Munin: Browsing Doktorgradsavhandlinger (NT-fak) by Author

Model based Statistics for Protein Sequence Families

Ahmed, Said Hassan (Doctoral thesis; Doktorgradsavhandling, 01-Jul-2011)

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Statistical Analysis of Multilook Polarimetric Radar Images with the Mellin Transform

Anfinsen, Stian Normann (Doctoral thesis; Doktorgradsavhandling, 19-May-2010)

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Abstract:

This thesis presents methods for statistical analysis of the probability distributions used to model multilook polarimetric radar images. The methods are based on a matrix-variate version of Mellin's integral transform. The proposed theoretical framework is referred to as Mellin kind statistics. It is an extension of a theory recently developed for single polarisation amplitude and intensity data to the complex matrix-variate case describing multilook polarimetric images. This generalisation is made possible by the rediscovery of a generalised Mellin transform, which is defined for functions of positive definite Hermitian matrices. The domain makes it suited for application to the distributions used to model the polarimetric covariance and coherency matrix. The analysis tools include the matrix-variate Mellin kind characteristic function, which is defined with the Mellin transform in place of the conventional Fourier transform. Matrix log-moments and matrix log-cumulants are retrieved from this function. The matrix log-cumulants are used in a moment based approach to parameter estimation of the distribution parameters. The estimators make efficient use of all the statistical information in the polarimetric covariance matrix, and are superior to all known alternatives. The matrix log-cumulants are also used to construct the first known goodness-of-fit test for matrix distributions based on the multilook polarimetric product model. The algorithms are interpreted by means of a highly informative graphical visualisation tool displaying a space spanned by certain matrix log-cumulants. It is demonstrated that the matrix-variate Mellin transform is the natural tool for analysing multilook polarimetric radar images. This conclusion is based on the simple and elegant mathematical expressions obtained, the superb statistical properties of developed estimators, as well as the intuitive interpretations offered by the Mellin kind statistics.

URI:

http://hdl.handle.net/10037/2471

File(s) in this item: 5

paper_1.pdf (5.533Mb)

paper_2.pdf (613.3Kb)

paper_3.pdf (1.662Mb)

thesis_entire.pdf (9.069Mb)

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Processes and dynamics during deglaciation of a polar continental shelf. Examples from the marine-based Barents Sea Ice Sheet

Bjarnadottir, Lilja Run (Doctoral thesis; Doktorgradsavhandling, 20-Dec-2012)

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Abstract:	The main objective of this PhD thesis was to reconstruct the pattern and main processes of the last deglaciation of the Barents Sea Ice Sheet. The thesis consists of an introductory part and five papers. The conclusions presented in the papers were based on data acquired with a suite of marine geophysical and geological methods, including multibeam-swath bathymetry data, chirp data, airgun and sparker seismic data and sediment (gravity) cores. Bathymetric data were used for identification and mapping of main geomorphic features on the seafloor. The distribution, geometry, reflection signature and seismic/acoustic stratigraphy of seabed sediments, were assessed based on chirp and seismic data. Sediment core analyses provided information about the depositional environment and age constraints for deglaciation. The primary focus was on two main study areas. The first area is Kveithola, a small submarine trough on the western margin of the continental shelf (NW of Bjørnøya). Results from Kveithola are presented in papers 1-2. In the first paper, the sedimentary environment in the trough from the time it was deglaciated before ~14.2 cal ka ago until the last sign of glacimarine sedimentation in the trough ~10.3 cal ka ago, is reconstructed. The second paper summarises both the complex retreat history of the Kveithola Ice Stream and the following glacimarine sedimentation in a conceptual model. The second study area was the central Barents Sea, which is addressed in papers 3-5. The third paper includes a map showing the distribution of large tunnel valleys on the seafloor, along with descriptions and discussions of their attributes, genesis and relevance for glacial history. The fourth paper focuses on the seafloor of upper Bjørnøyrenna, where a landform assemblage related to ice stream stagnation is presented and a new model of ice stream retreat in meltwater-dominated areas is introduced. In the final paper a new reconstruction of the deglaciation of the central Barents Sea is presented. The reconstruction includes main ice flow patterns, prolonged ice margin positions and glacial dynamics during the retreat of the ice sheet, based on both new and old data.
Description:	The papers of this thesis are not available in Munin: 1. Rüther, D.C., Bjarnadóttir, L.R., Junttila, J., Husum, K., Rasmussen, T.L., Lucchi, R.G. and Andreassen, K.: 'Pattern and timing of the north-western Barents Sea Ice Sheet deglaciation and indications of episodic Holocene deposition', Boreas (2012), vol. 41(3):494-512. Available at http://dx.doi.org/10.1111/j.1502-3885.2011.00244.x 2. Bjarnadóttir, L.R., Rüther, D.C., Winsborrow, M.C.M. and Andreassen, K.: 'Grounding line dynamics of the Kveithola ice stream, W Barents Sea, as identified from seabed geomorphology and shallow seismic stratigraphy', Boreas (2013), vol. 42(1):84–107. Available at http://dx.doi.org/10.1111/j.1502-3885.2012.00273.x 3. Bjarnadóttir, L.R., Winsborrow, M.C.M. and Andreassen, K.: 'Tunnel valleys in the Barents Sea' (manuscript) 4. Andreassen, K., Winsborrow, M.C.M., Bjarnadóttir, L.R. and Rüther, D.C.: 'Landform assemblage from the collapse of the Bjørnøyrenna palaeo-ice stream, northern Barents Sea' (manuscript) 5. Bjarnadóttir, L.R., Winsborrow, M.C. and Andreassen, K.: 'Deglaciation of the central Barents Sea' (manuscript)
URI:	http://hdl.handle.net/10037/5146

File(s) in this item: 1

thesis.pdf (3.445Mb)

Minor element abundances in the corona and solar wind

Byhring, Hanne Sigrun (Doctoral thesis; Doktorgradsavhandling, 21-Oct-2011)

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Abstract:	Using a time-dependent numerical model that spans the chromosphere, corona and solar wind, abundance variations resulting from gravitational settling in the chromosphere and corona have been studied. \noindent Gravitational settling in the chromosphere may lead to a depletion in the abundances of minor elements in the solar wind relative to the photosphere. The observed overabundance (relative to the photosphere) of elements with a first ionization potential (FIP) lower than 10~eV in the solar wind, and the underabundance of high-FIP elements such as He and Ne is a long standing problem in solar physics. In Paper~I and Paper~II, we study the significance of the magnetic flux tube expansion factor on the abundances of high-FIP elements He, Ne and O in the solar wind. With a low expansion factor, of order 15-20, we can reproduce the observed fast solar wind He abundance, but a high expansion factor, of order 40-100, is required to reproduce the observed fast solar wind Ne abundance. \noindent In the corona, gravitational settling leads to local abundance enhancements. The magnitude and location of a coronal abundance enhancement depends on the minor element heating rate and the background plasma parameters. Observations of minor element abundances in the corona, in combination with modelling, may place constraints on the minor element heating rates, thereby providing new constraints for models and theories on coronal heating. \noindent In Paper~I it is shown that, for proton-electron plasma parameters in accordance with observations from polar coronal holes, a coronal He abundance enhancement will occur in the region 1.2 - 2~$R_\odot$, where no observations of the He abundance exist. It can only be avoided by strong heating of the He ions, which leads to very high outflow velocities for both He and protons in the corona. In Paper~II we show that such high outflow velocities in the corona causes O and Ne to be pushed far out of ionization equilibrium, and leads to ion fractions for O and Ne that are not in accordance with in-situ observations in the fast solar wind. The results from Paper~I and Paper~II suggest that He abundance enhancements are common in the region above 1.2~$R_\odot$. In Paper~II we also investigate minor element abundance enhancements in the corona in a H-He background, using O as an example. We find that for O temperatures and outflow velocities in accordance with observations from coronal holes, coronal O abundance enhancements will occur at heights above 1.3~$R_\odot$. \noindent In Paper~III we study Fe elemental abundance enhancements in the slow solar wind. The results are compared to the observations of \cite{Habbaletal2007}, who found evidence of coronal density enhancements of Fe$^{+10}$ and Fe$^{+12}$, particularly along streamer edges. We show that the observations of \cite{Habbaletal2007} are consistent with an Fe elemental abundance enhancement, but owing to existing uncertainties about the plasma conditions in the source regions of the slow solar wind we cannot place any strong constraints on the coronal Fe heating rate. However, by comparing the modeled Fe ion fractions with in-situ observations in the slow solar wind we find that a background model with coronal hole-like densities and a high outflow velocity in the corona provides the best fit to observations.
Description:	The papers of this thesis are not available in Munin: 1. H. S. Byhring: 'The helium abundance in polar coronal holes and the fast solar wind', The Astrophysical Journal (2011) 738:172 (7pp). Available at http://dx.doi.org/10.1088/0004-637X/738/2/172 2. H.S Byhring, R. Esser and Ø. Lie-Svendsen: 'O and Ne in a H-He fast solar wind', (accepted paper in The Astrophysical Journal). 3. H. S. Byhring, S. R. Cranmer, Ø. Lie-Svendsen, S. R. Habbal, and R. Esser: 'Modeling iron abdundance enhancements in the slow solar wind', The Astrophysical Journal (2011) 732:119 (12pp). Available at http://dx.doi.org/10.1088/0004-637X/732/2/119
URI:	http://hdl.handle.net/10037/3658

File(s) in this item: 1

thesis.pdf (443.7Kb)

Non-Gaussian statistical analysis of polarimetric synthetic aperture radar images

Doulgeris, Anthony Paul (Doctoral thesis; Doktorgradsavhandling, 18-Feb-2011)

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Abstract:	This thesis describes general methods to analyse polarimetric synthetic aperture radar images, with the primary application of unsupervised image segmentation. The fundamental physics of electromagnetic scattering from distributed targets leads to the image phenomenon called speckle. Speckle is shown to be potentially non-Gaussian and several statistical distributions are investigated. Non-Gaussianity and polarimetry both hold pertinent information about the target medium and methods that utilise both attributes are developed. Two approaches are proposed: a local feature extraction method; and a model-based clustering algorithm. The local feature extraction approach creates a new six-dimensional description of the image by extending standard polarimetric features with a non-Gaussianity measure. Importantly, the non-Gaussianity measure is model independent and therefore does not unduly constrain the analysis. This may be used for subsequent image analysis or for physical parameter extraction, and unsupervised image segmentation is demonstrated with good results. The model-based approach describes a Bayesian clustering algorithm for the K-Wishart model and incorporates both non-Gaussianity and polarimetry. The initial implementation required several key parameters to be given in advance. When compared to the more common Wishart model, the K-Wishart gives similar results for Gaussian image regions, but performs better for non-Gaussian regions. Further development of the model-based method resulted in a novel technique to automatically determine the number of distinct classes supported by the data, given the model and a statistical confidence level. All relevant parameters are subsequently estimated within the algorithm and no special initialisation is required. These are significant advances from existing methods, where key parameters are predetermined and the number of classes are found after many full clustering results are obtained. The methods are general and apply to all coherent imaging systems that exhibit product model based statistics. The methods are demonstrated on several real radar images and with different numbers of polarimetric channels.
Description:	Paper number 2 of the thesis is not available in Munin due to publisher's restrictions: Anthony P. Doulgeris, Stian Normann Anfinsen and Torbjørn Eltoft: ’Classification With a Non-Gaussian Model for PolSAR Data’, IEEE transactions on geoscience and remote sensing (2008), vol. 46, no. 10, pp. 2999-3009 Available at http://dx.doi.org/ 10.1109/TGRS.2008.923025
URI:	http://hdl.handle.net/10037/2962

File(s) in this item: 3

paper1.pdf (14.58Mb)

paper3.pdf (2.733Mb)

thesis.pdf (957.5Kb)

Angles as tool for grasping space. Teaching of angles based on students’ experiences with physical activities and body movement

Fyhn, Anne Birgitte (Doctoral thesis; Doktorgradsavhandling, 13-Jun-2007)

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Abstract:	The thesis enlightens how the choice of context as well as the approach to mathematics is important in introducing the concepts of angles. The analyses indicate that students should not be introduced to measuring angles before they are able to sort out angles according to their sizes. Angles can be introduced by use of the students’ bodies in a climbing context, where the word angle refers to bent shape. Climbing is an activity which to a large extent is experienced as exciting and fun. The idea is to base the teaching on the students’ talk about climbing. The teacher’s job is to guide the students to build up their understanding of angles as a tool for improved climbing technique. The students’ use of drawing and text in describing and explaining angles in a climbing context is analysed. These analyses indicate that the teaching should point out differences between narrative and analytical text and drawing and then the students’ analytical drawings can function as basis for their further work with geometry. The thesis focuses on students’ mathematising of climbing and on how the participating teachers relate to this activity. The analyses indicate that the teachers need some experience with inductive teaching of mathematics in some practical context before they are able to grasp the value of their students’ mathematising. Thus two DVDs are made. The first one shows how inductive physical geometry activities can function as basis for written and oral tasks in mathematics. The second DVD shows how students can mathematise climbing with respect to angles, and how experiences from one climbing situation can function as basis for adapting the teaching of angles to the students’ different levels of understanding.
Description:	DVD 1, which is part of the thesis introduction, is not made available in Munin due to restrictions in the Personal Data Act.
URI:	http://hdl.handle.net/10037/994

File(s) in this item: 8

climbingangles_2007_no.wmv (63.10Mb)

climbingangles_2007.wmv (66.94Mb)

dvd_info.pdf (75.34Kb)

Paper_I.pdf (344.7Kb)

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Synthesis of a novel class of antitubercular peptidomimetics based on β-aminoboronates.

Gorovoy, Alexey (Doctoral thesis; Doktorgradsavhandling, 16-Nov-2012)

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Abstract:	The unique properties of antimicrobial peptides have attracted the attention of chemists since the 1970’s. This class of compounds provides additional tools in the treatment of infections and the work described in this thesis was therefore focused on the synthesis of short peptidomimetics on the basis of modified amino acids and evaluation of their antimicrobial activity. The compounds of choice were β-aminoboronic acid derivatives with different substitution patterns and this work describes the development of a synthetic approach to the synthesis of this class of compounds. The skeleton of a β-amino acid was built using a step-wise approach utilizing the Matteson homologation. New chiral centers were obtained with high levels of diastereoselectivity provided by the use of chiral directors with particular configurations. The variety of β-aminoboronates was provided not only by different substituents in positions α- and β- to boron, but also by the opposite configurations of these chiral centers. As their configuration was dependent on the chiral directors used, several attempts to obtain all possible stereoisomers were undertaken. Derivatives of β-aminoboronic acid were coupled with different amino acids (both natural and non-natural) and the library of (~70) short peptidoids was characterized and tested on the set of microorganisms (Mycobacterium tuberculosis, Staphylococcus aureus, Escherichia coli, Streptococcus pyogenes, Pseudomonas aeruginosa and Candida albicans). High activity of the synthesized compounds against Mycobacterium tuberculosis (H37Rv) induced additional investigations on a set of resistant strains of this pathogen. Lead compounds has shown activity against all resistant strains tested. Investigation of the affinity of our compounds to secreted and internal chorismate mutase showed the absence of binding and led to the exlusion of this mechanism of inhibition from consideration. Antifungal activity (including resistant strains) was detected in one of the molecules synthesized. The low levels of toxicity of the lead compounds are very encouraging with regard to the prospects for developing drugs based on these compounds.
Description:	Papers 2, 3 and 4 of this thesis are not available in Munin: 2. Alexey S. Gorovoy, Olga V. Gozhina, John Sigurd Svendsen, Anna A. Domorad, George V. Tetz, Victor V. Tetz and Tore Lejon: 'Boron containing peptidomimetics : a novel class of selective anti-tubercular drugs' (manuscript) 3. Alexey S. Gorovoy, Tore Lejon, Anton Liaimer: 'β-Aminoboronate based peptidomimetic as potential antifungal agent' (manuscript) 4. Alexey S. Gorovoy, Olga Gozhina, John-Sigurd Svendsen, George V. Tetz, Anna Domorad, Victor V. Tetz and Tore Lejon: ''Syntheses and anti-tubercular activity of β-substituted and α,β-disubstituted β-aminoboronates and boronic' acids' (manuscript).
URI:	http://hdl.handle.net/10037/4653

File(s) in this item: 2

paper_1.pdf (2.213Mb)

thesis.pdf (16.53Mb)

Studies of ionospheric parameters by means of electron plasma lines observed by EISCAT

Guio, Patrick (Doctoral thesis; Doktorgradsavhandling, 18-Dec-1998)

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Abstract:

This work presents a study of the electron plasma lines observed by the incoherent scatter radar EISCAT. The work is focusing on two parts. On one hand, the design of a plasma line experiment for the EISCAT system with an improved spatial resolution. On the other hand, the comparison of the plasma line data collected with the EISCAT radar with an improved model for the intensity and the Doppler frequency shift of the plasma lines. In order to improve the spatial resolution of the plasma line experiment we have designed the first experiment that implements the recent technique of alternating code. The experiment has been run successfully with an altitude resolution of 3kmas opposed to 40– 50km obtained with the conventional techniques. Because it is very difficult to construct a self-consistent model of the velocity distribution function encompassing all of the relevant energy range, we have made an ad hoc model by separating the distribution into two parts: the thermal and the supra-thermal population. The thermal population is represented by the Spitzer function that takes into account the effect of an electric field and/or a temperature gradient. The supra-thermal population is derived from the angular energy flux of the supra-thermal electrons calculated by a numerical electron transport model. A numerical code has been developed to calculate the dielectric function and the reduced one-dimensional velocity distribution for any arbitrary two-dimensional velocity distribution which are needed to model the intensity and the Doppler frequency shift of the plasma lines. We have been able to reproduce peculiar features of the intensity as well as the Doppler shift of the plasma lines with data collected with the EISCAT VHF radar. Especially, two sharp peaks in the supra-thermal distribution were identified as the signature of photo-ionisation of N2and Oand were observed in the measured data. The effect of the temperature gradient—which produces a decisive correction to the Doppler shift of the plasma lines—was taken into accountmore accurately than previously by numerical evaluation of the singular integrals rather than by the use of the first terms of a series expansion as done in other studies. This is important because it has allowed a model for the first time to reproduce accurately the intensity and the Doppler shift of the plasma line as measured by actual experiment.

URI:

http://hdl.handle.net/10037/2976

File(s) in this item: 6

article_1.pdf (505.2Kb)

article_2.pdf (1.308Mb)

article_3.pdf (126.7Kb)

article_4.pdf (1.779Mb)

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Interactive Visualization on High-Resolution Tiled Display Walls with Network Accessible Compute- and Display-Resources

Hagen, Tor-Magne Stien (Doctoral thesis; Doktorgradsavhandling, 26-Sep-2011)

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Abstract:	The vast volume of scientific data produced today requires tools that can enable scientists to explore large amounts of data to extract meaningful information. One such tool is interactive visualization. The amount of data that can be simultaneously visualized on a computer display is proportional to the display’s resolution. While computer systems in general have seen a remarkable increase in performance the last decades, display resolution has not evolved at the same rate. Increased resolution can be provided by tiling several displays in a grid. A system comprised of multiple displays tiled in such a grid is referred to as a display wall. Display walls provide orders of magnitude more resolution than typical desktop displays, and can provide insight into problems not possible to visualize on desktop displays. However, their distributed and parallel architecture creates several challenges for designing systems that can support interactive visualization. One challenge is compatibility issues with existing software designed for personal desktop computers. Another set of challenges include identifying characteristics of visualization systems that can: (i) Maintain synchronous state and display-output when executed over multiple display nodes; (ii) scale to multiple display nodes without being limited by shared interconnect bottlenecks; (iii) utilize additional computational resources such as desktop computers, clusters and supercomputers for workload distribution; and (iv) use data from local and remote compute- and data-resources with interactive performance. This dissertation presents Network Accessible Compute (NAC) resources and Network Accessible Display (NAD) resources for interactive visualization of data on displays ranging from laptops to high-resolution tiled display walls. A NAD is a display having functionality that enables usage over a network connection. A NAC is a computational resource that can produce content for network accessible displays. A system consisting of NACs and NADs is either push-based (NACs provide NADs with content) or pull-based (NADs request content from NACs). To attack the compatibility challenge, a push-based system was developed. The system enables several simultaneous users to mirror multiple regions from the desktop of their computers (NACs) onto nearby NADs (among others a 22 megapixel display wall) without requiring usage of separate DVI/VGA cables, permanent installation of third party software or opening firewall ports. The system has lower performance than that of a DVI/VGA cable approach, but increases flexibility such as the possibility to share network accessible displays from multiple computers. At a resolution of 800 by 600 pixels, the system can mirror dynamic content between a NAC and a NAD at 38.6 frames per second (FPS). At 1600x1200 pixels, the refresh rate is 12.85 FPS. The bottleneck of the system is frame buffer capturing and encoding/decoding of pixels. These two functional parts are executed in sequence, limiting the usage of additional CPU cores. By pipelining and executing these parts on separate CPU cores, higher frame rates can be expected and by a factor of two in the best case. To attack all presented challenges, a pull-based system, WallScope, was developed. WallScope enables interactive visualization of local and remote data sets on high-resolution tiled display walls. The WallScope architecture comprises a compute-side and a display-side. The compute-side comprises a set of static and dynamic NACs. Static NACs are considered permanent to the system once added. This type of NAC typically has strict underlying security and access policies. Examples of such NACs are clusters, grids and supercomputers. Dynamic NACs are compute resources that can register on-the-fly to become compute nodes in the system. Examples of this type of NAC are laptops and desktop computers. The display-side comprises of a set of NADs and a data set containing data customized for the particular application domain of the NADs. NADs are based on a sort-first rendering approach where a visualization client is executed on each display-node. The state of these visualization clients is provided by a separate state server, enabling central control of load and refresh-rate. Based on the state received from the state server, the visualization clients request content from the data set. The data set is live in that it translates these requests into compute messages and forwards them to available NACs. Results of the computations are returned to the NADs for the final rendering. The live data set is close to the NADs, both in terms of bandwidth and latency, to enable interactive visualization. WallScope can visualize the Earth, gigapixel images, and other data available through the live data set. When visualizing the Earth on a 28-node display wall by combining the Blue Marble data set with the Landsat data set using a set of static NACs, the bottleneck of WallScope is the computation involved in combining the data sets. However, the time used to combine data sets on the NACs decreases by a factor of 23 when going from 1 to 26 compute nodes. The display-side can decode 414.2 megapixels of images per second (19 frames per second) when visualizing the Earth. The decoding process is multi-threaded and higher frame rates are expected using multi-core CPUs. WallScope can rasterize a 350-page PDF document into 550 megapixels of image-tiles and display these image-tiles on a 28-node display wall in 74.66 seconds (PNG) and 20.66 seconds (JPG) using a single quad-core desktop computer as a dynamic NAC. This time is reduced to 4.20 seconds (PNG) and 2.40 seconds (JPG) using 28 quad-core NACs. This shows that the application output from personal desktop computers can be decoupled from the resolution of the local desktop and display for usage on high-resolution tiled display walls. It also shows that the performance can be increased by adding computational resources giving a resulting speedup of 17.77 (PNG) and 8.59 (JPG) using 28 compute nodes. Three principles are formulated based on the concepts and systems researched and developed: (i) Establishing the end-to-end principle through customization, is a principle stating that the setup and interaction between a display-side and a compute-side in a visualization context can be performed by customizing one or both sides; (ii) Personal Computer (PC) – Personal Compute Resource (PCR) duality states that a user’s computer is both a PC and a PCR, implying that desktop applications can be utilized locally using attached interaction devices and display(s), or remotely by other visualization systems for domain specific production of data based on a user’s personal desktop install; and (iii) domain specific best-effort synchronization stating that for distributed visualization systems running on tiled display walls, state handling can be performed using a best-effort synchronization approach, where visualization clients eventually will get the correct state after a given period of time. Compared to state-of-the-art systems presented in the literature, the contributions of this dissertation enable utilization of a broader range of compute resources from a display wall, while at the same time providing better control over where to provide functionality and where to distribute workload between compute-nodes and display-nodes in a visualization context.
Description:	Papers number 2-7 and appendix B and C of this thesis are not available in Munin: 2. Hagen, T-M.S., Johnsen, E.S., Stødle, D., Bjorndalen, J.M. and Anshus, O.: 'Liberating the Desktop', First International Conference on Advances in Computer-Human Interaction (2008), pp 89-94. Available at http://dx.doi.org/10.1109/ACHI.2008.20 3. Tor-Magne Stien Hagen, Oleg Jakobsen, Phuong Hoai Ha, and Otto J. Anshus: 'Comparing the Performance of Multiple Single-Cores versus a Single Multi-Core' (manuscript) 4. Tor-Magne Stien Hagen, Phuong Hoai Ha, and Otto J. Anshus: 'Experimental Fault-Tolerant Synchronization for Reliable Computation on Graphics Processors' (manuscript) 5. Tor-Magne Stien Hagen, Daniel Stødle and Otto J. Anshus: 'On-Demand High-Performance Visualization of Spatial Data on High-Resolution Tiled Display Walls', Proceedings of the International Conference on Imaging Theory and Applications and International Conference on Information Visualization Theory and Applications (2010), pages 112-119. Available at http://dx.doi.org/10.5220/0002849601120119 6. Bård Fjukstad, Tor-Magne Stien Hagen, Daniel Stødle, Phuong Hoai Ha, John Markus Bjørndalen and Otto Anshus: 'Interactive Weather Simulation and Visualization on a Display Wall with Many-Core Compute Nodes', Para 2010 – State of the Art in Scientific and Parallel Computing. Available at http://vefir.hi.is/para10/extab/para10-paper-60 7. Tor-Magne Stien Hagen, Daniel Stødle, John Markus Bjørndalen, and Otto Anshus: 'A Step towards Making Local and Remote Desktop Applications Interoperable with High-Resolution Tiled Display Walls', Lecture Notes in Computer Science (2011), Volume 6723/2011, 194-207. Available at http://dx.doi.org/10.1007/978-3-642-21387-8_15
URI:	http://hdl.handle.net/10037/3672

File(s) in this item: 2

paper_1.pdf (2.029Mb)

thesis.pdf (8.025Mb)

Quality of service aware binding in open systems

Hanssen, Øyvind (Doctoral thesis; Doktorgradsavhandling, 07-Feb-2008)

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Abstract:	This thesis addresses negotiation of bindings in QoS aware open systems and in particular how to characterize possible contracts, requirements and capabilities of heterogeneous environments. Our approach is (1) to use trading of policies as the principle for negotiation and (2) the use of declared or rule-based conformance for QoS statements to be used in negotiation and (3) a middleware binding framework supporting negotiable bindings. A policy is an architectural entity which encapsulates a potential QoS contract plus a resource and implementation configuration to enforce the contract. The contract part (profile) consists of an obligation to be matched with requirements and an expectation to be matched with descriptions of the environment. A policy may encapsulate how implementation components and properties of environments are combined to achieve a QoS level. Policy trading is the proposed principle for negotiation. Potential contracts may be orthogonal to interfaces and interface types, and are associated with some trading service. Negotiation is essentially to collect requirements and environment descriptions from participants and match these with policies. We investigate an approach to contract matching based on declared conformance. An important contribution is the development of a declarative expression language for profiles, requirement and environment descriptions used in negotiation at run-time. We propose to define conformance as rule bases. Such rule bases can be compiled to efficient conformance checking code. We propose two composition operators to combine expressions at run-time and develop the foundations of a generic conformance checking algorithm for profile expressions. A prototype binding framework is developed, supporting activation of bindings, pluggable binder and activator components. The framework is extended to support negotiation using policy trading and profile expressions. The approach is validated by examples and proof of concept implementations. A profile model compiler, a policy trader and the binding framework are implemented and applied to example applications.
Description:	The trial lecture of the thesis defence is available in Munin at http://hdl.handle.net/10037/2840.
URI:	http://hdl.handle.net/10037/1350

File(s) in this item: 2

appendix.pdf (5.377Mb)

thesis.pdf (1.284Mb)

Ice Shelf - Ocean Interaction in the Eastern Weddell Sea, Antarctica

Hattermann, Tore (Doctoral thesis; Doktorgradsavhandling, 10-Dec-2012)

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Abstract:	This thesis investigates the interaction of the Antarctic ice shelves along the coast of Dronning Maud Land with the ocean circulation in the Eastern Weddell Sea. A set of direct oceanic observations below the Fimbul Ice Shelf, which were acquired during three Antarctic field seasons in the austral summers 2009/10, 2010/11 and 2011/12, is a central element of the presented work. This new oceanographic dataset is complemented by a high-resolution state-of-the-art ice shelf - ocean circulation model. The results provide an estimate of the amount of basal melting at the Fimbul Ice Shelf, and revise the physical processes that determine the ocean heat fluxes over the East Antarctic continental slope. A major finding is that deep-ocean heat fluxes towards the ice are much more constrained than predicted by previous ocean models, causing substantially lower rates of basal melting than earlier suggested. The predicted basal melting is consistent with mass balance estimates from satellite data and implicates that the Fimbul Ice Shelf is currently not subject to rapid basal mass loss. Furthermore, the complex interplay of the processes within the coastal, frontal system, and their respective role in transporting heat for melting towards the ice is examined. The results emphasize the importance of oceanic eddies within the coastal circulation for controlling the inflow of Warm Deep Water into the ice shelf cavities. A realistic representation of the effect of the mesoscale eddy overturning is thus a crucial requirement in order to simulate basal melting along the Weddell Sea coast in the present and future climate. The results also imply that fresh, and solar-heated Antarctic Surface Water plays a central role for the ice shelf cavity exchange. Being produced by sea ice melting at the ocean surface, this water mass directly enters the cavity and increases the melting of shallow ice. Due to its buoyancy, the presence of Antarctic Surface Water also alters the coastal dynamics and regulates the inflow of warm water at depth, thus showing that a more detailed understanding of the role of this water mass for basal melting around Antarctica will need further attention. Finally, the results suggest a direct relationship between the simulated basal melting and only a few deterministic parameters of the coastal circulation, which is used to derive a simple parameterization of for basal melting at the Fimbul Ice Shelf.
Description:	Papers 3 and 4 are not available in Munin: 3. T. Hattermann, L. H. Smedsrud, O. A. Nøst, J. M. Lilly, and B. Galton-Fenzi: 'Modeling basal melting below the Fimbul Ice Shelf, Antarctica' (manuscript) 4. Q. Zhou, T. Hattermann and O. A. Nøst: 'Wind-driven spreading of fresh Antarctica Surface Water below ice shelves in the Eastern Weddell Sea' (manuscript)
URI:	http://hdl.handle.net/10037/5147

File(s) in this item: 3

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Changing circumstances : implications for trophic dynamics and species conservation in the Fennoscandian tundra

Henden, John-André (Doctoral thesis; Doktorgradsavhandling, 16-Mar-2009)

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Abstract:	A special case of population fluctuation is multi-annual population cycles. While such population cycles exist in several ecosystems, they are more prominent in northern (e.g.tundra) ecosystems, especially among key stone herbivore species. These herbivores providean important ecosystem function in the sense of pulsed flows of resources (i.e. for predators) and disturbances (i.e. for vegetation) throughout the ecosystem. However, the circumstances on the tundra are changing. For instance, large scale collapse of population cycles of many herbivors has been reported, as well as northward expansion of novel predators (e.g. red fox). These changes, heavily connected to climate changes, are capable of disrupting the function and structure of such systems. Overall this thesis aims to outline and evaluate the recent dramatic changes in multi-annual population cycles of many herbivores and the possible implications of such changes on the trophic dynamics and species conservation in the Fennoscandinavian tundra ecosystem. First I show that the recent collapse of multi-annual population cyclles are now a widespread phenomenon, extending several species and ecosystem barriers. Next I show, based on long time series of fox bounty data, that these recent changes have some historical analogies. Specifically, I show that the highly publicized patterns (e.g. geographic gradients, large scale synchrony) in Fennoscandian small rodent cycle have been buject to large spatio-temporal trensitions in their patterns, being highly non-stationary. I also demonstrate that collapse of cycles similar to the recent events, though on a smaller spatial extent, have occurred earlier and that these incidents seem to concur with shifts between cold and warm climatic periods. Then I demonstrate wich aspects of the recent changes in the dynamics of key prey species is likely to heavily affect the viability and existence of tundra predatirs strongly adapted to the pulsed flow of resources provided bycyclically fluctuating prey populations. Furthermore, the effect of recent and future projections of climate change may facilitate the establishment of novel predator species, which may act as dominant competitors for native species for habitat and prey. I here show that increased competition with red fox may be detrimental to arctic fox viability, especially if subsidies (e.g. reindeer carcasses) are available to the dominant competitor. Finally, I show that attempts to conserve native predators, such as the arctic fox, should take into account the factors that govern their demography and thus population dynamics. I show thet the effect of management action is highly dependent onthe phase of the demographic cycle of arctic fox. This means that management intervantion should be continous, but most focused to moments in time where the effect is expected to be most pronounced.
Description:	Papers number 1,2 and 3 of the thesis are not available in Munin due to publishers' restrictions. 1.Rolf A. Ims, John-André Henden, Siw T. Killengreen.: "Collapsing population cycles." Trends in Ecology & Evolution; 23(2): 79-86 (Science Direct). Available at http://dx.doi.org/10.1016/j.tree.2007.10.010 2.John-André Henden, Rolf A. Ims, Nigel G. Yoccoz.: "Nonstationary spatio-temporal small rodent dynamics: evidence from long-term Norwegian fox bounty data." Journal of Animal Ecology; 78(3): 636-645 (Wiley). Available at http://dx.doi.org/10.1111/j.1365-2656.2008.01510.x 3.John-André Henden , Bård-Jørgen Bårdsen, Nigel G. Yoccoz, Rolf A. Ims.: " Impacts of differential prey dynamics on the potential recovery of endangered arctic fox populations." Journal of Applied Ecology Journal of Applied Ecology; 45(4): 1086-1093 (Wiley). Available at http://dx.doi.org/10.1111/j.1365-2664.2008.01515.x
URI:	http://hdl.handle.net/10037/2585

File(s) in this item: 3

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thesis.pdf (5.725Mb)

Scale-space methodology applied to spectral feature detection, multinormality testing and the k-sample problem, and wavelet variance analysis

Hindberg, Kristian (Doctoral thesis; Doktorgradsavhandling, 23-Mar-2012)

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Abstract:	The number of scale-space statistical algorithms has been greatly increased over the last 15 years. The concept originated from computer vision, introduced in Lindeberg (1994). The seminal paper by Chaudhuri and Marron (1999) brought the scale-space concept into smoothing of curves and kernel density estimation through the SiZer tool. By using all relevant smoothing bandwidths, i.e., the scale part, SiZer allows the user to look for interesting features in the smoothed curves or density estimates simultaneously on all bandwidths. In the years following, a number of classical statistical problems were also included in the family of scale-space algorithms. In this thesis, new scale-space algorithms for four such classical statistical problems are suggested. Paper II presents two closely related problems, addressed with highly similar approaches. Paper I addresses spectral scale-space analysis. Peaks found in the estimated spectral density function of evenly sampled stationary signals are typically of great interest for scientists. A peak found at a given frequency translates to potential (hidden) periodicities in a data set. Therefore, algorithms to determine which spectral peaks that really are significant are important in real-world applications. The presented algorithm uses the infamous periodogram, for reasons explained later. The different Fourier frequencies are the space part of the algorithm, while the scale part is introduced through a smoothing parameter of an assumed prior distribution. By using the Integrated Nested Laplace Approximation, a full posterior distribution can be constructed, from which the needed p-values are found. Unlike Papers I and III, Paper II presents a scale-space approach without introducing a prior distribution. Through two similar algorithms, two different questions are addressed: 1) Can a multivariate data set be considered to originate from some unspecified multivariate Gaussian distribution? 2) Can k multivariate data sets be considered to originate from some unspecified multivariate distribution? The scale part of both algorithms is connected to a weighted summation across neighboring dimensions. The number of dimensions that are summed across is given by the scale parameter. The space parameter is connected to the time or location index of the data series. The algorithms do not need to invert estimated covariance matrices, thereby they can handle the High Dimension Low Sample Size case, where most comparable methods fail. Paper III brings the scale-space concept into long-range dependence and wavelet analysis. The basis of this third paper is the wavelet coefficients resulting from linear filtering of the data with localized wavelet filters of increasing widths. The variance of these coefficients forms the wavelet variance. The space part is connected to the different wavelet filters/scales. As in Paper I, the scale part is connected to the smoothing parameter of the prior distribution. The degree of long-range dependence is fully characterized by the Hurst parameter. This parameter can be estimated through linear regression of the natural logarithm of the wavelet variance. Determining for which scales this regression should be done is not trivial, an issue which the presented algorithm addresses. A time-divided/local wavelet analysis for detecting non-stationarities in the data is also presented in Paper III.
Description:	The papers of this thesis are not available in Munin: 1. Sigrunn H. Sørbye, Kristian Hindberg, Lena R. Olsen and Håvard Rue: 'Bayesian multiscale feature detection of log-spectral densities', Computational Statistics and Data Analysis (2009), vol. 53, num. 11, pp. 3746-3754. Available at http://dx.doi.org/10.1016/j.csda.2009.03.020 2. Kristian Hindberg, Jan Hannig and Fred Godtliebsen: 'A novel scale-space approach for multinormality testing and the k-sample problem' (manuscript submitted to Computational Statistics and Data Analysis) 3. Kristian Hindberg, Donald B. Percival, Tor Arne Øigård, Stilian A. Stoev, Fred Godtliebsen and Murad S. Taqqu: 'A scale-space wavelet visualization tool for exploring non-stationarities in long-range dependent time series', (manuscript)
URI:	http://hdl.handle.net/10037/4324

File(s) in this item: 1

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Practical Fault-Tolerance for Mobile Agents

Jacobsen, Kjetil (Doctoral thesis; Doktorgradsavhandling, 18-Oct-2011)

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Abstract:	The amount of computational resources available on the Internet is increasing. Effectively using these resources for distributed computations is challenging. An infrastructure called computational grids provides tools for structuring and deploying large-scale distributed computations on the Internet. One of the key problems in computational grids is managing the available computational resources; tools based on mobile agents are being advocated to solve this problem. However, to be widely adopted, such tools must be robust towards failures in the grid environment, and thus require effective mechanisms for mobile agent fault-tolerance. To gain insight on how grid applications perform on the Internet, this dissertation investigates two master-worker algorithms, one based on group communication and one based on message flooding. Both algorithms are executed in simulations using Internet communication traces. The results from running and evaluating the algorithms are used to infer requirements for our mobile agent fault-tolerance approach. This dissertation then derives a fault-tolerant mobile agent protocol. The protocol is rooted in the primary-backup approach, where a set of backups monitor the progress of the mobile agent during the computation. The protocol allows the set of backups to be changed during the computation to adapt to the current network topology. The dissertation then describes an implementation of our protocol on top of a mobile agent platform, and evaluates the performance of the protocol. The results show that explicit management of backups can be beneficial to performance, and that our protocol is applicable outside the scope of mobile agent computations.
Description:	The papers of this thesis are not available in Munin due to publishers' restrictions: 1. Kjetil Jacobsen and Dag Johansen: 'Ubiquitous devices united : enabling distributed computing through mobile code', In Proceedings of the 1999 ACM Symposium on Applied Computing (ACM SAC 1999), pages 399–404. Available at http://dx.doi.org/10.1145/298151.298395 2. Dag Johansen, Keith Marzullo, Fred B. Schneider, Kjetil Jacobsen and Dmitrii Zagorodnov: 'NAP : Practical Fault-Tolerance for Itinerant Computations', In Proceedings of the 19th IEEE International Conference on Distributed Computing Systems (ICDCS,1999), pages 180–189. Available at http://dx.doi.org/10.1109/ICDCS.1999.776519 3. Kjetil Jacobsen, Xianan Zhang and Keith Marzullo: 'Group membership and wide-area master-worker computations', In Proceedings of the 23rd IEEE International Conference on Distributed Computing Systems (ICDCS 2003), pages 570–579. Available at http://dx.doi.org/10.1109/ICDCS.2003.1203508
URI:	http://hdl.handle.net/10037/3661

File(s) in this item: 1

thesis.pdf (1.684Mb)

Benthic foraminifera in an Arctic fjord : recent distribution and fauna of the last two millennia

Jernas, Patrycja Ewa (Doctoral thesis; Doktorgradsavhandling, 13-Sep-2012)

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Abstract:	The main objective of the PhD study was to improve the knowledge about the ecology of the benthic foraminiferal faunas thus increasing the precision of benthic foraminifera as indicators for modern and past Arctic fjord and shelf environments. The investigation of living (stained) benthic foraminifera assemblages in Kongsfjorden (western Svalbard) was performed on inter-annual and seasonal time scale. The fauna was subsequently compared to the environmental conditions including e.g. hydrology, primary productivity as well as the sediment structure, oxygen profiling, pore-water chemistry, in order to identify the driving forces leading to faunal variations. The newly gained knowledge on benthic foraminifera ecology was applied to interpret paleoceanographic changes the past 2000 years recorded in the two marine sediment cores from the Kongsfjorden and Hinlopen Troughs (northern Svalbard). The results show that living benthic foraminiferal faunas in Kongsfjorden are mainly controlled by the food supply from pelagic production which is closely related to the timing and amount of Atlantic Water (AW) inflow in addition to the release of suspended matter from the surrounding glaciers. The strongest response to the high seasonal productivity and related summer intrusions of AW is shown by dominant Nonionellina labradorica. Further, the study shows that benthic foraminifera inhabiting the micro-environments prefer to live in proximity to the bio-irrigation system (burrows, tubes), what allows them to use more extensively the oxygen and labile organic matter storage. The two paleorecords show a distinct faunal signal from AD 1200-1500 attributed to the development of highly productive oceanographic fronts between the Arctic and Atlantic water masses. This period is followed by more severe conditions from AD 1500-1900 corresponding to the Little Ice Age. The observed long term trends indicate the overall gradual reduction in glacial influence and a possible oceanographic warming of the NW Svalbard shelf over the last two millennia.
Description:	The papers of this thesis are not available in Munin: 1. Jernas, P., Klitgaard-Kristensen, D., Husum, K., Koç, N., Tverberg, V., Loubere, P., Prins, M and Dijkstra, N.: 'Response of modern Arctic benthic foraminiferal fauna to annual environmental changes; evidence from Kongsfjorden, Svalbard (forthcoming in Marine Micropaleontology). 2. Jernas, P., Klitgaard-Kristensen, D., Husum, K., Wilson, L. and Koç, N.: 'Paleoenvironmental changes of the last two millennia on the western and northern Svalbard shelf' (forthcoming in Boreas). 3. Jernas, P., Husum K., Klitgaard-Kristensen D., Forwick, M. and Koç, N.: 'Seasonal composition of recent benthic foraminifera in surface sediments of Kongsfjorden, Svalbard' (manuscript) 4. Loubere, P., Jacobson, B., Kritgaard-Kristensen, D., Husum, K., Jernas, P. and Richaud, M.: 'The structure of benthic environments and the paleochemical record of foraminifera', Deep Sea Research, Part 1: Oceanographic Research Papers (2011), vol. 58, no. 5:535-545. Available at http://dx.doi.org/10.1016/j.dsr.2011.02.011
URI:	http://hdl.handle.net/10037/4647

File(s) in this item: 1

thesis.pdf (705.7Kb)

Low-frequency noise characterization of silicon-germanium resistors and devices

Johansen, Jarle Andre (Doctoral thesis; Doktorgradsavhandling, 03-Jun-2004)

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Abstract:

The main topic of this thesis is experimental low-frequency electrical noise characterization of semiconductor devices. In particular, we concentrate on applications of the silicon-germanium alloy (SiGe). Low-frequency electrical noise is a sensitive measure of defects and non-idealities in semiconductor devices, which directly or indirectly impact device performance and reliability. Thus, it is of prime importance to be able to characterize the noise in semiconductor devices. We compare the low-frequency noise from poly-crystalline silicon-germanium thin film resistors with different germanium content, film thickness and doping level. The noise level decreases with increasing doping density. We find that the germanium content and film thickness have little influence on the noise level. The noise was found to stem from mobility fluctuations in the depletion region of the grains. We compare the low-frequency noise of silicon based field-effect transistors with poly-crystalline gates, made from silicon and silicon-germanium. The output noise level for N-MOSFETs is independent of the gate material, whereas for P-MOSFETs the silicon-germanium gate material results in lower noise. Analysis of fluctuating physical quantities, points towards mobility fluctuations for P-MOS, and number fluctuations for N-MOS. We present results from measurement of the low-frequency electrical noise in Al- GaInP QuantumWell Lasers. Experimental evidence of a connection between the noise and device reliability is found, and hence, low-frequency noise measurements can be used as a non-destructive reliability indicator for laser diodes. The low-frequency noise in state-of-the-art silicon-germanium Heterojunction Bipolar Transistors (HBTs) is explored. Device geometrical down-scaling induces a deviceto- device noise variation, caused by small sets of noise generating traps, that are different from device to device. We use proton irradiation to introduce additional traps, and find that it can reduce the noise variation without increasing the noise level significantly. Aggressive down-scaling normally results in higher low-frequency noise. However, we find that the latest generation of SiGe HBTs (> 200 GHz) breaks this trend, and only a residual background noise remains, resulting in record values of low-frequency noise level and noise corner frequency. We present, and apply, recent statistical tools to probe for non-linear coupling between frequency components in a noise signal. These tools are applied to low-frequency noise time series with Random Telegraph Signal (RTS) noise from small geometry SiGe HBTs. The noise in small HBTs is shown to be non-Gaussian and non-linear. The nonlinearity is shown to originate from the RTS component of the noise.

URI:

http://hdl.handle.net/10037/345

File(s) in this item: 1

thesis.pdf (2.912Mb)

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