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- Abenius, Erik, et al.
(författare)
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A General Approach for Time-Domain Simulation of Waveguides in 3D
- 2004
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Ingår i: Proc. EMB 04, Computational Electromagnetics. - Göteborg, Sweden : Department of Electromagnetics, Chalmers University of Technology. - 9163160765 ; , s. 220-226
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 2. |
- Abenius, Erik, 1971-
(författare)
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Direct and Inverse Methods for Waveguides and Scattering Problems in the Time Domain
- 2005
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Numerical simulation is an important tool in understanding the electromagnetic field and how it interacts with the environment. Different topics for time-domain finite-difference (FDTD) and finite-element (FETD) methods for Maxwell's equations are treated in this thesis. Subcell models are of vital importance for the efficient modeling of small objects that are not resolved by the grid. A novel model for thin sheets using shell elements is proposed. This approach has the advantage of taking into account discontinuities in the normal component of the electric field, unlike previous models based on impedance boundary conditions (IBCs). Several results are presented to illustrate the capabilities of the shell element approach. Waveguides are of fundamental importance in many microwave applications, for example in antenna feeds. The key issues of excitation and truncation of waveguides are addressed. A complex frequency shifted form of the uniaxial perfectly matched layer (UPML) absorbing boundary condition (ABC) in FETD is developed. Prism elements are used to promote automatic grid generation and enhance the performance. Results are presented where reflection errors below -70dB are obtained for different types of waveguides, including inhomogeneous cases. Excitation and analysis via the scattering parameters are achieved using waveguide modes computed by a general frequency-domain mode solver for the vector Helmholtz equation. Huygens surfaces are used in both FDTD and FETD for excitation in waveguide ports. Inverse problems have received an increased interest due to the availability of powerful computers. An important application is non-destructive evaluation of material. A time-domain, minimization approach is presented where exact gradients are computed using the adjoint problem. The approach is applied to a general form of Maxwell's equations including dispersive media and UPML. Successful reconstruction examples are presented both using synthetic and experimental measurement data. Parameter reduction of complex geometries using simplified models is an interesting topic that leads to an inverse problem. Gradients for subcell parameters are derived and a successful reconstruction example is presented for a combined dielectric sheet and slot geometry.
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| 8. |
- Abenius, Erik
(författare)
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Time-Domain Inverse Electromagnetic Scattering using FDTD and Gradient-based Minimization
- 2004
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The thesis addresses time-domain inverse electromagneticscattering for determining unknown characteristics of an objectfrom observations of the scattered .eld. Applications includenon-destructive characterization of media and optimization ofmaterial properties, for example the design of radar absorbingmaterials.A nother interesting application is the parameteroptimization of subcell models to avoid detailed modeling ofcomplex geometries. The inverse problem is formulated as an optimal controlproblem where the cost function to be minimized is thedi.erence between the estimated and observed .elds, and thecontrol parameters are the unknown object characteristics. Theproblem is solved in a deterministic gradient-basedoptimization algorithm using a parallel 2D FDTD scheme for thedirect problem.This approach is computationally intensive sincethe direct problem needs to be solved in every optimizationiteration in order to compute an estimated .eld.H ighlyaccurate analytical gradients are computed from the adjointformulation.In addition to giving better accuracy than .nitedi.erences, the analytical gradients also have the advantage ofonly requiring one direct and one adjoint problem to be solvedregardless of the number of parameters. When absorbing boundary conditions are used to truncate thecomputational domain, the equations are non-reversible and theentire time-history of the direct solution needs to be storedfor the gradient computation.Ho wever, using an additionaldirect simulation and a restart procedure it is possible tokeep the storage at an acceptable level. The inverse method has been successfully applied to a widerange of industrial problems within the European project,IMPACT (Inverse Methods for Wave Propagation Applications inTime-Domain).T he results presented here includecharacterization of layered dispersive media, determination ofparameters in subcell models for thin sheets and narrow slotsand optimization problems where the observed .eld is given bydesign objectives.
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| 9. |
- Abenius, Erik, et al.
(författare)
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Waveguide Truncation Using UPML in the Finite-Element Time-Domain Method
- 2005
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- An important part of numerical waveguide modeling is the termination of the waveguide using artificial boundaries. In this paper we develop a perfectly matched layer (PML) for waveguides in the finite-element time-domain method (FETD). The PML is discretized by prism elements aligned with the direction of propagation of the waveguide. Assuming that the waveguide is discretized by tetrahedra such a grid is easily generated from a cross-sectional surface in the waveguide. The proposed method has the advantage of being general with regard to the geometry and material of the waveguide. Previous works on PML for FETD have reported problems with late-time instability. While still present in the current approach, our results indicate that the instability is less severe for the prism element PML compared to a tetrahedral PML. Moreover, it may be controlled by increasing the number of grid points in the absorbing layer. It should be noted that the instability appears long after the energy has been attenuated and therefore pose no problems in practical computations. The performance of the suggested scheme is demonstrated for several waveguide problems, including an inhomogeneous case.
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| 10. |
- Jörnsten, Rebecka, 1971, et al.
(författare)
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Network modeling of the transcriptional effects of copy number aberrations in glioblastoma
- 2011
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Ingår i: Molecular Systems Biology. - : EMBO. - 1744-4292. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- DNA copy number aberrations (CNAs) are a hallmark of cancer genomes. However, little is known about how such changes affect global gene expression. We develop a modeling framework, EPoC (Endogenous Perturbation analysis of Cancer), to (1) detect disease-driving CNAs and their effect on target mRNA expression, and to (2) stratify cancer patients into long- and short-term survivors. Our method constructs causal network models of gene expression by combining genome-wide DNA- and RNA-level data. Prognostic scores are obtained from a singular value decomposition of the networks. By applying EPoC to glioblastoma data from The Cancer Genome Atlas consortium, we demonstrate that the resulting network models contain known disease-relevant hub genes, reveal interesting candidate hubs, and uncover predictors of patient survival. Targeted validations in four glioblastoma cell lines support selected predictions, and implicate the p53-interacting protein Necdin in suppressing glioblastoma cell growth. We conclude that large-scale network modeling of the effects of CNAs on gene expression may provide insights into the biology of human cancer. Free software in MATLAB and R is provided.
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