EU-Funded Project HiddenBio
Hidden states and currents in biological systems
The possibility to infer information about hidden degrees of freedom from time series is a key challenge in many disciplines, especially single-molecule spectroscopy, climate science, and epidemiology. Hidden degrees of freedom are often essential, as they reflect the approach to, and mechanism of, critical transitions. Current approaches neglect certain information encoded in the time ordering, which prevents accessing hidden information.
In HiddenBio we approach time series as “shadows” of high-dimensional dynamics, resting on the fact that hidden properties of a high-dimensional landscape imprint onto the time ordering of projected states along individual trajectories. We are focusing on additive functionals of projected paths that are easily inferred from data, and analyse their statistics and measure concentration by theory and by inferring them from single-molecule data.
Our goal is the systematic exploration of hidden states, parallel pathways, and buried currents directly from time series, especially those probed in experiments on single-molecules and assemblies at the mesoscale, in and (far) out of thermodynamic equilibrium.
Publications
Purely quantum memory in closed systems observed via imperfect measurements
Author(s): Jorge Tabanera-Bravo; Aljaž Godec
Published in: Quantum, Volume 9, 2025
Publisher: Vienna, Austria
DOI: 10.22331
Towards Markov-State Holography
Author(s): Xizhu. Zhao, D. E. Makarov; Aljaž Godec
Published in: New Journal of Physics, Issue 27, 2025, ISSN 1367-2630
Publisher: Cambridge, England
DOI: 10.1088
Thermodynamic correlation inequalities for finite times and transients
Author(s): Cai Dieball; Aljaž Godec
Published in: Journal of Physics A: Mathematical and Theoretical, Issue 58, 2025, ISSN 1751-8121
Publisher: Cambridge, England
DOI: 10.1088
Soft Matter
Author(s): Cai Dieball; Yasamin Mohebi Satalsari; Angel B. Zuccolotto-Bernez; Stefan U. Egelhaaf; Manuel A. Escobedo-Sánchez; Aljaž Godec
Published in: Soft Matter, 2025, ISSN 1744-683X
Publisher: Cambridge, England : Royal Society of Chemistry
DOI: 10.48550/ARXIV.2410.07026
Physical Review Letters
Author(s): Cai Dieball; Aljaž Godec
Published in: Physical Review Letters, 2024, ISSN 0031-9007
Publisher: New York : American Physical Society
DOI: 10.48550/ARXIV.2403.00048
Perspective: Time irreversibility in systems observed at coarse resolution
Author(s): Cai Dieball, Aljaž Godec
Published in: The Journal of Chemical Physics, Issue 162, 2025, ISSN 0021-9606
Publisher: AIP Publishing
DOI: 10.1063/5.0251089
Multiple Pareto-optimal solutions of the dissipation-adaptation trade-off
Author(s): Jorge Tabanera-Bravo, Aljaž Godec
Published in: Physical Review Research, Issue 7, 2025, ISSN 2643-1564
Publisher: American Physical Society (APS)
DOI: 10.1103/PHYSREVRESEARCH.7.013020
Physical Review Letters
Author(s): Xizhu Zhao; David Hartich; Aljaž Godec
Published in: Physical Review Letters, 2024, ISSN 0031-9007
Publisher: New York : American Physical Society
DOI: 10.1103/PHYSREVLETT.132.147101