https://3demmethods.i2pc.es/index.php?action=history&feed=atom&title=2024Parkhurst_IceSimulation 2026-05-24T22:00:47Z Revision history for this page on the wiki MediaWiki 1.44.2 https://3demmethods.i2pc.es/index.php?title=2024Parkhurst_IceSimulation&diff=4566&oldid=prev 2024-07-16T07:30:04Z

<p>Created page with &quot;== Citation == Parkhurst, James M. / Cavalleri, Anna / Dumoux, Maud / Basham, Mark / Clare, Daniel / Siebert, C. Alistair / Evans, Gwyndaf / Naismith, James H. / Kirkland, Angus / Essex, Jonathan W. Computational models of amorphous ice for accurate simulation of cryo-EM images of biological samples. 2024. Ultramicroscopy, Vol. 256, p. 113882 == Abstract == Simulations of cryo-electron microscopy (cryo-EM) images of biological samples can be used to produce test datas...&quot;</p> <p><b>New page</b></p><div>== Citation ==<br /> <br /> Parkhurst, James M. / Cavalleri, Anna / Dumoux, Maud / Basham, Mark / Clare, Daniel / Siebert, C. Alistair / Evans, Gwyndaf / Naismith, James H. / Kirkland, Angus / Essex, Jonathan W. Computational models of amorphous ice for accurate simulation of cryo-EM images of biological samples. 2024. Ultramicroscopy, Vol. 256, p. 113882<br /> <br /> == Abstract ==<br /> <br /> Simulations of cryo-electron microscopy (cryo-EM) images of biological samples can be used to produce test<br /> datasets to support the development of instrumentation, methods, and software, as well as to assess data<br /> acquisition and analysis strategies. To be useful, these simulations need to be based on physically realistic models<br /> which include large volumes of amorphous ice. The gold standard model for EM image simulation is a physical<br /> atom-based ice model produced using molecular dynamics simulations. Although practical for small sample<br /> volumes; for simulation of cryo-EM data from large sample volumes, this can be too computationally expensive.<br /> We have evaluated a Gaussian Random Field (GRF) ice model which is shown to be more computationally<br /> efficient for large sample volumes. The simulated EM images are compared with the gold standard atom-based<br /> ice model approach and shown to be directly comparable. Comparison with experimentally acquired data shows<br /> the Gaussian random field ice model produces realistic simulations. The software required has been implemented<br /> in the Parakeet software package and the underlying atomic models are available online for use by the wider<br /> community.<br /> <br /> == Keywords ==<br /> <br /> == Links ==<br /> <br /> https://www.sciencedirect.com/science/article/pii/S0304399123001997<br /> <br /> == Related software ==<br /> <br /> == Related methods ==<br /> <br /> == Comments ==</div>

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