Publications

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Journal articles

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. M. Sadeghi, “Formation of membrane invaginations by curvature-inducing peripheral proteins: free energy profiles, kinetics, and membrane-mediated effects”, bioRxiv (2022) 515891.
  7. M. Sadeghi, “Investigating the entropic nature of membrane-mediated interactions driving the aggregation of peripheral proteins”, Soft Matter (2022) 18:3917-3927.
  8. 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.
  9. 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.
  10. M. Sadeghi and F. Noé, “Hydrodynamic coupling for particle-based solvent-free membrane models”, The Journal of Chemical Physics (2021) 155:114108.
  11. M. Sadeghi and F. Noé, “Large-scale simulation of biomembranes incorporating realistic kinetics into coarse-grained models”, Nature Communications (2020) 11:2951.
  12. 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.
  13. 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.
  14. 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.
  15. M. Sadeghi, G. A. Parsafar, “Density-induced molecular arrangements of water inside carbon nanotubes”, Physcial Chemistry Chemical Physics (2013) 15:7379-7388.
  16. M. Sadeghi, G. A. Parsafar, “Toward an equation of state for water inside carbon nanotubes”, Journal of Physcial Chemistry B (2012) 116:4943-4951.
  17. 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.
  18. 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.
  19. M. Sadeghi , R. Naghdabadi, “Nonlinear vibration analysis of single-layer graphene sheets”, Nanotechnology (2010) 21:105705.
  20. 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.
  21. 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
  22. 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).