@article{Sadeghi2021a,
abstract = {The great challenge with biological membrane systems is the wide range of scales involved, from nanometers and picoseconds for individual lipids to the micrometers and beyond millisecond for cellul...},
author = {Sadeghi, Mohsen and No{\'{e}}, Frank},
doi = {10.1063/5.0061623},
file = {:home/sadeghi/Dokumente/Mendeley Desktop/Sadeghi, No{\'{e}} - 2021 - Hydrodynamic coupling for particle-based solvent-free membrane models.pdf:pdf},
issn = {0021-9606},
journal = {J. Chem. Phys.},
month = {sep},
number = {11},
pages = {114108},
publisher = {AIP Publishing LLCAIP Publishing},
title = {{Hydrodynamic coupling for particle-based solvent-free membrane models}},
url = {https://aip.scitation.org/doi/abs/10.1063/5.0061623},
volume = {155},
year = {2021}
}
@article{Sadeghi2018,
abstract = {We present a simple and computationally efficient coarse-grained and solvent-free model for simulating lipid bilayer membranes. In order to be used in concert with particle-based reaction-diffusion simulations, the model is purely based on interacting and reacting particles, each representing a coarse patch of a lipid monolayer. Particle interactions include nearest-neighbor bond-stretching and angle-bending and are parameterized so as to reproduce the local membrane mechanics given by the Helfrich energy density over a range of relevant curvatures. In-plane fluidity is implemented with Monte Carlo bond-flipping moves. The physical accuracy of the model is verified by five tests: (i) Power spectrum analysis of equilibrium thermal undulations is used to verify that the particle-based representation correctly captures the dynamics predicted by the continuum model of fluid membranes. (ii) It is verified that the input bending stiffness, against which the potential parameters are optimized, is accurately recovered. (iii) Isothermal area compressibility modulus of the membrane is calculated and is shown to be tunable to reproduce available values for different lipid bilayers, independent of the bending rigidity. (iv) Simulation of two-dimensional shear flow under a gravity force is employed to measure the effective in-plane viscosity of the membrane model and show the possibility of modeling membranes with specified viscosities. (v) Interaction of the bilayer membrane with a spherical nanoparticle is modeled as a test case for large membrane deformations and budding involved in cellular processes such as endocytosis. The results are shown to coincide well with the predicted behavior of continuum models, and the membrane model successfully mimics the expected budding behavior. We expect our model to be of high practical usability for ultra coarse-grained molecular dynamics or particle-based reaction-diffusion simulations of biological systems.},
author = {Sadeghi, M. and Weikl, T. R. and No{\'{e}}, F.},
doi = {10.1063/1.5009107},
file = {:home/sadeghi/Dokumente/Mendeley Desktop/Sadeghi, Weikl, No{\'{e}} - 2018 - Particle-based membrane model for mesoscopic simulation of cellular dynamics.pdf:pdf},
journal = {J. Chem. Phys.},
number = {4},
pages = {044901},
title = {{Particle-based membrane model for mesoscopic simulation of cellular dynamics}},
volume = {148},
year = {2018}
}
@article{Albrecht2016a,
abstract = {The axon initial segment (AIS) is enriched in specific adaptor, cytoskeletal, and transmembrane molecules. During AIS establishment, a membrane diffusion barrier is formed between the axonal and somatodendritic domains. Recently, an axonal periodic pattern of actin, spectrin, and ankyrin forming 190-nm-spaced, ring-like structures has been discovered. However, whether this structure is related to the diffusion barrier function is unclear. Here, we performed single-particle tracking time-course experiments on hippocampal neurons during AIS development. We analyzed the mobility of lipid-anchored molecules by high-speed single-particle tracking and correlated positions of membrane molecules with the nanoscopic organization of the AIS cytoskeleton. We observe a strong reduction in mobility early in AIS development. Membrane protein motion in the AIS plasma membrane is confined to a repetitive pattern of {\~{}}190-nm-spaced segments along the AIS axis as early as day in vitro 4, and this pattern alternates with actin rings. Mathematical modeling shows that diffusion barriers between the segments significantly reduce lateral diffusion along the axon.},
author = {Albrecht, David and Winterflood, Christian M. and Sadeghi, Mohsen and Tschager, Thomas and No{\'{e}}, Frank and Ewers, Helge},
doi = {10.1083/jcb.201603108},
file = {:home/sadeghi/Dokumente/Mendeley Desktop/Albrecht et al. - 2016 - Nanoscopic compartmentalization of membrane protein motion at the axon initial segment.pdf:pdf},
isbn = {1540-8140},
issn = {15408140},
journal = {J. Cell Biol.},
number = {1},
pmid = {27697928},
title = {{Nanoscopic compartmentalization of membrane protein motion at the axon initial segment}},
volume = {215},
year = {2016}
}
@article{Bogdanow2022,
abstract = {Herpesviruses assemble large enveloped particles that are difficult to characterize structurally due to their size, fragility and complex proteome with partially amorphous nature. Here we use cross-linking mass spectrometry and quantitative proteomics to derive a spatially resolved interactome map of intact human cytomegalovirus virions. This enabled the de novo allocation of 32 viral proteins into four spatially resolved virion layers, each organized by a dominant viral scaffold protein. The viral protein UL32 engages with all layers in an N-to-C-terminal radial orientation bridging nucleocapsid to viral membrane. In addition, we observed the layer-specific recruitment of 82 host proteins, a subset of which are constitutively and selectively incorporated via specific host-virus interactions. We uncover how the recruitment of PP1 phosphatase and 14-3-3 proteins by UL32 affects early and late steps during viral biogenesis. Collectively, this study provides global structural insights into the native configuration of virus and host protein interactions inside herpesvirus particles. {\#}{\#}{\#} Competing Interest Statement The authors have declared no competing interest.},
author = {Bogdanow, Boris and Gruska, Iris and M{\"{u}}hlberg, Lars and Protze, Jonas and Hohensee, Svea and Vetter, Barbara and Lehmann, Martin and Sadeghi, Mohsen and Wiebusch, L{\"{u}}der and Liu, Fan},
file = {:home/sadeghi/Dokumente/Mendeley Desktop/Bogdanow et al. - 2023 - Spatial, Quantitative and Functional Deconstruction of Virus and Host Protein Interactions Inside Intact Cytome.pdf:pdf},
journal = {Nat. Microbiol.},
pages = {[accepted]},
title = {{Spatial, Quantitative and Functional Deconstruction of Virus and Host Protein Interactions Inside Intact Cytomegalovirus Particles}},
url = {https://www.biorxiv.org/content/10.1101/2022.05.02.490278v1},
year = {2023}
}
@article{Sadeghi2020,
abstract = {Biomembranes are two-dimensional assemblies of phospholipids that are only a few nanometres thick, but form micrometre-sized structures vital to cellular function. Explicit molecular modelling of biologically relevant membrane systems is computationally expensive due to the large number of solvent particles and slow membrane kinetics. Coarse-grained solvent-free membrane models offer efficient sampling but sacrifice realistic kinetics, thereby limiting the ability to predict pathways and mechanisms of membrane processes. Here, we present a framework for integrating coarse-grained membrane models with continuum-based hydrodynamics. This framework facilitates efficient simulation of large biomembrane systems with large timesteps, while achieving realistic equilibrium and non-equilibrium kinetics. It helps to bridge between the nanometer/nanosecond spatiotemporal resolutions of coarse-grained models and biologically relevant time- and lengthscales. As a demonstration, we investigate fluctuations of red blood cells, with varying cytoplasmic viscosities, in 150-milliseconds-long trajectories, and compare kinetic properties against single-cell experimental observations.},
author = {Sadeghi, Mohsen and No{\'{e}}, Frank},
doi = {10.1038/s41467-020-16424-0},
file = {:home/sadeghi/Dokumente/Mendeley Desktop/Sadeghi, No{\'{e}} - 2020 - Large-scale simulation of biomembranes incorporating realistic kinetics into coarse-grained models.pdf:pdf},
issn = {20411723},
journal = {Nat. Commun.},
keywords = {Biological physics,Computational biophysics,Computational models},
number = {1},
pages = {2951},
pmid = {32528158},
publisher = {Cold Spring Harbor Laboratory},
title = {{Large-scale simulation of biomembranes incorporating realistic kinetics into coarse-grained models}},
url = {https://doi.org/10.1038/s41467-020-16424-0 http://www.nature.com/articles/s41467-020-16424-0},
volume = {11},
year = {2020}
}
@article{Sadeghi2021b,
abstract = {Shaping and remodeling of biomembranes is essential for cellular trafficking, with membrane-binding peripheral proteins playing the key role in it. Significant membrane remodeling as in endo-and exocytosis is often due to clusters or aggregates of many proteins whose interactions may be direct or mediated via the membrane. While computer simulation could be an important tool to disentangle these interactions and understand what drives cooperative protein interactions in membrane remodeling, this has so far been extremely challenging: protein-membrane systems involve time-and lengthscales that make detailed atomistic simulations impractical, while most coarse-grained models lack the degree of detail needed to resolve the dynamics and physical effect of protein and membrane flexibility. Here, we develop a coarse-grained model of the bilayer membrane bestrewed with rotationally-symmetric flexible membrane-bound proteins. We show how this model can be param-eterized based on local curvatures, protein flexibility, and the in-plane dynamics of proteins. We measure the effective interaction potential for the membrane-mediated interactions between peripheral proteins. Furthermore, we investigate the kinetics, equilibrium distributions, and the free energy landscape governing the formation and break-up of protein clusters on the surface of the membrane. We demonstrate how the flexibility of the protein plays a deciding role in highly selective macroscopic aggregation behavior. Finally, we present large-scale simulations of membrane tubulation, and discuss the sequence of events and the stability of intermediates.},
author = {Sadeghi, Mohsen and No{\'{e}}, Frank},
doi = {10.1101/2021.04.09.439228},
file = {:home/sadeghi/Dokumente/Mendeley Desktop/Sadeghi, No{\'{e}} - 2021 - Thermodynamics and kinetics of aggregation of flexible peripheral membrane proteins(2).pdf:pdf},
journal = {J. Phys. Chem. Lett.},
month = {apr},
pages = {10497--10504},
publisher = {Cold Spring Harbor Laboratory},
title = {{Thermodynamics and kinetics of aggregation of flexible peripheral membrane proteins}},
url = {https://doi.org/10.1021/acs.jpclett.1c02954},
volume = {12},
year = {2021}
}
@article{Montazeri2010,
abstract = {Various experimental and theoretical investigations have been carried out to determine the elastic properties of nanotubes in the axial direction. Their behavior in transverse directions, however, has not been well studied. In this paper, a combination of molecular dynamics (MD) and continuum-based elasticity model is used to predict the transverse-isotropic elastic properties of single-walled carbon nanotubes (SWCNTs). From this modeling study, five independent elastic constants of an SWCNT in transverse directions are obtained by analyzing its deformations under four different loading conditions, namely, axial tension, torsion, uniform and non-uniform radial pressure. To find the elastic constants in the transverse directions, the strain energy due to radial pressure is calculated from the MD simulation. Then, a continuum-based model is implemented to find the relation between the strain energy and maximum pressure under these two loading conditions. Based on the energy equivalence between the MD simulation and the continuum-based model, the transverse-isotropic elastic constants of SWCNTs are computed. The effectiveness of this approach is demonstrated by comparing the results with previous experimental and computational works. ?? 2010 Elsevier B.V. All rights reserved.},
author = {Montazeri, A. and Sadeghi, M. and Naghdabadi, R. and Rafii-Tabar, H.},
doi = {10.1016/j.commatsci.2010.05.047},
file = {:home/sadeghi/Dokumente/Mendeley Desktop/Montazeri et al. - 2010 - Computational modeling of the transverse-isotropic elastic properties of single-walled carbon nanotubes.pdf:pdf},
issn = {09270256},
journal = {Comput. Mater. Sci.},
keywords = {Continuum-based elasticity theory,Molecular dynamics simulation,Single-walled carbon nanotubes,Transverse-isotropic material},
number = {3},
pages = {544--551},
title = {{Computational modeling of the transverse-isotropic elastic properties of single-walled carbon nanotubes}},
volume = {49},
year = {2010}
}
@article{DeJong-Bolm2022,
abstract = {Multiplexed cellular imaging typically relies on the sequential application of detection probes, such as antibodies or DNA barcodes, which is complex and time-consuming. To address this, we developed here protein nanobarcodes, composed of combinations of epitopes recognized by specific sets of nanobodies. The nanobarcodes are read in a single imaging step, relying on nanobodies conjugated to distinct fluorophores, which enables a precise analysis of large numbers of protein combinations.},
author = {{De Jong-Bolm}, Dani{\"{e}}lle and Sadeghi, Mohsen and Bao, Guobin and Klaehn, Gabriele and Hoff, Merle and Mittelmeier, Lucas and {Buket Basmanav}, F and Opazo, Felipe and No{\'{e}}, Frank and Rizzoli, Silvio O},
doi = {10.1101/2022.06.03.494744},
file = {:home/sadeghi/Dokumente/Mendeley Desktop/De Jong-Bolm et al. - 2022 - Protein nanobarcodes enable single-step multiplexed fluorescence imaging.pdf:pdf},
journal = {bioRxiv},
month = {jun},
pages = {2022.06.03.494744},
publisher = {Cold Spring Harbor Laboratory},
title = {{Protein nanobarcodes enable single-step multiplexed fluorescence imaging}},
url = {https://www.biorxiv.org/content/10.1101/2022.06.03.494744v1 https://www.biorxiv.org/content/10.1101/2022.06.03.494744v1.abstract https://doi.org/10.1101/2022.06.03.494744},
year = {2022}
}
@misc{Sadeghi2019,
abstract = {The great challenge with simulating bilayer membranes is the the wide range of scales involved, from nanometer/picosecond pertaining to individual lipids, to the micrometer/millisecond scale of biological membranes. While solvent-free coarse-grained membrane models are convenient for large-scale simulations, and promising to provide insight into slow cellular processes involving membranes, the fact remains that these models cannot be trusted to reproduce the kinetics of lipid bilayer motion, even at their scales of interest. This is due to the fact that the dynamics of the solvent cannot be ignored at any scale, while a secondary, composition-dependent time-scale due to the in-plane diffusion of the lipids is also present. Thus, developing an implicit method that incorporates both dynamics into a unified approach remains a challenge. Here, we lay out a framework for implementing anisotropic stochastic dynamics based on semi-analytical solutions to Stokes hydrodynamic equations. We show how this approach offers realistic kinetics for membranes at both time-scales, while still offering very large timesteps. Using this framework, we study dispersion relation of planar membrane patches and show it to coincide very well with continuum-based predictions. We also demonstrate how the in-plane viscosity and diffusion can be tuned independently to empirical range of values.},
archivePrefix = {arXiv},
arxivId = {1909.02722},
author = {Sadeghi, Mohsen and No{\'{e}}, Frank},
booktitle = {arXiv},
eprint = {1909.02722},
file = {:home/sadeghi/Dokumente/Mendeley Desktop/Sadeghi, No{\'{e}} - 2019 - First-principle hydrodynamics and kinetics for solvent-free coarse-grained membrane models.pdf:pdf},
issn = {23318422},
month = {sep},
pages = {arXiv 1909.02722},
title = {{First-principle hydrodynamics and kinetics for solvent-free coarse-grained membrane models}},
url = {https://arxiv.org/abs/1909.02722},
year = {2019}
}
@article{Galama2023,
abstract = {The dynamics of molecules are governed by rare event transitions between long-lived (metastable) states. To explore these transitions efficiently, many enhanced sampling protocols have been introdu...},
author = {Galama, Maaike M. and Wu, Hao and Kr{\"{a}}mer, Andreas and Sadeghi, Mohsen and No{\'{e}}, Frank},
doi = {10.1021/ACS.JCTC.2C00976},
file = {:home/sadeghi/Dokumente/Mendeley Desktop/Galama et al. - 2023 - Stochastic Approximation to MBAR and TRAM Batchwise Free Energy Estimation.pdf:pdf},
issn = {1549-9618},
journal = {J. Chem. Theory Comput.},
month = {jan},
publisher = {American Chemical Society},
title = {{Stochastic Approximation to MBAR and TRAM: Batchwise Free Energy Estimation}},
url = {https://pubs.acs.org/doi/full/10.1021/acs.jctc.2c00976},
year = {2023}
}
@article{Sadeghi2021,
author = {Sadeghi, Mohsen and No{\'{e}}, Frank},
doi = {10.1007/s00249-021-01558-w},
file = {:home/sadeghi/Dokumente/Mendeley Desktop/Sadeghi, No{\'{e}} - 2021 - 13th EBSA congress, July 24-28, 2021, Vienna, Austria.pdf:pdf},
issn = {1432-1017},
journal = {Eur. Biophys. J.},
number = {1},
pages = {S171},
title = {{13th EBSA congress, July 24-28, 2021, Vienna, Austria}},
url = {https://doi.org/10.1007/s00249-021-01558-w},
volume = {50},
year = {2021}
}
@article{Sadeghi2010a,
abstract = {In this paper, a hybrid atomistic-structural element for studying the mechanical behaviour of carbon nanotubes is introduced. Non-linear formulation for this element is derived based on empirical inter-atomic potentials. This hybrid element is capable of taking into account the non-linear nature of inter-atomic forces as well as the non-linearity arising from large deformations. Using these capabilities, the stability analysis of carbon nanotubes under axial compressive loading is performed and the post-buckling behaviour is predicted. Also, the dependence of axial buckling force on nanotube radius is shown.},
author = {Sadeghi, M and Naghdabadi, R},
file = {:home/sadeghi/Dokumente/Mendeley Desktop/Sadeghi, Naghdabadi - 2010 - Stability analysis of carbon nanotubes using a hybrid atomistic-structural element.pdf:pdf},
journal = {Int. J. Nanomanufacturing},
keywords = {carbon nanotubes,hybrid-atomistic-structural element,inter-atomic potential,large deformations,post-buckling,stability},
number = {34},
pages = {366--375},
title = {{Stability analysis of carbon nanotubes using a hybrid atomistic-structural element}},
volume = {54},
year = {2010}
}
@article{Sadeghi2012,
author = {Sadeghi, M. and Parsafar, G. A.},
doi = {10.1021/jp211647e},
file = {:home/sadeghi/Dokumente/Mendeley Desktop/Sadeghi, Parsafar - 2012 - Toward an equation of state for water inside carbon nanotubes.pdf:pdf},
issn = {15205207},
journal = {J. Phys. Chem. B},
number = {16},
pages = {4943--4951},
title = {{Toward an equation of state for water inside carbon nanotubes}},
volume = {116},
year = {2012}
}
@article{Sadeghi2010,
abstract = {Recent experiments have shown the applicability of single-layer graphene sheets (SLGSs) as electromechanical resonators. Existing theoretical models, based on linear continuum or atomistic methods, are limited to the study of linear vibrations of SLGSs. Here we introduce a hybrid atomistic-structural element which is capable of modelling nonlinear behaviour of graphene sheets. This hybrid element is based on an empirical inter-atomic potential function and can model the nonlinear dynamic response of SLGSs. Using this element, nonlinear vibrational analysis of SLGSs is performed. It is shown that the nonlinear vibrational analysis of SLGSs predicts significantly higher fundamental frequencies. Also, the effects of vibration amplitude as well as the geometry of the SLGSs on the fundamental frequency are studied and predictive relations between the fundamental frequency, the SLGS length and the non-dimensional vibration amplitude are presented. The results are verified with experimental observations and are in remarkable agreement.},
author = {Sadeghi, M and Naghdabadi, R},
doi = {10.1088/0957-4484/21/10/105705},
isbn = {0957-4484},
issn = {0957-4484},
journal = {Nanotechnology},
number = {10},
pages = {105705},
pmid = {20154368},
title = {{Nonlinear vibrational analysis of single-layer graphene sheets.}},
volume = {21},
year = {2010}
}
@article{Sadeghi2020b,
abstract = {The great challenge with biological membrane systems is the wide range of scales involved, from nanometers and picoseconds for individual lipids, to the micrometers and beyond millisecond for cellular signalling processes. While solvent-free coarse-grained membrane models are convenient for large-scale simulations, and promising to provide insight into slow processes involving membranes, these models usually have unrealistic kinetics. One major obstacle is the lack of an equally convenient way of introducing hydrodynamic coupling without significantly increasing the computational cost of the model. To address this, we introduce a framework based on anisotropic Langevin dynamics, for which major in-plane and out-of-plane hydrodynamic effects are modeled via friction and diffusion tensors from analytical or semi-analytical solutions to Stokes hydrodynamic equations. Using this framework, we obtain accurate dispersion relations for planar membrane patches, both free-standing and in the vicinity of a wall. We also briefly discuss how non-equilibrium dynamics is affected by hydrodynamic interactions.},
archivePrefix = {arXiv},
arxivId = {1909.02722},
author = {Sadeghi, Mohsen and No{\'{e}}, Frank},
eprint = {1909.02722},
file = {:home/sadeghi/Dokumente/Mendeley Desktop/Sadeghi, No{\'{e}} - 2020 - Hydrodynamic coupling for particle-based solvent-free membrane models.pdf:pdf},
journal = {arXiv},
month = {sep},
pages = {1909.02722},
publisher = {arXiv},
title = {{Hydrodynamic coupling for particle-based solvent-free membrane models}},
url = {http://arxiv.org/abs/1909.02722},
year = {2020}
}
@article{Dimou2019,
abstract = {FGF2 is exported from cells by an unconventional secretory mechanism. Here, we directly visualized individual FGF2 membrane translocation events at the plasma membrane using live cell TIRF microscopy. This process was dependent on both PI(4,5)P 2 –mediated recruitment of FGF2 at the inner leaflet and heparan sulfates capturing FGF2 at the outer plasma membrane leaflet. By simultaneous imaging of both FGF2 membrane recruitment and the appearance of FGF2 at the cell surface, we revealed the kinetics of FGF2 membrane translocation in living cells with an average duration of ∼200 ms. Furthermore, we directly demonstrated FGF2 oligomers at the inner leaflet of living cells with a FGF2 dimer being the most prominent species. We propose this dimer to represent a key intermediate in the formation of higher FGF2 oligomers that form membrane pores and put forward a kinetic model explaining the mechanism by which membrane-inserted FGF2 oligomers serve as dynamic translocation intermediates during unconventional secretion of FGF2.},
author = {Dimou, Eleni and Cosentino, Katia and Platonova, Evgenia and Ros, Uris and Sadeghi, Mohsen and Kashyap, Purba and Katsinelos, Taxiarchis and Wegehingel, Sabine and No{\'{e}}, Frank and Garc{\'{i}}a-S{\'{a}}ez, Ana J and Ewers, Helge and Nickel, Walter},
doi = {10.1083/jcb.201802008},
file = {:home/sadeghi/Dokumente/Mendeley Desktop/Dimou et al. - 2019 - Single event visualization of unconventional secretion of FGF2.pdf:pdf},
issn = {15408140},
journal = {J. Cell Biol.},
number = {2},
pages = {683--699},
title = {{Single event visualization of unconventional secretion of FGF2}},
url = {http://doi.org/10.1083/jcb.201802008},
volume = {218},
year = {2019}
}
@article{Sadeghi2022a,
abstract = {Peripheral membrane-associated proteins are known to accumulate on the surface of biomembranes as result of membrane-mediated interactions. For a pair of rotationally-symmetric curvature-inducing proteins, membrane mechanics at the low-temperature limit predicts pure repulsion. On the other hand, temperature-dependent entropic forces arise between pairs of stiff-binding proteins suppressing membrane fluctuations. These Casimir-like interactions have thus been suggested as candidates for attractive force leading to aggregation. With dense assemblies of peripheral proteins on the membrane, both these abstractions encounter multi-body complications. Here, we make use of a particle-based membrane model augmented with flexible peripheral proteins to quantify purely membrane-mediated interactions and investigate their underlying nature. We introduce a continuous reaction coordinate corresponding to the progression of protein aggregation. We obtain free energy and entropy landscapes for different surface concentrations along this reaction coordinate. In parallel, we investigate time-dependent estimates of membrane entropy corresponding to membrane undulations and coarse-grained tilt field and how they also change dynamically with protein aggregation. Congruent outcomes of the two approaches point to the conclusion that for low surface concentrations, interactions with an entropic nature may drive the aggregation. But at high concentrations, energetic contributions due to concerted membrane deformation by protein clusters are dominant. {\#}{\#}{\#} Competing Interest Statement The authors have declared no competing interest.},
author = {Sadeghi, Mohsen},
doi = {10.1039/d2sm00118g},
file = {:home/sadeghi/Dokumente/Mendeley Desktop/Sadeghi - 2022 - Investigating the entropic nature of membrane-mediated interactions driving the aggregation of peripheral proteins(2).pdf:pdf},
journal = {Soft Matter},
pages = {3917 -- 3927},
title = {{Investigating the entropic nature of membrane-mediated interactions driving the aggregation of peripheral proteins}},
url = {https://doi.org/10.1039/D2SM00118G},
volume = {18},
year = {2022}
}
@article{Niaki2012,
abstract = {Dynamic and static fracture properties of Graphene Sheets (GSs) and Carbon nanotubes (CNTs) with different sizes are investigated based on an empirical inter-atomic potential function that can simulate nonlinear large deflections of nanostructures. Dynamic fracture of GSs and CNTs are studied based on wave propagation analysis in these nanostructures in a wide range of strain-rates. It is shown that wave propagation velocity is independent from strain-rate while dependent on the nanostructure size and approaches to 2.2??10 4m/s for long GSs. Also, fracture strain shows extensive changes versus strain-rate, which has not been reported before. Fracture stress is determined as 115GPa for GSs and 122GPa for CNTs which are independent from the strain-rate; in contrast to the fracture strain. Moreover, fracture strain drops at extremely high strain-rates for GSs and CNTs. These features are considered as capability of carbon nanostructures for reinforcing nanocomposites especially under impact loadings up to high strain-rates. ?? 2012 Elsevier Ltd.},
author = {Niaki, S. A. and Mianroodi, J. R. and Sadeghi, M. and Naghdabadi, R.},
doi = {10.1016/j.compstruct.2012.02.027},
file = {:home/sadeghi/Dokumente/Mendeley Desktop/Niaki et al. - 2012 - Dynamic and static fracture analyses of graphene sheets and carbon nanotubes.pdf:pdf},
issn = {02638223},
journal = {Compos. Struct.},
keywords = {Carbon nanotube,Dynamic fracture,Finite element method,Graphene sheet,Static fracture,Wave propagation},
number = {8},
pages = {2365--2372},
title = {{Dynamic and static fracture analyses of graphene sheets and carbon nanotubes}},
volume = {94},
year = {2012}
}
@article{Sadeghi2008,
author = {Sadeghi, M and Ozmaian, M and Naghdabadi, R},
doi = {10.1088/0022-3727/41/20/205411},
file = {:home/sadeghi/Dokumente/Mendeley Desktop/Sadeghi, Ozmaian, Naghdabadi - 2008 - Stability analysis of carbon nanotubes under electric fields and compressive loading.pdf:pdf},
issn = {0022-3727},
journal = {J. Phys. D. Appl. Phys.},
number = {20},
pages = {205411},
title = {{Stability analysis of carbon nanotubes under electric fields and compressive loading}},
url = {http://stacks.iop.org/0022-3727/41/i=20/a=205411?key=crossref.ca4e84ef79b67f706bdc905a65b64ffa},
volume = {41},
year = {2008}
}
@article{Dyhr2022,
abstract = {Cryo-soft X-ray tomography (cryo-SXT) is a powerful method to investigate the ultrastructure of cells, offering resolution in the tens of nm range and strong contrast for membranous structures without requirement for labeling or chemical fixation. The short acquisition time and the relatively large volumes acquired allow for fast acquisition of large amounts of tomographic image data. Segmentation of these data into accessible features is a necessary step in gaining biologically relevant information from cryo-soft X-ray tomograms. However, manual image segmentation still requires several orders of magnitude more time than data acquisition. To address this challenge, we have here developed an end-to-end automated 3D-segmentation pipeline based on semi-supervised deep learning. Our approach is suitable for high-throughput analysis of large amounts of tomographic data, while being robust when faced with limited manual annotations and variations in the tomographic conditions. We validate our approach by extracting three-dimensional information on cellular ultrastructure and by quantifying nanoscopic morphological parameters of filopodia in mammalian cells.Competing Interest StatementThe authors have declared no competing interest.},
author = {Dyhr, Michael C A and Sadeghi, Mohsen and Moynova, Ralitsa and Knappe, Carolin and Kepsutlu, Burcu and Werner, Stephan and Schneider, Gerd and McNally, James and Noe, Frank and Ewers, Helge},
doi = {10.1101/2022.05.16.492055},
journal = {bioRxiv},
pages = {2022.05.16.492055},
publisher = {Cold Spring Harbor Laboratory},
title = {{3D-surface reconstruction of cellular cryo-soft X-ray microscopy tomograms using semi-supervised deep learning}},
url = {https://www.biorxiv.org/content/early/2022/05/16/2022.05.16.492055},
year = {2022}
}
@article{Montazeri2011,
abstract = {A combination of molecular dynamics (MD), continuum elasticity and FEM is used to predict the effect of CNT orientation on the shear modulus of SWCNT- polymer nanocomposites. We first develop a transverse-isotropic elastic model of SWCNTs based on the continuum ...},
author = {Montazeri, A and Sadeghi, M and Naghdabadi, R and Rafii-Tabar, H},
doi = {10.1016/j.physleta.2011.02.065},
file = {:home/sadeghi/Dokumente/Mendeley Desktop/Montazeri et al. - 2011 - Multiscale modeling of the effect of carbon nanotube orientation on the shear deformation properties of reinfo.pdf:pdf},
isbn = {0375-9601},
issn = {0375-9601},
journal = {Phys. Lett. A},
keywords = {Molecular dynamics simulation,Multiscale modeling,Orientation,SWCNT-polymer nanocomposite,Shear modulus},
number = {14},
pages = {1588--1597},
title = {{Multiscale modeling of the effect of carbon nanotube orientation on the shear deformation properties of reinforced polymer-based composites}},
url = {www.elsevier.com/locate/pla http://www.sciencedirect.com/science/article/pii/S0375960111002763},
volume = {375},
year = {2011}
}
@article{Sadeghi2022,
abstract = {Peripheral membrane-associated proteins are known to accumulate on the surface of biomembranes as result of membrane-mediated interactions. For a pair of rotationally-symmetric curvature-inducing proteins, membrane mechanics at the low-temperature limit predicts pure repulsion. On the other hand, temperature-dependent entropic forces arise between pairs of stiff-binding proteins suppressing membrane fluctuations. These Casimir-like interactions have thus been suggested as candidates for attractive force leading to aggregation. With dense assemblies of peripheral proteins on the membrane, both these abstractions encounter multi-body complications. Here, we make use of a particle-based membrane model augmented with flexible peripheral proteins to quantify purely membrane-mediated interactions and investigate their underlying nature. We introduce a continuous reaction coordinate corresponding to the progression of protein aggregation. We obtain free energy and entropy landscapes for different surface concentrations along this reaction coordinate. In parallel, we investigate time-dependent estimates of membrane entropy corresponding to membrane undulations and coarse-grained tilt field and how they also change dynamically with protein aggregation. Congruent outcomes of the two approaches point to the conclusion that for low surface concentrations, interactions with an entropic nature may drive the aggregation. But at high concentrations, energetic contributions due to concerted membrane deformation by protein clusters are dominant. {\#}{\#}{\#} Competing Interest Statement The authors have declared no competing interest.},
author = {Sadeghi, Mohsen},
doi = {10.1101/2022.01.24.477571},
file = {:home/sadeghi/Dokumente/Mendeley Desktop/Sadeghi - 2022 - Investigating the entropic nature of membrane-mediated interactions driving the aggregation of peripheral proteins.pdf:pdf},
journal = {bioRxiv},
month = {jan},
pages = {2022.01.24.477571},
publisher = {Cold Spring Harbor Laboratory},
title = {{Investigating the entropic nature of membrane-mediated interactions driving the aggregation of peripheral proteins}},
url = {https://www.biorxiv.org/content/10.1101/2022.01.24.477571v1 https://www.biorxiv.org/content/10.1101/2022.01.24.477571v1.abstract},
year = {2022}
}
@article{Sadeghi2023,
abstract = {Curvature-inducing peripheral proteins have been observed to spontaneously remodel bilayer membranes, resulting in membrane invaginations and formation of membrane tubules. In case of proteins such as cholera and Shiga toxin that bend the membrane with locally isotropic curvatures, the resulting membrane-mediated interactions are rather small. Thus, the process in which these proteins form dense clusters on the membrane and collectively induce invaginations is extremely slow, progressing over several minutes. This makes it virtually impossible to directly simulate the pathway leading to membrane tubulation even with highly coarse-grained models. Here, we present a steered molecular dynamics protocol through which the peripheral proteins are forced to gather on a membrane patch and form a tubular invagination. Using thermodynamic integration, we obtain the free energy profile of this process and discuss its different stages. We show how protein stiffness, which also determines local membrane curvature, affects the free energy landscape and the organization of proteins in the invaginated region. Furthermore, we estimate the kinetics of the described pathway modeled as a Markovian stochastic process, and compare the implied timescales with their experimental counterparts. {\#}{\#}{\#} Competing Interest Statement The authors have declared no competing interest.},
author = {Sadeghi, Mohsen},
doi = {10.1101/2022.11.09.515891},
file = {:home/sadeghi/Dokumente/Mendeley Desktop/Sadeghi - 2023 - Free energy profile and kinetics of the formation of membrane invaginations by membrane-bending peripheral proteins.pdf:pdf},
journal = {bioRxiv},
month = {mar},
pages = {2022.11.09.515891},
publisher = {Cold Spring Harbor Laboratory},
title = {{Free energy profile and kinetics of the formation of membrane invaginations by membrane-bending peripheral proteins}},
url = {https://www.biorxiv.org/content/10.1101/2022.11.09.515891v2 https://www.biorxiv.org/content/10.1101/2022.11.09.515891v2.abstract},
year = {2023}
}
@article{Sadeghi2013,
abstract = {Water inside carbon nanotubes is an interesting confined system, and its theoretical and applied aspects have been studied extensively. The confinement in nanometer-and sub-nanometer-sized nanotubes gives rise to new molecular arrangements of water and affects its physical properties drastically. In order to study these new arrangements, Monte Carlo simulations of water inside carbon nanotubes have been performed. Simulations are carried out for water with a wide range of density inside carbon nanotubes with different diameters. It is observed that at constant temperature, the density of water dictates the presence of water clusters, filled states, and different ordered phases. The transitions between these states and their effects on the physical properties of this system are studied in detail.},
author = {Sadeghi, M and Parsafar, G A},
doi = {10.1039/c3cp44563a},
file = {:home/sadeghi/Dokumente/Mendeley Desktop/Sadeghi, Parsafar - 2013 - Density-induced molecular arrangements of water inside carbon nanotubes.pdf:pdf},
isbn = {1463-9076},
issn = {1463-9084},
journal = {Phys. Chem. Chem. Phys.},
number = {15},
pages = {7379--7388},
pmid = {23579195},
title = {{Density-induced molecular arrangements of water inside carbon nanotubes}},
volume = {15},
year = {2013}
}