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- Aurell, Erik, et al.
(författare)
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Self-gravitating systems in a three-dimensional expanding universe
- 2002. - 1
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Ingår i: European journal of physics. - 0143-0807 .- 1361-6404.
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Tidskriftsartikel (refereegranskat)abstract
- The non-linear evolution of one-dimensional perturbations in a three-dimensional expanding Universe is considered. A general Lagrangian scheme is derived, and compared to two previously introduced approximate models. These models are simulated with heap-based event-driven numerical procedure that allows for the study of large systems, averaged over many realisations of random initial conditions. One of the models is shown to be qualitatively, and, in some respects, concerning mass aggregation, quantitatively similar to the adhesion model.
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| 3. |
- Bongini, Lorenzo, et al.
(författare)
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Resolving the geometry of biomolecules imaged by cryo electron tomography
- 2007
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Ingår i: Journal of Microscopy. - : Wiley. - 0022-2720 .- 1365-2818. ; 228:2, s. 174-184
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we describe two methods for computerized analysis of cryo electron tomography reconstructions of biomolecules. Both methods aim at quantifying the degree of structural flexibility of macromolecules and eventually resolving the inner dynamics through automatized protocols. The first method performs a Brownian dynamics evolution of a simplified molecular model into a fictitious force field generated by the tomograms. This procedure enables us to dock the simplified model into the experimental profiles. The second uses a fuzzy framework to delineate the subparts of the proteins and subsequently determine their interdomain relations. The two methods are discussed and their complementarities highlighted with reference to the case of the immunoglobulin antibody. Both artificial maps, constructed from immunoglobulin G entries in the Protein Data Bank and real tomograms are analyzed. Robustness issues and agreement with previously reported measurements are discussed.
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| 7. |
- Svensson, Stina, et al.
(författare)
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Using a fuzzy framework for delineation and decomposition of immunoglobulin G in cryo electron tomographic images
- 2006
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Ingår i: Proceedings The 18th International Conference on Pattern Recognition (ICPR 2006). - 0769525210 ; , s. 961-
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Konferensbidrag (refereegranskat)abstract
- In structural studies of proteins, the first task is to identify the different parts of the protein. We present a robust method using a fuzzy framework for delineating a protein and to identify its parts. The method is used in a study of the immunoglobulin G antibody, individually imaged using cryo electron tomography, with satisfactory results.
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| 8. |
- Öktem, Ozan, 1969-, et al.
(författare)
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Electron tomography : A short overview with an emphasis on the absorption potential model for the forward problem
- 2008
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Ingår i: Inverse Problems. - : Institute of Physics (IOP). - 0266-5611 .- 1361-6420. ; 24:1, s. 013001-
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Tidskriftsartikel (refereegranskat)abstract
- This review of the development and current status of electron tomography deals mainly with the mathematical and algorithmic aspects. After a very brief description of the role of electron tomography in structural biology, we turn our attention to the derivation of the forward operator. Starting from the Schrodinger equation, the electron - specimen interaction is modelled as a diffraction tomography problem and the picture is completed by adding a description of the optical system of the transmission electron microscope. The first- order Born approximation enables one to explicitly express the intensity for any finite wavenumber in terms of the propagation operator acting on the specimen convolved with a point spread function, derived from the optics in the transmission electron microscope. Next, we focus on the difficulties that cause the reconstruction problem to be quite challenging. Special emphasis is put on explaining the extremely low signal- to- noise ratio in the data combined with the incomplete data problems, which lead to severe ill- posedness. The next step is to derive the standard phase contrast model used in the electron tomography community. The above- mentioned expression for the intensity generalizes the standard phase contrast model which can be obtained by replacing the propagation operator by its high- energy limit, the x- ray transform, as the wavenumber tends to infinity. The importance of more carefully including the wave nature of the electron - specimen interaction is supported by performing an asymptotic analysis of the intensity as the wavenumber tends to infinity. Next we provide an overview of the various reconstruction methods that have been employed in electron tomography and we conclude by mentioning a number of open problems. Besides providing an introduction to electron tomography written in the 'language of inverse problems', the authors hope to raise interest among experts in integral geometry and regularization theory for the mathematical and algorithmic difficulties that are encountered in electron tomography.
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