Publications

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Journal articles

  1. J. Kroll, U. Kravčenko, M. Sadeghi, C. A. Diebolder, L. Ivanov, M. Lubas, T. Sprink, M. Schacherl, M. Kudryashev, C. Rosenmund “Dynamic nanoscale architecture of synaptic vesicle fusion in mouse hippocampal neurons”, bioRxiv (2025) 635788.
  2. N. Wehlitz, M. Sadeghi, A. Montefusco, C. Schütte, G. A. Pavliotis, S. Winkelmann “Approximating particle-based clustering dynamics by stochastic PDEs”, SIAM Journal on Applied Dynamical Systems (2025) 24(2):1676661.
  3. J. Rentsch, S. Bandstra, B. Sezen, P. S. Sigrist, F. Bottanelli, B. Schmerl, S. A. Shoichet, F. Noé, M. Sadeghi H. Ewers “Sub-membrane actin rings compartmentalize the plasma membrane”, The Journal of Cell Biology (2024) 223 (4): e202310138.
  4. D. de Jong-Bolm, M. Sadeghi, G. Bao, G. Klaehn, M. Hoff, L. Mittelmeier, F. B. Basmanav, F. Opazo, F. Noé, S. O. Rizzoli, “Protein nanobarcodes enable single-step multiplexed fluorescence imaging”, PLoS Biology (2023) 21(12):e3002427.
  5. B. Bogdanow, I. Gruska, L. Mühlberg, J. Protze, S. Hohensee, B. Vetter, M. Lehmann, M. Sadeghi, L. Wiebusch, F. Liu “Spatially resolved protein map of intact human cytomegalovirus virions”, Nature Microbiology (2023) 8:1732-1747.
  6. M. Dyhr, M. Sadeghi, R. Moynova, C. Knappe, B. Kepsutlu, S. Werner, G. Schneider, J. McNally, F. Noé, H. Ewers, “3D-surface reconstruction of cellular cryo-soft X-ray microscopy tomograms using semi-supervised deep learning”, Proceedings of the National Academy of Sciences (2023) 120 (24): e2209938120.
  7. M. M. Galama, H. Wu, A. Krämer, M. Sadeghi, Frank Noé, “Stochastic approximation to MBAR and TRAM: batch-wise free energy estimation”, Journal of Chemical Theory and Computation (2022) 19(3):758-766.
  8. M. Sadeghi, “Formation of membrane invaginations by curvature-inducing peripheral proteins: free energy profiles, kinetics, and membrane-mediated effects”, bioRxiv (2022) 515891.
  9. M. Sadeghi, “Investigating the entropic nature of membrane-mediated interactions driving the aggregation of peripheral proteins”, Soft Matter (2022) 18:3917-3927.
  10. M. Sadeghi and F. Noé, “Thermodynamics and kinetics of aggregation of flexible peripheral membrane proteins”, The Journal of Physical Chemistry Letters (2021) 12:10497-10504.
  11. M. Sadeghi and F. Noé, “Aggregation of flexible membrane-bound proteins: thermodynamic and kinetic insights from large-scale simulations”, European Biophysics Journal with Biophysics Letters (2021) 50 (S1):171.
  12. M. Sadeghi and F. Noé, “Hydrodynamic coupling for particle-based solvent-free membrane models”, The Journal of Chemical Physics (2021) 155:114108.
  13. M. Sadeghi and F. Noé, “Large-scale simulation of biomembranes incorporating realistic kinetics into coarse-grained models”, Nature Communications (2020) 11:2951.
  14. E. Dimou, K. Cosentino, E. Platonova, U. Ros, M. Sadeghi, P. Kashyap, T. Katsinelos, S. Wegehingel, F. Noé, A. J. García-Sáez, H. Ewers, W. Nickel “Single event visualization of unconventional secretion of FGF2”, The Journal of Cell Biology (2018) 218(2):683-699.
  15. M. Sadeghi, T. R. Weikl, F. Noé, “Particle-based membrane model for mesoscopic simulation of cellular dynamics”, The Journal of Chemical Physics (2018) 148:044901.
  16. D. Albrecht, C. M. Winterflood, M. Sadeghi, T. Tschager, F. Noé, H. Ewers, “Nanoscopic compartmentalization of membrane protein motion at the axon initial segment”, The Journal of Cell Biology (2016) 215(1):37-46.
  17. M. Sadeghi, G. A. Parsafar, “Density-induced molecular arrangements of water inside carbon nanotubes”, Physcial Chemistry Chemical Physics (2013) 15:7379-7388.
  18. M. Sadeghi, G. A. Parsafar, “Toward an equation of state for water inside carbon nanotubes”, Journal of Physcial Chemistry B (2012) 116:4943-4951.
  19. S.A. Niaki, J.R. Mianroodi, M. Sadeghi, R. Naghdabadi, “Dynamic and static fracture analyses of graphene sheets and carbon nanotubes”, Composite Structures (2012) 94(8):2365-2372.
  20. A. Montazeri, M. Sadeghi , R. Naghdabadi, H. Rafii-Tabar, “Multiscale modeling of the effect of carbon nanotube orientation on the shear deformation properties of reinforced polymer-based composites”, Physics Letters A (2011) 375:1588-1597.
  21. M. Sadeghi , R. Naghdabadi, “Nonlinear vibration analysis of single-layer graphene sheets”, Nanotechnology (2010) 21:105705.
  22. A. Montazeri, M. Sadeghi , R. Naghdabadi, H. Rafii-Tabar, “Computational modeling of the transverse-isotropic elastic properties of single-walled carbon nanotubes”, Computational Materials Science (2010) 49:544-551.
  23. M. Sadeghi , R. Naghdabadi, “Stability analysis of carbon nanotubes using a hybrid atomistic-structural element”, International Journal of Nanomanufacturing (2009) 5(3/4):366-375
  24. M. Sadeghi , M. Ozmaian, R. Naghdabadi, “Stability analysis of carbon nanotubes under electric fields and compressive loading”, Journal of Physics D: Applied Physics (2008) 41:205411.

Books and book chapters

  1. M. Sadeghi and D. Rosenberger, 2024 “Dynamic framework for large-scale modeling of membranes and peripheral proteins” in MIE 701: Biophysical Approaches for the Study of Membrane Structure Part B, ed. Markus Deserno, Tobias Baumgart, (Elsevier: Methods in Enzymology, Academic Press).
  2. M. Sadeghi 2010 “Nonlinear mechanical analysis of carbon nanostructures: Numerical simulation using the hybrid atomistic-structural method” (Saarbrücken: Lambert Academic Publishing).