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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).

Non-equilibrium Markov state modeling of periodically driven biomolecules
Fabian Knoch, Thomas Speck
The Journal of Chemical Physics 150 (5), 054103 (2019);

Molecular dynamics simulations allow us to study the structure and dynamics of single biomolecules in microscopic detail. However, many processes occur on time scales beyond the reach of fully atomistic simulations and require coarse-grained multiscale models. While systematic approaches to construct such models have become available, these typically rely on microscopic dynamics that obey detailed balance. In vivo, however, biomolecules are constantly driven away from equilibrium in order to perform specific functions and thus break detailed balance. Here we introduce a method to construct Markov state models for systems that are driven through periodically changing one (or several) external parameter. We illustrate the method for alanine dipeptide, a widely used benchmark molecule for computational methods, exposed to a time-dependent electric field.

Highly controlled optical transport of cold atoms into a hollow-core fiber
Maria Langbecker, Ronja Wirtz, Fabian Knoch, Mohammad Noaman, Thomas Speck, Patrick Windpassinger
New Journal of Physics 20 (8), 083038 (2018);

Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding
Fabian Knoch, Ken Schäfer, Gregor Diezemann, Thomas Speck
The Journal of Chemical Physics 148 (4), 044109 (2018);

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

Nonequilibrium Markov state modeling of the globule-stretch transition
Fabian Knoch, Thomas Speck
Physical Review E 95 (1), (2017);

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);

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

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

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);


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