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
Molecular Systems Design & Engineering,
(2018);
doi:10.1039/c7me00080d
Nonequilibrium Markov state modeling of the globule-stretch transition
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
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
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
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
New Journal of Physics 17 (11),
115004
(2015);
doi:10.1088/1367-2630/17/11/115004
Contact
- Prof. Dr. Thomas Speck
- Institut für Physik
- Universität Mainz
- Staudingerweg 9
- D-55128 Mainz
- Tel: +49 6131 39 26915
- Fax: +49 6131 39 20496
- thomas.specktxmA@puni-mainz.de
- http://www.komet331.physik.uni-mainz.de/speck.php