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.
Publications
Topological chiral random walker
S. Osat, E. Meyberg, J. Metson, T. Speck
Arxiv preprint
Link: https://doi.org/10.48550/arXiv.2602.12020
Mutual linearity is a generic property of steady-state Markov networks
Robin Bebon, Thomas Speck
Physical Review Letters 136, 137401 (2026)
Link: https://doi.org/10.1103/jcm3-57d8
Impact of currents on non-equilibrium coexistence in chemically driven mixtures
Ellen Meyberg, Joshua F. Robinson, Thomas Speck
The Journal of Chemical Physics 165, 044118 (2026)
Link: https://doi.org/10.1063/5.0336459
Proton First: Rationalizing a Proton Transfer in a Protein-Fragment Complex
H. Vatheuer, J. Paulus, L. Johannknecht, G. Keller, R.M. Ziora, L.S. Stelzl, P. Czodrowski
CHEMMEDCHEM 20, 202500244 (2025)
Link: https://doi.org/10.1002/cmdc.202500244
Sequence determinants of protein phase separation and recognition by protein phase-separated condensates through molecular dynamics and active learning
A. Changiarath, A. Arya, V.A. Xenidis, J. Padeken, L.S. Stelzl
Faraday Discussions 256, 235-254 (2025)
Link: https://doi.org/10.1039/d4fd00099d
Steady inhomogeneous shear flows as mechanical phase transitions
Thomas Speck
Physical Review E 111, 015430 (2025)
Link: https://doi.org/10.1103/PhysRevE.111.015430
Molecular simulations of enzymatic phosphorylation of disordered proteins and their condensates
E. Zippo, D. Dormann, T. Speck, L.S. Stelzl
Nature Communications 16, 4649 (2025)
Link: https://doi.org/10.1038/s41467-025-59676-4
Dependencies between effective parameters in coarse-grained models for phase separation of DNA-based fluids
Soumen De Karmakar, Thomas Speck
The Journal of Chemical Physics 161, 234907 (2024)
Link: https://doi.org/10.1063/5.0232651
Structural ensembles of disordered proteins from hierarchical chain growth and simulatio
Lisa M. Pietrek, Lukas Stelzl, Gerhard Hummer
Current Opinion in Structural Biology 78, 102501 (2023)
Link: https://doi.org/0.1016/j.sbi.2022.102501
Critical behavior of active Brownian particles: Connection to field theories
Thomas Speck
Physical Review E 105, 064601 (2022)
Link: https://doi.org/10.1103/PhysRevE.105.064601
Single-chain and condensed-state behavior of hnRNPA1 from molecular simulations
D.J. Bauer, L.S. Stelzl, A. Nikoubashman
The Journal of Chemical Physics 165, 044118 (2022)
Link: https://doi.org/10.1063/5.0105540
Modeling of biomolecular machines in non-equilibrium steady states
Thomas Speck
The Journal of Chemical Physics 155, 230901 (2021)
Link: https://doi.org/10.1063/5.0070922
Classical nucleation theory for the crystallization kinetics in sheared liquids
David Richard, Thomas Speck
Physical Review E 99, 062801 (2019)
Link: https://doi.org/10.1103/PhysRevE.99.062801
Non-equilibrium Markov state modeling of periodically driven biomolecules
Fabian Knoch, Thomas Speck
The Journal of Chemical Physics 150 (5), 054103 (2019)
Link: https://doi.org/10.1063/1.5055818
Communication: Is directed percolation in colloid-polymer mixtures linked to dynamic arrest?
David Richard, Patrick C. Royall, Thomas Speck
The Journal of Chemical Physics 148, 241101 (2018)
Link: https://doi.org/10.1063/1.5037680
Crystallization of hard spheres revisited. I. Extracting kinetics and free energy landscape from forward flux sampling
David Richard, Thomas Speck
The Journal of Chemical Physics 148, 124110 (2018)
Link: https://doi.org/10.1063/1.5016277
Crystallization of hard spheres revisited. II. Thermodynamic modeling, nucleation work, and the surface of tension
David Richard, Thomas Speck
The Journal of Chemical Physics 148, 224102 (2018)
Link: https://doi.org/10.1063/1.5025394
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)
Link: https://doi.org/10.1088/1367-2630/aad9bb
Unfolding dynamics of small peptides biased by constant mechanical forces
Fabian Knoch, Thomas Speck
Molecular Systems Design and Engineering, (2018)
Link: https://doi.org/10.1039/c7me00080d
Coupling between criticality and gelation in ``sticky{''} spheres: a structural analysis
David Richard, James Hallett, Thomas Speck
Soft Matter 14, 5554-5564 (2018)
Link: https://doi.org/10.1039/c8sm00389k
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)
Link: https://doi.org/10.1063/1.5010435
Estimation of the critical behavior in an active colloidal system with Vicsek-like interactions
Benjamin Trefz, Jonathan T. Siebert, Thomas Speck, Kurt Binder, Peter Virnau
The Journal of Chemical Physics 146, 074901 (2017)
Link: https://doi.org/10.1063/1.4975812
Nonequilibrium Markov state modeling of the globule-stretch transition
Fabian Knoch, Thomas Speck
Physical Review E95 (1), (2017)
Link: https://doi.org/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)
Link: https://doi.org/10.1063/1.4979124
Gold nanorods as plasmonic sensors for particle diffusion
Verena Wulf, Fabian Knoch, Thomas Speck, Carsten Sönnichsen
The Journal of Physical Chemistry Lett. 7, 4951-4955 (2016)
Link: https://doi.org/10.1021/acs.jpclett.6b02165
Special Issue on Structure in Glassy and Jammed Systems
Patrick C. Royall and Thomas Speck
J. Stat. Mech. 054045 (2016)
Link: https://doi.org/10.1088/1742-5468/2016/05/054045
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)
Link: https://doi.org/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)
Link: https://doi.org/10.1039/c6sm00485g
The role of shear in crystallization kinetics: From suppression to enhancement
David Richard, Thomas Speck
Sci. Rep. 5, 14610 (2015)
Link: https://doi.org/10.1038/srep14610
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)
Link: https://doi.org/10.1088/1367-2630/17/11/115004