Computational models of amorphous ice for accurate simulation of cryo-EM images of biological samples
Ultramicroscopy. 2023 Nov 4;256:113882. doi: 10.1016/j.ultramic.2023.113882. Online ahead of print.ABSTRACTSimulations of cryo-electron microscopy (cryo-EM) images of biological samples can be used to produce test datasets to support the development of instrumentation, methods, and software, as well as to assess data acquisition and analysis strategies. To be useful, these simulations need to be based on physically realistic models which include large volumes of amorphous ice. The gold standard model for EM image simulation is a physical atom-based ice model produced using molecular dynamics simulations. Although practical...
Source: Ultramicroscopy - November 18, 2023 Category: Laboratory Medicine Authors: James M Parkhurst Anna Cavalleri Maud Dumoux Mark Basham Daniel Clare C Alistair Siebert Gwyndaf Evans James H Naismith Angus Kirkland Jonathan W Essex Source Type: research
Computational models of amorphous ice for accurate simulation of cryo-EM images of biological samples
Ultramicroscopy. 2023 Nov 4;256:113882. doi: 10.1016/j.ultramic.2023.113882. Online ahead of print.ABSTRACTSimulations of cryo-electron microscopy (cryo-EM) images of biological samples can be used to produce test datasets to support the development of instrumentation, methods, and software, as well as to assess data acquisition and analysis strategies. To be useful, these simulations need to be based on physically realistic models which include large volumes of amorphous ice. The gold standard model for EM image simulation is a physical atom-based ice model produced using molecular dynamics simulations. Although practical...
Source: Ultramicroscopy - November 18, 2023 Category: Laboratory Medicine Authors: James M Parkhurst Anna Cavalleri Maud Dumoux Mark Basham Daniel Clare C Alistair Siebert Gwyndaf Evans James H Naismith Angus Kirkland Jonathan W Essex Source Type: research
Computational models of amorphous ice for accurate simulation of cryo-EM images of biological samples
Ultramicroscopy. 2023 Nov 4;256:113882. doi: 10.1016/j.ultramic.2023.113882. Online ahead of print.ABSTRACTSimulations of cryo-electron microscopy (cryo-EM) images of biological samples can be used to produce test datasets to support the development of instrumentation, methods, and software, as well as to assess data acquisition and analysis strategies. To be useful, these simulations need to be based on physically realistic models which include large volumes of amorphous ice. The gold standard model for EM image simulation is a physical atom-based ice model produced using molecular dynamics simulations. Although practical...
Source: Ultramicroscopy - November 18, 2023 Category: Laboratory Medicine Authors: James M Parkhurst Anna Cavalleri Maud Dumoux Mark Basham Daniel Clare C Alistair Siebert Gwyndaf Evans James H Naismith Angus Kirkland Jonathan W Essex Source Type: research
Prediction of primary knock-on damage during electron microscopy characterization of lithium-containing materials
In this study, we investigated this damage by determining the probability of knock-on damage and performing Monte Carlo simulation. For this objective, the threshold displacement energies (TDEs) were computed using sudden approximation technique for three sets of materials, including pure elements, LiX (X = F, Cl, Br), and Li2MSiO4 (M = Fe, Co, Mn). By including the Climbing-Image Nudge Elastic Band (CI-NEB) method into the sudden approximation approach, it was found that the accuracy of the predicted TDEs could be improved. Results also indicated that at moderate electron energies, the knock-on damage for Li in both its e...
Source: Ultramicroscopy - November 17, 2023 Category: Laboratory Medicine Authors: Ali Jaberi Nicolas Brodusch Jun Song Raynald Gauvin Source Type: research
Improving the temporal resolution of event-based electron detectors using neural network cluster analysis
Ultramicroscopy. 2023 Nov 11;256:113881. doi: 10.1016/j.ultramic.2023.113881. Online ahead of print.ABSTRACTNovel event-based electron detector platforms provide an avenue to extend the temporal resolution of electron microscopy into the ultrafast domain. Here, we characterize the timing accuracy of a detector based on a TimePix3 architecture using femtosecond electron pulse trains as a reference. With a large dataset of event clusters triggered by individual incident electrons, a neural network is trained to predict the electron arrival time. Corrected timings of event clusters show a temporal resolution of 2 ns, a 1.6-fo...
Source: Ultramicroscopy - November 17, 2023 Category: Laboratory Medicine Authors: Alexander Schr öder Christopher Rathje Leon van Velzen Maurits Kelder Sascha Sch äfer Source Type: research
Prediction of primary knock-on damage during electron microscopy characterization of lithium-containing materials
In this study, we investigated this damage by determining the probability of knock-on damage and performing Monte Carlo simulation. For this objective, the threshold displacement energies (TDEs) were computed using sudden approximation technique for three sets of materials, including pure elements, LiX (X = F, Cl, Br), and Li2MSiO4 (M = Fe, Co, Mn). By including the Climbing-Image Nudge Elastic Band (CI-NEB) method into the sudden approximation approach, it was found that the accuracy of the predicted TDEs could be improved. Results also indicated that at moderate electron energies, the knock-on damage for Li in both its e...
Source: Ultramicroscopy - November 17, 2023 Category: Laboratory Medicine Authors: Ali Jaberi Nicolas Brodusch Jun Song Raynald Gauvin Source Type: research
Improving the temporal resolution of event-based electron detectors using neural network cluster analysis
Ultramicroscopy. 2023 Nov 11;256:113881. doi: 10.1016/j.ultramic.2023.113881. Online ahead of print.ABSTRACTNovel event-based electron detector platforms provide an avenue to extend the temporal resolution of electron microscopy into the ultrafast domain. Here, we characterize the timing accuracy of a detector based on a TimePix3 architecture using femtosecond electron pulse trains as a reference. With a large dataset of event clusters triggered by individual incident electrons, a neural network is trained to predict the electron arrival time. Corrected timings of event clusters show a temporal resolution of 2 ns, a 1.6-fo...
Source: Ultramicroscopy - November 17, 2023 Category: Laboratory Medicine Authors: Alexander Schr öder Christopher Rathje Leon van Velzen Maurits Kelder Sascha Sch äfer Source Type: research
Reconstruction of Angstrom resolution exit-waves by the application of drift-corrected phase-shifting off-axis electron holography
Ultramicroscopy. 2023 Oct 22;256:113880. doi: 10.1016/j.ultramic.2023.113880. Online ahead of print.ABSTRACTPhase-shifting electron holography is an excellent method to reveal electron wave phase information with very high phase sensitivity over a large range of spatial frequencies. It circumvents the limiting trade-off between fringe spacing and visibility of standard off-axis holography. Previous implementations have been limited by the independent drift of biprism and sample. We demonstrate here an advanced drift correction scheme for the hologram series that exploits the presence of an interface of the TEM specimen to ...
Source: Ultramicroscopy - November 12, 2023 Category: Laboratory Medicine Authors: J Lindner U Ross T Meyer V Boureau M Seibt Ch Jooss Source Type: research
Reconstruction of Angstrom resolution exit-waves by the application of drift-corrected phase-shifting off-axis electron holography
Ultramicroscopy. 2023 Oct 22;256:113880. doi: 10.1016/j.ultramic.2023.113880. Online ahead of print.ABSTRACTPhase-shifting electron holography is an excellent method to reveal electron wave phase information with very high phase sensitivity over a large range of spatial frequencies. It circumvents the limiting trade-off between fringe spacing and visibility of standard off-axis holography. Previous implementations have been limited by the independent drift of biprism and sample. We demonstrate here an advanced drift correction scheme for the hologram series that exploits the presence of an interface of the TEM specimen to ...
Source: Ultramicroscopy - November 12, 2023 Category: Laboratory Medicine Authors: J Lindner U Ross T Meyer V Boureau M Seibt Ch Jooss Source Type: research
Reconstruction of Angstrom resolution exit-waves by the application of drift-corrected phase-shifting off-axis electron holography
Ultramicroscopy. 2023 Oct 22;256:113880. doi: 10.1016/j.ultramic.2023.113880. Online ahead of print.ABSTRACTPhase-shifting electron holography is an excellent method to reveal electron wave phase information with very high phase sensitivity over a large range of spatial frequencies. It circumvents the limiting trade-off between fringe spacing and visibility of standard off-axis holography. Previous implementations have been limited by the independent drift of biprism and sample. We demonstrate here an advanced drift correction scheme for the hologram series that exploits the presence of an interface of the TEM specimen to ...
Source: Ultramicroscopy - November 12, 2023 Category: Laboratory Medicine Authors: J Lindner U Ross T Meyer V Boureau M Seibt Ch Jooss Source Type: research
Reconstruction of Angstrom resolution exit-waves by the application of drift-corrected phase-shifting off-axis electron holography
Ultramicroscopy. 2023 Oct 22;256:113880. doi: 10.1016/j.ultramic.2023.113880. Online ahead of print.ABSTRACTPhase-shifting electron holography is an excellent method to reveal electron wave phase information with very high phase sensitivity over a large range of spatial frequencies. It circumvents the limiting trade-off between fringe spacing and visibility of standard off-axis holography. Previous implementations have been limited by the independent drift of biprism and sample. We demonstrate here an advanced drift correction scheme for the hologram series that exploits the presence of an interface of the TEM specimen to ...
Source: Ultramicroscopy - November 12, 2023 Category: Laboratory Medicine Authors: J Lindner U Ross T Meyer V Boureau M Seibt Ch Jooss Source Type: research
On central focusing for contrast optimization in direct electron ptychography of thick samples
Ultramicroscopy. 2023 Nov 3;256:113879. doi: 10.1016/j.ultramic.2023.113879. Online ahead of print.ABSTRACTPtychography provides high dose efficiency images that can reveal light elements next to heavy atoms. However, despite ptychography having an otherwise single signed contrast transfer function, contrast reversals can occur when the projected potential becomes strong for both direct and iterative inversion ptychography methods. It has recently been shown that these reversals can often be counteracted in direct ptychography methods by adapting the focus. Here we provide an explanation of why the best contrast is often f...
Source: Ultramicroscopy - November 9, 2023 Category: Laboratory Medicine Authors: C Gao C Hofer T J Pennycook Source Type: research
On central focusing for contrast optimization in direct electron ptychography of thick samples
Ultramicroscopy. 2023 Nov 3;256:113879. doi: 10.1016/j.ultramic.2023.113879. Online ahead of print.ABSTRACTPtychography provides high dose efficiency images that can reveal light elements next to heavy atoms. However, despite ptychography having an otherwise single signed contrast transfer function, contrast reversals can occur when the projected potential becomes strong for both direct and iterative inversion ptychography methods. It has recently been shown that these reversals can often be counteracted in direct ptychography methods by adapting the focus. Here we provide an explanation of why the best contrast is often f...
Source: Ultramicroscopy - November 9, 2023 Category: Laboratory Medicine Authors: C Gao C Hofer T J Pennycook Source Type: research
On central focusing for contrast optimization in direct electron ptychography of thick samples
Ultramicroscopy. 2023 Nov 3;256:113879. doi: 10.1016/j.ultramic.2023.113879. Online ahead of print.ABSTRACTPtychography provides high dose efficiency images that can reveal light elements next to heavy atoms. However, despite ptychography having an otherwise single signed contrast transfer function, contrast reversals can occur when the projected potential becomes strong for both direct and iterative inversion ptychography methods. It has recently been shown that these reversals can often be counteracted in direct ptychography methods by adapting the focus. Here we provide an explanation of why the best contrast is often f...
Source: Ultramicroscopy - November 9, 2023 Category: Laboratory Medicine Authors: C Gao C Hofer T J Pennycook Source Type: research
On central focusing for contrast optimization in direct electron ptychography of thick samples
Ultramicroscopy. 2023 Nov 3;256:113879. doi: 10.1016/j.ultramic.2023.113879. Online ahead of print.ABSTRACTPtychography provides high dose efficiency images that can reveal light elements next to heavy atoms. However, despite ptychography having an otherwise single signed contrast transfer function, contrast reversals can occur when the projected potential becomes strong for both direct and iterative inversion ptychography methods. It has recently been shown that these reversals can often be counteracted in direct ptychography methods by adapting the focus. Here we provide an explanation of why the best contrast is often f...
Source: Ultramicroscopy - November 9, 2023 Category: Laboratory Medicine Authors: C Gao C Hofer T J Pennycook Source Type: research
