Publications of the Mathemathical bioPhysics Group

Link to publication list based on the Max Planck Repository MPG.PuRe

 

Last change: November 30, 2024

 

Most recent publications

within the last two months
(chronological order)
  • Goswami K, Cherstvy AG, Godec A, Metzler R. Anomalous diffusion of active Brownian particles in responsive elastic gels: Nonergodicity, non-Gaussianity, and distributions of trapping times. Phys. Rev. E 110, 044609 (2024)   [pdf] [doi]
     
  • Hartich D, Godec A. Comment on 'Inferring broken detailed balance in the absence of observable currents'. Nature Communications 15, 8678 (2024)   [pdf] [preprint] [doi] [arXiv]
     
  

2024

(alphabetical order)
  1. Blom K, Song K, Vouga E, Godec A, Makarov DE. Milestoning estimators of dissipation in systems observed at a coarse resolution. PNAS 121 (17), E2318333121 (2024)   [pdf] [preprint] [doi] [arXiv]
     
  2. Dieball C, Godec A. Thermodynamic Bounds on Generalized Transport: From Single-Molecule to Bulk Observables. Phys. Rev. Let. 133 (6), 067101-067107 (2024)   [pdf] [doi]
     
  3. Goswami K, Cherstvy AG, Godec A, Metzler R. Anomalous diffusion of active Brownian particles in responsive elastic gels: Nonergodicity, non-Gaussianity, and distributions of trapping times. Phys. Rev. E 110, 044609 (2024)   [pdf] [doi]
     
  4. Hartich D, Godec A. Comment on 'Inferring broken detailed balance in the absence of observable currents'. Nature Communications 15, 8678 (2024)   [pdf] [preprint] [doi] [arXiv]
     
  5. Ibáñez M, Dieball C, Lasanta A, Godec A, Rica RA. Heating and Cooling are Fundamentally Asymmetric and Evolve Along Distinct Pathways. Nature Phys. 20, 135–141 (2024)   [pdf] [preprint] [doi] [arXiv]
     
  6. Miao M, Makarov DE, Blom K. Nonequilibrium statistical mechanics of money/energy exchange models. J. Phys. A 57 (15), 155003 (2024)   [pdf] [doi]
     
  7. 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. J. Phys. A: Math. Theor. 57, 365001 - 365020 (2024)   [pdf] [doi]
     
  8. Zhao X, Hartich D, Godec A. Emergence of Memory in Equilibrium versus Nonequilibrium Systems. Phys. Rev. Lett. 132, 147101 (2024)   [pdf] [preprint] [doi] [arXiv]
     
  

2023

(alphabetical order)
  1. Bebon R., Godec A. Controlling Uncertainty of Empirical First-Passage Times in the Small-Sample Regime. Phys. Rev. Lett. 131, 237101 (2023)   [pdf] [preprint] [doi] [arXiv]
     
  2. Blom K, Godec A. Global Speed Limit for Finite-Time Dynamical Phase Transition and Nonequilibrium Relaxation. arXiv (submitted on 2022-09-28) (review) (2023)   [preprint] [arXiv]
     
  3. Blom K, Ziethen N, Zwicker D, Godec A. Thermodynamically consistent phase-field theory including nearest-neighbor pair correlations. Phys. Rev. Res. 5, 013135 (2023)   [pdf] [doi]
     
  4. De H, Godec A. Vorticity and level-set variations of invariant current bound steady-state dissipation. arXiv (submitted on 2023-06-23) (review) (2023)   [preprint] [arXiv]
     
  5. Dieball C, Godec A. Direct Route to Thermodynamic Uncertainty Relations and Their Saturation. Phys. Rev. Lett. 130, 087101 (2023)   [pdf] [preprint] [doi] [arXiv]
     
  6. Dieball C, Godec A. Feynman-Kac theory of time-integrated functionals: Itô versus functional calculus. J. Phys. A: Math. Theor. 56, 155002-155013 (2023)   [pdf] [preprint] [doi] [arXiv]
     
  7. Dieball C, Wellecke G, Godec A. Asymmetric thermal relaxation in driven systems: Rotations go opposite ways. Phys. Rev. Res. 5, L042030 (2023)   [pdf] [preprint] [doi] [arXiv]
     
  8. Godec A, Makarov DE. Challenges in Inferring the Directionality of Active Molecular Processes from Single-Molecule Fluorescence Resonance Energy Transfer Trajectories. J. Phys. Chem. Lett. 14, 49 - 56 (2023)   [pdf] [doi]
     
  9. Hartich D, Godec A. Violation of local detailed balance upon lumping despite a clear timescale separation. Phys. Review Res. 5 (3), L032017 (2023)   [pdf] [doi]
     
  10. Vossel M, de Groot BL, Godec A. The allosteric lever: towards a principle of specific allosteric response. arXiv (submitted on 2023-11-20) (review) (2023)   [preprint] [arXiv]
     
  

2022

(alphabetical order)
  1. Blom K, Godec, A. Global Speed Limit for Finite-Time Dynamical Phase Transition in Nonequilibrium Relaxation. arXiv (submitted on 28-Sep-2022) (preprint) (2022)   [preprint] [arXiv]
     
  2. Dieball C, Godec A. Coarse Graining Empirical Densities and Currents in Continuous-Space Steady States. Phys. Rev. Res. 4, 033243-033266 (2022)   [pdf] [preprint] [doi] [arXiv]
     
  3. Dieball C, Godec A. Mathematical, Thermodynamical, and Experimental Necessity for Coarse Graining Empirical Densities and Currents in Continuous Space. Phys. Rev. Lett. (2022)   [pdf] [arXiv]
     
  4. Dieball C, Godec A. On correlations and fluctuations of time-averaged densities and currents with general time-dependence. J. Phys. A: Mat. and Theor. 55, 475001-475013 (2022)   [pdf] [preprint] [doi] [arXiv]
     
  5. Dieball C, Krapf D, Weiss M, Godec A. Scattering fingerprints of two-state dynamics. New J. Phys. 24, 023004 (2022)   [pdf] [preprint] [doi] [arXiv]
     
  6. Li J, Xie JF, Godec A, Weninger KR, Liu C, Smith JC, Hong L. Non-ergodicity of a globular protein extending beyond its functional timescale. Chem. Sci. 13, 9668-9677 (2022)   [pdf] [doi]
     
  7. Zunke C, Bewerunge J, Platten F, Egelhaaf SU, Godec A. First-passage statistics of colloids on fractals: Theory and experimental realization. Sci. Adv. 8, eabk0627 (2022)   [pdf] [doi]
     
  

2021

(alphabetical order)
  1. Blom K, Godec A. Criticality in Cell Adhesion. Phys. Rev. X 11 (3), 031067 (35) (2021)   [pdf] [doi]
     
  2. Hartich D, Godec A. Emergent Memory and Kinetic Hysteresis in Strongly Driven Networks. Phys. Rev. X 11, 041047 (2021)   [pdf] [doi]
     
  3. Hartich D, Godec A. Thermodynamic Uncertainty Relation Bounds the Extent of Anomalous Diffusion. Phys. Rev. Lett. 127 (8), 080601 (2021)   [pdf] [doi]
     
  4. Hartich D, Godec A. Violation of Local Detailed Balance Despite a Clear Time-Scale Separation. arXiv (submitted on 29-11-2021) (preprint) (2021)   [preprint] [arXiv]
     
  5. Lapolla A, Godec A. BetheSF V2: 3-point propagator and additional external potentials. Comput. Phys. Comm. 269, 108131 (2021)   [pdf] [doi]
     
  6. Lapolla A, Godec A. BetheSF: Efficient computation of the exact tagged-particle propagator in single-file systems via the Bethe eigenspectrum. Comput. Phys. Comm. 258, 107569 (2021)   [pdf] [doi]
     
  7. Lapolla A, Godec A. Toolbox for quantifying memory in dynamics along reaction coordinates. Phys. Rev. Res. 3, L022018 (2021)   [pdf] [doi]
     
  8. Lapolla A, Vossel M, Godec A. Time- and ensemble-average statistical mechanics of the Gaussian network model. J. Phys. A: Math. Theor. 54, 355601 (30pp) (2021)   [pdf] [doi]
     
  

2020

(alphabetical order)
  1. Lapolla A, Godec A. Faster Uphill Relaxation in Thermodynamically Equidistant Temperature Quenches. Phys. Rev. Lett. 125, 110602 (2020)   [pdf] [suppl] [doi]
     
  2. Lapolla A, Godec A. Single-file diffusion in a bi-stable potential: Signatures of memory in the barrier-crossing of a tagged-particle. JCP 153, 194104 (2020)   [pdf] [doi]
     
  3. Lapolla A, Hartich D, Godec A. Spectral theory of fluctuations in time-average statistical mechanics of reversible and driven systems. Phys. Rev. Res. 2, 043084 (2020)   [pdf] [doi]
     
  4. Ukmar-Godec T, Fang P, Ibáñez de Opakua A, Henneberg F, Godec A, Pan KT, Cima-Omori MS, Chari A, Mandelkow E, Urlaub H, Zweckstetter M. Proteasomal degradation of the intrinsically disordered protein tau at single-residue resolution. Sci. Adv. 6, eaba3916, 1-12 (2020)   [pdf] [suppl] [doi]
     
  

2019

(alphabetical order)
  1. Hartich D, Godec A. Extreme value statistics of ergodic Markov processes from first passage times in the large deviation limit. J. Phys. A: Math. Theor. 52, 244001 (2019)   [pdf] [doi]
     
  2. Hartich D, Godec A. Interlacing relaxation and first-passage phenomena in reversible discrete and continuous space Markovian dynamics. J. Stat. Mech. , 024002 (2019)   [pdf] [preprint] [doi] [arXiv]
     
  3. Lapolla A, Godec A. Manifestations of Projection-Induced Memory: General Theory and the Tilted Single File. Frontiers Phys. 11 (7), Art. 182 (2019)   [pdf] [preprint] [doi] [arXiv]
     
  

2018

(alphabetical order)
  1. Hartich D, Godec A. Duality between relaxation and first passage in reversible Markov dynamics: rugged energy landscapes disentangled. New J. Phys. 20, 112002 (2018)   [pdf] [doi]
     
  2. Lapolla A, Godec A. Unfolding tagged particle histories in single-file diffusion: exact single- and two-tag local times beyond large deviation theory. New J. Phys. 20, 113021 (2018)   [pdf] [doi]
     
  

2017

(alphabetical order)
  1. Godec A, Metzler R. First passage time statistics for two-channel diffusion. J. Phys. A: Mathem. and Theor. 50 (8), 084001 (2017)   [doi]
     
  2. Schwarzl M, Godec A, Metzler R. Quantifying non-ergodicity of anomalous diffusion with higher order moments. Sci. Rep. 7, 3878 (2017)   [pdf] [doi]
     
  3. Ukmar-Godec T, Bertinetti L, Dunlop J, Godec A, Grabiger M, Masic A, Nguyen H, Zlotnikov I, Zaslansky P, Faivre D. A tooth without mineral: materials nano architecturing via cation-mediated protein assembly. Adv. Mater. 29 (27), 1701171 (2017)   [pdf] [suppl] [doi]
     
  

2016

(alphabetical order)
  1. Godec A, Metzler R. Active transport improves the precision of linear long distance molecular signalling. J. Phys. A: Mathem. and Theor. 49 (36), 364001 (2016)   [doi]
     
  2. Godec A, Metzler R. First passage time distribution in heterogeneity controlled kinetics: Going beyond the mean first passage time. Sci. Rep. 6, 20349 (2016)   [pdf] [doi]
     
  3. Godec A, Metzler R. Universal proximity effect in target search kinetics in the few-encounter limit. Phys. Rev. X 6 (4), 041037 (2016)   [pdf] [suppl] [doi]
     
  4. 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. J. Phys. A: Mathem. and Theor. 49 (22), 225601 (2016)   [doi]
     
  

2015

(alphabetical order)
  1. Godec A, Metzler R. Optimization and universality of Brownian search in a basic model of quenched heterogeneous media. Phys. Rev. E 91 (5), 052134 (2015)   [pdf] [doi]
     
  2. Godec A, Metzler R. Signal focusing through active transport. Phys. Rev. E 92 (1), 010701® (2015)   [pdf] [suppl] [doi]
     
  3. Krüsemann H, Godec A, Metzler R. Ageing first passage time density in continuous time random walks and quenched energy landscapes. J. Phys. A: Mathem. and Theor. 48 (28), 285001 (2015)   [doi]
     
  

2014

(alphabetical order)
  1. Bauer M, Godec A, Metzler R. Diffusion of finite-size particles in two-dimensional channels with random wall configurations. Phys. Chem. Chem. Phys. 16 (13), 6118 - 6128 (2014)   [pdf] [doi]
     
  2. Godec A, Bauer M, Metzler R. Collective dynamics effect transient subdiffusion of inert tracers in flexible gel networks. New J.Phys. 16, 092002 (2014)   [pdf] [doi]
     
  3. Godec A, Chechkin AV, Barkai E, Kantz H, Metzler R. Localisation and universal fluctuations in ultraslow diffusion processes. J. Phys. A: Mathem. and Theor. 47 (49), 492002 (2014)   [doi]
     
  4. Krüsemann H, Godec A, Metzler R. First-passage statistics for aging diffusion in systems with annealed and quenched disorder. Phys. Rev. E 89 (4), 040101® (2014)   [pdf] [doi]
     
  

2013

(alphabetical order)
  1. Godec A, Metzler R. Finite-time effects and ultraweak ergodicity breaking in superdiffusive dynamics. Phys. Rev. Lett. 110 (2), 020603 (2013)   [pdf] [doi]
     
  2. Godec A, Metzler R. Linear response, fluctuation-dissipation, and finite-system-size effects in superdiffusion. Phys. Rev. E 88 (1), 012116 (2013)   [pdf] [doi]
     
  3. Godec A, Smith JC, Merzel F. Soft collective fluctuations governing hydrophobic association. Phys. Rev. Lett. 111 (12-20), 127801 (2013)   [pdf] [doi]
     
  

2012

(alphabetical order)
  1. Godec A, Merzel F. Physical origin underlying the entropy loss upon hydrophobic hydration. J. Am. Chem. Soc. 134 (42), 17575 - 17581 (2012)   [suppl] [doi]
     
  2. 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. J. Mater. Chem. 22 (3), 1112 - 1120 (2012)   [suppl] [doi]
     
  3. Znidarsic A, Godec A, Gaberscek M. pH-based one pot synthesis of biocompatible olive shaped inorganic particles. Mater. Res. Bull. 47 (4), 967 - 973 (2012)   [doi]
     
  

2011

(alphabetical order)
  1. Godec A, Smith JC, Merzel F. Increase of both order and disorder in the first hydration shell with increasing solute polarity. Phys. Rev. Lett. 107 (26), 267801 (2011)   [pdf] [doi]
     
  2. Godec A, Ukmar T, Gaberscek M, Merzel F. Inversion of pore size dependence of solute transport kinetics from increasingly attractive ordered porous matrix. Europhys. Lett. 92 (6), 60011 (2011)   [pdf] [doi]
     
  3. Ukmar T, Gaberscek M, Merzel F, Godec A. Modus operandi of controlled release from mesoporous matrices: A theoretical perspective. Phys. Chem. Chem. Phys. 13 (3), 15311 - 15317 (2011)   [suppl] [doi]
     
  4. 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. Phys. Chem. Chem. Phys. 13 (35), 16046 - 16054 (2011)   [suppl] [doi]
     
  5. Ukmar T, Maver U, Planinsek O, Kaucic V, Gaberscek M, Godec A. Understanding controlled drug release from mesoporous silicates: Theory and experiment. J. Contr. Rel. 155 (3), 409 - 417 (2011)   [suppl]
     
  

2010

(alphabetical order)
  1. 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. Phys. Chem. Chem. Phys. 12 (41), 13566 - 13573 (2010)   [doi]
     
  2. 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. Coll. Surf. A: Physicochem. Eng. Asp. 371 (1-3), 119 - 125 (2010)   [doi]
     
  3. 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. J. Pharm. Sci. 99 (4), 1968 - 1981 (2010)   [doi]
     
  

2009

(alphabetical order)
  1. Godec A, Gaberscek M, Jamnik J, Merzel F. Nonlinear diffusion in two-dimensional ordered porous media based on a free volume theory. J. Chem. Phys. 131 (23), 234106 (2009)   [pdf] [doi]
     
  2. 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. J. Sol. Chem. 38 (1), 135 - 146 (2009)   [doi]
     
  3. Ukmar T, Godec A, Maver U, Planinsek O, Bele M, Jamnik J, Gaberscek M. Suspensions of modified TiO2 nanoparticles with supreme UV filtering ability. J. Mat. Chem. 19 (43), 8176 - 8183 (2009)   [suppl] [doi]
     
  

2007

(alphabetical order)
  1. Godec A, Maver U, Bele M, Planinsek O, Srcic S, Gaberscek Mc, Jamnik J. Vitrification from solution in restricted space: Formation and stabilization of amorphous nifedipine in a nanoporous silica xerogel carrier. Intern. J. Pharm. 343 (1-2), 131 - 140 (2007)   [doi]
     
  2. 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. Intern. J. Pharm. 330 (1-2), 164 - 174 (2007)   [doi]
     


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