Publications of the Mathemathical bioPhysics Group

Journal Article

Dieball, C.; Godec, A.: Perspective: Time irreversibility in systems observed at coarse resolution. The Journal of Chemical Physics 162, 090901 (2025)

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Journal Article

Dieball, C.; Mohebi Satalsari, Y.; Zuccolotto-Bernez, A. B.; Egelhaaf, S. U.; Escobedo-Sánchez, M. A.; Godec, A.: Precisely controlled colloids: a playground for path-wise non-equilibrium physics. Soft Matter 21 (11), pp. 2170 - 2181 (2025)

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Journal Article

Blom, K.; Thiele, U.; Godec, A.: Local order controls the onset of oscillations in the nonreciprocal Ising model. Physical Review E 111 (2), 024207 (2025)

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Journal Article

Tabanera-Bravo, J.; Godec, A.: Multiple Pareto-optimal solutions of the dissipation-adaptation trade-off. Physical Review Research 7, 013020 (2025)

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Journal Article

Goswami, K.; Cherstvy, A. G.; Godec, A.; Metzler, R.: Anomalous diffusion of active Brownian particles in responsive elastic gels: Nonergodicity, non-Gaussianity, and distributions of trapping times. Physical Review E 110, 044609 (2024)

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Journal Article

Hartich, D.; Godec, A.: Comment on “Inferring broken detailed balance in the absence of observable currents”. Nature Communications 15, 8678 (2024)

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Journal Article

Vollmar, L.; Bebon, R.; Schimpf, J.; Flietel, B.; Celiksoy, S.; Sönnichsen, C.; Godec, A.; Hugel, T.: Model-free inference of memory in conformational dynamics of a multi-domain protein. Journal of Physics A 57 (36), 365001 (2024)

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Journal Article

Dieball, C.; Godec, A.: Thermodynamic Bounds on Generalized Transport: From Single-Molecule to Bulk Observables. Physical Review Letters 133 (6), 067101 (2024)

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10.

Journal Article

Dunlop, J.; Cerisola, F.; Tabanera-Bravo, J.; Anders, J.: Thermodynamically optimal protocols for dual-purpose qubit operations. Physical Review Research 6 (3), 033005 (2024)

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11.

Journal Article

Blom, K.; Song, K.; Vouga, E.; Godec, A.; Makarov, D. E.: Milestoning estimators of dissipation in systems observed at a coarse resolution. PNAS 121 (17), e2318333121 (2024)

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12.

Journal Article

Miao, M.; Makarov, D. E.; Blom, K.: Nonequilibrium statistical mechanics of money/energy exchange models. Journal of Physics A 57 (15), 155003 (2024)

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13.

Journal Article

Zhao, X.; Hartich, D.; Godec, A.: Emergence of Memory in Equilibrium versus Nonequilibrium Systems. Physical Review Letters 132 (14), 147101 (2024)

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14.

Journal Article

Ibáñez, M.; Dieball, C.; Lasanta, A.; Godec, A.; Rica, R. A.: Heating and cooling are fundamentally asymmetric and evolve along distinct pathways. Nature Physics 20, pp. 135 - 141 (2024)

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15.

Journal Article

Dieball, C.; Wellecke, G.; Godec, A.: Asymmetric thermal relaxation in driven systems: Rotations go opposite ways. Physical Review Research 5 (4), L042030 (2023)

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16.

Journal Article

Hartich, D.; Godec, A.: Violation of local detailed balance upon lumping despite a clear timescale separation. Physical Review Research 5 (3), L032017 (2023)

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17.

Journal Article

Dieball, C.; Godec, A.: Feynman-Kac theory of time-integrated functionals: Itô versus functional calculus. Journal of Physics A 56 (15), 155002 (2023)

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18.

Journal Article

Dieball, C.; Godec, A.: Direct Route to Thermodynamic Uncertainty Relations and Their Saturation. Physical Review Letters 130 (8), 087101 (2023)

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19.

Journal Article

Blom, K.; Ziethen, N.; Zwicker, D.; Godec, A.: Thermodynamically consistent phase-field theory including nearest-neighbor pair correlations. Physical Review Research 5 (1), 013135 (2023)

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20.

Journal Article

Godec, A.; Makarov, D. E.: Challenges in Inferring the Directionality of Active Molecular Processes from Single-Molecule Fluorescence Resonance Energy Transfer Trajectories. The Journal of Physical Chemistry Letters 14 (1), pp. 49 - 56 (2023)

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21.

Journal Article

Bebon, R.; Godec, A.: Controlling Uncertainty of Empirical First-Passage Times in the Small-Sample Regime. Physical Review Letters 131 (23), 237101 (2023)

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22.

Journal Article

Dieball, C.; Godec, A.: On correlations and fluctuations of time-averaged densities and currents with general time-dependence. Journal of Physics A 55 (47), 475001 (2022)

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23.

Journal Article

Dieball, C.; Godec, A.: Mathematical, thermodynamical, and experimental necessity for coarse graining empirical densities and currents in continuous space. Physical Review Letters 129 (14), 140601 (2022)

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24.

Journal Article

Dieball, C.; Godec, A.: Coarse graining empirical densities and currents in continuous-space steady states. Physical Review Research 4, 033243 (2022)

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25.

Journal Article

Li, J.; Xie, J.; Godec, A.; Weninger, K.; Liu, C.; Smith, J.; Hong, L.: Non-ergodicity of a globular protein extending beyond its functional timescale. Chemical Science 13, pp. 9668 - 9677 (2022)

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26.

Journal Article

Dieball, C.; Krapf, D.; Weiss, M.; Godec, A.: Scattering fingerprints of two-state dynamics. New Journal of Physics 24, 023004 (2022)

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27.

Journal Article

Zunke, C.; Bewerunge, J.; Platten, F.; Egelhaaf , S. U.; Godec, A.: First-passage statistics of colloids on fractals: Theory and experimental realization. Science Advances 8 (3), eabk0627 (2022)

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28.

Journal Article

Hartich, D.; Godec, A.: Emergent memory and kinetic hysteresis in strongly driven networks. Physical Review X 11 (4), 041047 (2021)

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29.

Journal Article

Lapolla, A.; Godec, A.: BetheSF V2: 3-point propagator and additional external potentials. Computer Physics Communications 269, 108131 (2021)

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30.

Journal Article

Blom, K.; Godec, A.: Criticality in cell adhesion. Physical Review X 11 (3), 031067 (2021)

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31.

Journal Article

Lapolla, A.; Vossel, M.; Godec, A.: Time- and ensemble-average statistical mechanics of the Gaussian network model. Journal of Physics A 54 (35), 355601 (2021)

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32.

Journal Article

Hartich, D.; Godec, A.: Thermodynamic uncertainty relation bounds the extent of anomalous diffusion. Physical Review Letters 127 (8), 080601 (2021)

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33.

Journal Article

Lapolla, A.; Godec, A.: Toolbox for quantifying memory in dynamics along reaction coordinates. Physical Review Research 3 (2), L022018 (2021)

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34.

Journal Article

Lapolla, A.; Godec, A.: BetheSF: Efficient computation of the exact tagged-particle propagator in single-file systems via the Bethe eigenspectrum. Computer Physics Communications 258, 107569 (2021)

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35.

Journal Article

Lapolla, A.; Hartich, D.; Godec, A.: Spectral theory of fluctuations in time-average statistical mechanics of reversible and driven systems. Physical Review Research 2 (4), 043084 (2020)

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36.

Journal Article

Lapolla, A.; Godec, A.: Single-file diffusion in a bi-stable potential: Signatures of memory in the barrier-crossing of a tagged-particle. The Journal of Chemical Physics 153 (19), 194104 (2020)

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37.

Journal Article

Lapolla, A.; Godec, A.: Faster uphill relaxation in thermodynamically equidistant temperature quenches. Physical Review Letters 125 (11), 110602 (2020)

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38.

Journal Article

Ukmar-Godec, T.; Fang, P.; Ibáñez de Opakua, A.; Henneberg, F.; Godec, A.; Pan, K. T.; Cima-Omori, M.-S.; Chari, A.; Mandelkow, E.; Urlaub, H. et al.; Zweckstetter, M.: Proteasomal degradation of the intrinsically disordered protein tau at single-residue resolution. Science Advances 6 (30), eaba3916 (2020)

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39.

Journal Article

Lapolla, A.; Godec, A.: Manifestations of projection-induced memory: General theory and the tilted single file. Frontiers in Physics 7, 182 (2019)

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40.

Journal Article

Hartich, D.; Godec, A.: Extreme value statistics of ergodic Markov processes from first passage times in the large deviation limit. Journal of Physics A: Mathematical and Theoretical 52, 244001 (2019)

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41.

Journal Article

Hartich, D.; Godec, A.: Interlacing relaxation and first-passage phenomena in reversible discrete and continuous space Markovian dynamics. Journal of Statistical Mechanics: Theory and Experiment 2019, 024002 (2019)

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42.

Journal Article

Hartich, D.; Godec, A.: Duality between relaxation and first passage in reversible Markov dynamics: Rugged energy landscapes disentangled. New Journal of Physics 20 (11), 112002 (2018)

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43.

Journal Article

Lapolla, A.; Godec, A.: Unfolding tagged particle histories in single-file diffusion: Exact single- and two-tag local times beyond large deviation theory. New Journal of Physics 20, 113021 (2018)

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44.

Journal Article

Ukmar-Godec, T.; Bertinetti, L.; Dunlop, J. W. C.; Godec, A.; Grabiger, M. A.; Masic, A.; Nguyen, H.; Zlotnikov, I.; Zaslansky, P.; Faivre, D.: Materials nanoarchitecturing via cation-mediated protein assembly: Making limpet teeth without mineral. Advanced Materials 29 (27), 1701171 (2017)

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45.

Journal Article

Schwarzl, M.; Godec, A.; Metzler, R.: Quantifying non-ergodicity of anomalous diffusion with higher order moments. Scientific Reports 7, 3878 (2017)

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46.

Journal Article

Godec, A.; Metzler, R.: First passage time statistics for two-channel diffusion. Journal of Physics A: Mathematical and Theoretical 50 (8), 084001 (2017)

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47.

Journal Article

Godec, A.; Metzler, R.: Universal proximity effect in target search kinetics in the few-encounter limit. Physical Review X 6 (4), 041037 (2016)

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48.

Journal Article

Godec, A.; Metzler, R.: Active transport improves the precision of linear long distance molecular signalling. Journal of Physics A: Mathematical and Theoretical 49 (36), 364001 (2016)

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49.

Journal Article

Schwarzl, M.; Godec, A.; Oshanin, G.; Metzler, R.: A single predator charging a herd of prey: Effects of self volume and predator–prey decision-making. Journal of Physics A: Mathematical and Theoretical (22), 225601 (2016)

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50.

Journal Article

Godec, A.; Metzler, R.: First passage time distribution in heterogeneity controlled kinetics: Going beyond the mean first passage time. Scientific Reports 6, 20349 (2016)

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51.

Journal Article

Godec, A.; Metzler, R.: Signal focusing through active transport. Physical Review E 92 (1), 010701(R) (2015)

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52.

Journal Article

Krüsemann, H.; Godec, A.; Metzler, R.: Ageing first passage time density in continuous time random walks and quenched energy landscapes. Journal of Physics A: Mathematical and Theoretical 48 (28), 285001 (2015)

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53.

Journal Article

Godec, A.; Metzler, R.: Optimization and universality of Brownian search in a basic model of quenched heterogeneous media. Physical Review E 91 (5), 052134 (2015)

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54.

Journal Article

Godec, A.; Chechkin, A. V.; Barkai, E.; Kantz, H.; Metzler, R.: Localisation and universal fluctuations in ultraslow diffusion processes. Journal of Physics A: Mathematical and Theoretical 47 (49), 492002 (2014)

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55.

Journal Article

Godec, A.; Bauer, M.; Metzler, R.: Collective dynamics effect transient subdiffusion of inert tracers in flexible gel networks. New Journal of Physics 16, 092002 (2014)

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56.

Journal Article

Krüsemann, H.; Godec, A.; Metzler, R.: First-passage statistics for aging diffusion in systems with annealed and quenched disorder. Physical Review E 89 (4), 040101(R) (2014)

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57.

Journal Article

Bauer, M.; Godec, A.; Metzler, R.: Diffusion of finite-size particles in two-dimensional channels with random wall configurations. Physical Chemistry Chemical Physics 16 (13), pp. 6118 - 6128 (2014)

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58.

Journal Article

Godec, A.; Smith, J. C.; Merzel, F.: Soft collective fluctuations governing hydrophobic association. Physical Review Letters 111 (12-20), 127801 (2013)

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59.

Journal Article

Godec, A.; Metzler, R.: Linear response, fluctuation-dissipation, and finite-system-size effects in superdiffusion. Physical Review E 88 (1), 012116 (2013)

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60.

Journal Article

Godec, A.; Metzler, R.: Finite-time effects and ultraweak ergodicity breaking in superdiffusive dynamics. Physical Review Letters 110 (2), 020603 (2013)

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61.

Journal Article

Godec, A.; Merzel, F.: Physical origin underlying the entropy loss upon hydrophobic hydration. Journal of the American Chemical Society 134 (42), pp. 17575 - 17581 (2012)

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62.

Journal Article

Znidarsic, A.; Godec, A.; Gaberscek , M.: pH-based one pot synthesis of biocompatible olive shaped inorganic particles. Materials Research Bulletin 47 (4), pp. 967 - 973 (2012)

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63.

Journal Article

Ukmar, T.; Maver, U.; Planinsek, O.; Pintar, A.; Kaucic, V.; Godec, A.; Gaberscek, M.: Guest-host van der Waals interactions decisively affect the molecular transport in mesoporous media. Journal of Materials Chemistry 22 (3), pp. 1112 - 1120 (2012)

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64.

Journal Article

Godec, A.; Smith, J. C.; Merzel, F.: Increase of both order and disorder in the first hydration shell with increasing solute polarity. Physical Review Letters 107 (26), 267801 (2011)

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65.

Journal Article

Ukmar, T.; Maver, U.; Planinsek, O.; Kaucic, V.; Gaberscek, M.; Godec, A.: Understanding controlled drug release from mesoporous silicates: Theory and experiment. Journal of Controlled Release 155 (3), pp. 409 - 417 (2011)

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66.

Journal Article

Godec, A.; Ukmar, T.; Gaberscek, M.; Merzel, F.: Inversion of pore size dependence of solute transport kinetics from increasingly attractive ordered porous matrix. Europhysics Letters 92 (6), 60011 (2011)

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67.

Journal Article

Ukmar, T.; Gaberscek, M.; Merzel, F.; Godec, A.: Modus operandi of controlled release from mesoporous matrices: A theoretical perspective. Physical Chemistry Chemical Physics 13 (3), pp. 15311 - 15317 (2011)

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68.

Journal Article

Ukmar, T.; Godec, A.; Planinsek, O.; Kaucic, V.; Mali, G.; Gaberscek, M.: The phase (trans)formation and physical state of a model drug in mesoscopic confinement. Physical Chemistry Chemical Physics 13 (35), pp. 16046 - 16054 (2011)

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69.

Journal Article

Maver, U.; Znidarsic, A.; Saboti, D.; Srcic, S.; Gaberscek, M.; Godec, A.; Planinsek , O.: The relation between the interfacial contact and SiO₂ coating efficiency and properties in the case of two clarithromycin polymorphs. Colloids and Surfaces A: Physicochemical and Engineering Aspects 371 (1-3), pp. 119 - 125 (2010)

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70.

Journal Article

Godec, A.; Gaberscek, M.; Jamnik , J.; Janezic, D.; Merzel, F.: Ion-size effect within the aqueous solution interface at the Pt(111) surface: Molecular dynamics studies. Physical Chemistry Chemical Physics 12 (41), pp. 13566 - 13573 (2010)

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71.

Journal Article

Planinsek, O.; Zadnik, J.; Kunaver, M.; Srcic, S.; Godec, A.: Structural evolution of indomethacin particles upon milling: Time-resolved quantification and localization of disordered structure studied by IGC and DSC. Journal of Pharmaceutical Sciences 99 (4), pp. 1968 - 1981 (2010)

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72.

Journal Article

Godec, A.; Gaberscek, M.; Jamnik , J.; Merzel, F.: Nonlinear diffusion in two-dimensional ordered porous media based on a free volume theory. The Journal of Chemical Physics 131 (23), 234106 (2009)

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73.

Journal Article

Godec, A.; Gaberscek, M.; Jamnik, J.: Comment on the article “A new understanding of the relationship between solubility and particle size” by W. Wu and G.H. Nancollas. Journal of Solution Chemistry 38 (1), pp. 135 - 146 (2009)

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74.

Journal Article

Ukmar, T.; Godec, A.; Maver, U.; Planinsek, O.; Bele, M.; Jamnik, J.; Gaberscek, M.: Suspensions of modified TiO2 nanoparticles with supreme UV filtering ability. Journal of Materials Chemistry 19 (43), pp. 8176 - 8183 (2009)

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75.

Journal Article

Godec, A.; Maver, U.; Bele, M.; Planinsek, O.; Srcic, S.; Gaberscek, M.c.; Jamnik, J.: Vitrification from solution in restricted space: Formation and stabilization of amorphous nifedipine in a nanoporous silica xerogel carrier. International Journal of Pharmaceutics 343 (1-2), pp. 131 - 140 (2007)

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76.

Journal Article

Maver, U.; Godec, A.; Bele, M.; Planinsek, O.; Gaberscek, M.; Srcic, S.; Jamnik, J.: Novel hybrid silica xerogels for stabilization and controlled release of drug. International Journal of Pharmaceutics 330 (1-2), pp. 164 - 174 (2007)

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Book Chapter (1)

77.

Book Chapter

Bebon, R.; Godec, A.: Concentration of Empirical First-Passage Times. In: Target Search Problems, pp. 31 - 53 (Eds. Grebenkov, D.; Metzler, R.; Oshanin, G.). Springer Nature Switzerland, Cham (2024)

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