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

Preserving dynamic information such as diffusion coefficients and transition rates in coarse-grained models is a persistent challenge in multi-scale simulations. This task becomes even more daunting when the original microscopic dynamics breaks detailed balance, corresponding to the system being driven away from thermal equilibrium. The aim of this project is to develop a comprehensive computational method to coarse-grain models from atomistic resolution to a few discrete states while preserving the statistics of the energetic exchange with their environment. In complex macro and biomolecules, these discrete states are identified with long-lived molecular conformations. In the second funding period, we are addressing the question how to model transitions that go beyond simple conformational transitions and involve a chemical transformation. To this end, we study a molecular rotor that is driven by light and performs asymmetric photoisomerization steps to achieve directional rotation. In the third funding period, we aim to broaden the scope of this project and to address applications. The systematic and physically accurate coarse-graining of driven systems is a current challenge in biology trying to unravel the function of biomolecular machines and the working of cells. In particular, we will elucidate how the interactions of disordered proteins are shaped by non-equilibrium phosphorylation dephosphorylation cycles.

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


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)
see publication


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)
see publication


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


Nonequilibrium Markov state modeling of the globule-stretch transition
Fabian Knoch, Thomas Speck
Physical Review E95 (1), (2017)
see publication


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)
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Polydisperse hard spheres: crystallization kinetics in small systems and role of local structure
Matteo Campo, Thomas Speck
Journal of Statistical Mechanics: Theory and Experiment 2016 (8), 084007 (2016)
see publication


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


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)
see publication