of systems driven into a non-equilibrium steady state
Fabian Knoch, Thomas Speck
New Journal of Physics 17 (11), 115004 (2015);
doi:10.1088/1367-2630/17/11/115004

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