Munin: Browsing Doktorgradsavhandlinger (NT-fak) by Author

Bonding in low-coordinate complexes : what, if anything, is special?

Tangen, Espen (Doctoral thesis; Doktorgradsavhandling, 14-Oct-2008)

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Abstract:	To contribute to the fundamental picture of the electronic structure of low-coordinate transition metal complexes, we have carried out a series of DFT studies on mono-imido and nitrosyl complexes for different metal ions (Mn^II/III, Fe^II/III/IV, Co^II/III) and different systems of basal ligands. These studies reveal striking similarities of the electronic structure for these systems. The distinction of bent versus linear NO units is attributed to the ranking of the dz2 and dxz/yz parentage MOs relative to each other. Without a ligand trans to the NO group, the antibonding metal dz2- NO σ orbital interaction is lessened by mixing in metal pz, causing the MO to shift away from the NO ligand. This exact same orbital interaction appears to explain the existence of middle to late first-row transition metal imido complexes.
Description:	The four papers of the thesis are not available in Munin, due to publishers' restrictions: 1. Tangen, E.; Svadberg, A.; Ghosh, A. "Toward Modeling H-NOX Domains: A DFT Study of Heme-NO Complexes as Hydrogen Bond Acceptors," Inorganic Chemistry 2005, 44, 7802-7805. (American Chemical Society) Available at http://dx.doi.org/10.1021/ic050486q 2. Tangen, E.; Conradie, J.; Ghosh, A. "The Challenge of Being Straight: Explaining the Linearity of a Low-Spin {FeNO}⁷ Unit in a Tropocoronand Complex," Inorganic Chemistry 2005, 44, 8699-8706. (American Chemical Society) Available at http://dx.doi.org/10.1021/ic050781a 3. Conradie, J.; Tangen, E.; Ghosh, A. "Trigonal bipyramidal iron(III) and manganese(III) oxo, sulfido, and selenido complexes. An electronic-structural overview," Journal of Inorganic Biochemistry 2006, 100, 707-715. (Elsevier Science) Available at http://dx.doi.org/10.1016/j.jinorgbio.2006.01.029 4. Tangen, E.; Conradie, J.; Ghosh, A. "Bonding in Low-Coordinate Environments: Electronic Structure of Pseudotetrahedral Iron-Imido Complexes," J. Chem. Theory Comput. 2007, 3, 448-457. (American Chemical Society) Available at http://dx.doi.org/10.1021/ct600318n
URI:	http://hdl.handle.net/10037/1725

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thesis.pdf (3.713Mb)

Higher-order SCF response functions in a quasi-energy formulation

Thorvaldsen, Andreas J. (Doctoral thesis; Doktorgradsavhandling, 30-Sep-2008)

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Abstract:	This thesis is concerned with computer modelling of molecules interacting with electromagnetic radiation (light, radio waves, etc.), static electric and magnetic fields (in the laboratory), as well as approximate treatments of the motions of the molecules' atomic nuclei (vibration). Compared to interactions between electrons or between electron and nucleus, these interactions are small, and well approximated by perturbation theory. Perturbation of isolated molecules in their ground state by time-dependent electromagnetic fields is known as 'response theory' (response functions), and permits study of both ground and excited states. For the 'self-consistent field' (SCF) class of electronic structure models, which includes the popular Kohn-Sham DFT models, this thesis presents a full hierachy of new formulas for response functions. Although there are several equivalent formulas for a given response function, one specific is typically preferable due to computational considerations. The derived formulas are expressed in terms of the atomic-orbital (AO) density matrix, and take into account time- and perturbation dependence of the AOs, such as magnetic-field-dependent 'London AOs' or 'gauge-including AOs', which are employed to obtain gauge-origin independent results with improved basis set convergence. The density matrix has an advantage over the more common molecular orbital (MO) parameterization in that it typically decays rapidly with the distance between atoms. For large molecules one may therefore truncate the density matrix. This can lead to great computational savings. We formulate response theory by applying perturbation theory to 'Floquet theory' (sometimes called optical Bloch equations), which is a semi-classical quantum field theory. The central quantity in Floquet theory is the 'quasi-energy', and this is therefore the 'quasi-energy formalism' of response theory. We have implemented the response function formulas in a local version of the DALTON quantum chemistry program, and demonstrate applications to the Cotton-Mouton birefringence, coherent anti-Stokes Raman scattering, electric-field-gradient induced birefringence, and to the vibrational corrections to hyperpolarizabilities.
Description:	Papers number 2,3 and 5 of the thesis are not available in Munin due to publishers' restrictions: 2. Thorvaldsen AJ, Ferrighi L, Ruud K, Ågren H, Coriani S, Jørgensen P.:"Analytic ab initio calculations of Coherent anti-Stokes Raman Scattering (CARS)." Physical Chemistry Chemical Physics 2009; 11: 2293-2304 (Royal Society of Chemistry). Available at http://dx.doi.org/10.1039/b812045e 3. Thorvaldsen AJ, Ruud K, Jaszunski M.:"Analytic calculations of vibrational hyperpolarizabilities in the atomic orbital basis."Journal of Physical Chemistry A 2009; 356(1-3): 177-186 (Elsevier) Available at http://dx.doi.org/10.1016/j.chemphys.2008.10.033 5. Shcherbin D, Thorvaldsen AJ, Ruud K, Rizzo A, Coriani S.:" Analytical calculations of nonlinear mixed electric and magnetic frequency-dependent molecular properties using London atomic orbitals: Buckingham birefringence." Physical Chemistry Chemical Physics 2009; 11: 816-825. (Royal Society of Chemistry). Available at http://dx.doi.org/10.1039/b815752a
URI:	http://hdl.handle.net/10037/2136

File(s) in this item: 3

paper_I.pdf (457.0Kb)

paper_IV.pdf (298.7Kb)

thesis.pdf (1.758Mb)

Cogset : A High-Performance MapReduce Engine

Viken Valvåg, Steffen (Doctoral thesis; Doktorgradsavhandling, 30-Jan-2012)

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Abstract:	MapReduce has become a widely employed programming model for large-scale data-intensive computations. Traditional MapReduce engines employ dynamic routing of data as a core mechanism for fault tolerance and load balancing. An alternative mechanism is static routing, which reduces the need to store temporary copies of intermediate data, but requires a tighter coupling between the components for storage and processing. The initial intuition motivating our work is that reading and writing less temporary data could improve performance, while the tight coupling of storage and processing could be leveraged to improve data locality. We therefore conjecture that a high-performance MapReduce engine can be based on static routing, while preserving the non-functional properties associated with traditional engines. To investigate this thesis, we design, implement, and experiment with Cogset, a distributed MapReduce engine that deviates considerably from the traditional design. We evaluate the performance of Cogset by comparing it to a widely used traditional MapReduce engine using a previously established benchmark. The results confirm our thesis that a high-performance MapReduce engine can be based on static routing, although analysis indicates that the reasons for Cogset's performance improvements are more subtle than expected. Through our work we develop a better understanding of static routing, its benefits and limitations, and its ramifications for a MapReduce engine. A secondary goal of our work is to explore how higher-level abstractions that are commonly built on top of MapReduce will interact with an execution engine based on static routing. Cogset is therefore designed with a generic, low-level core interface, upon which MapReduce is implemented as a relatively thin layer, as one of several supported programming interfaces. At its core, Cogset provides a few fundamental mechanisms for reliable and distributed storage of data, and parallel processing of statically partitioned data. While this dissertation mainly focuses on how these capabilities are leveraged to implement a distributed MapReduce engine, we also demonstrate how two other higher-level abstractions were built on top of Cogset. These may serve as alternative access points for data-intensive applications, and illustrate how some of the lessons learned from Cogset can be applicable in a broader context.
Description:	The papers of this thesis are not available in Munin: 1. Steffen Viken Valvåg and Dag Johansen: 'Oivos : simple and efficient distributed data processing' (2008). In Proceedings of the 2008 Tenth IEEE International Conference on High Performance Computing and Communications (HPCC 2008), pages 113– 122. IEEE Computer Society. Available at http://dx.doi.org/10.1109/HPCC.2008.105 2. Steffen Viken Valvåg and Dag Johansen: 'Update Maps : a new abstraction for High-Throughput Batch processing' (2009). In Proceedings of the 2009 IEEE International Conference on Networking, Architecture, and Storage (NAS 2009), pages 431–438. IEEE Computer Society. Available at http://dx.doi.org/10.1109/NAS.2009.73 3. Steffen Viken Valvåg and Dag Johansen: 'Cogset : a unified engine for reliable storage and parallel processing' (2009). In Proceedings of the 2009 Sixth IFIP International Conference on Network and Parallel Computing (NPC 2009), pages 174– 181. IEEE Computer Society. Available at http://dx.doi.org/10.1109/NPC.2009.23 4. Steffen Viken Valvåg, Dag Johansen, and Åge Kvalnes: 'Cogset vs. Hadoop : measurements and analysis', (2010). In Proceedings of the 2010 Second IEEE International Conference on Cloud Computing Technology and Science (CloudCom 2010), pages 768–775. IEEE Computer Society. Available at http://dx.doi.org/10.1109/CloudCom.2010.103
URI:	http://hdl.handle.net/10037/3817

File(s) in this item: 1

thesis.pdf (948.7Kb)

Behavioral and energetic response of Arctic-breeding seabirds to environmental variability.

Welcker, Jorg (Doctoral thesis; Doktorgradsavhandling, 16-Jun-2009)

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Abstract:	Knowledge about the extent to which organisms inhabitating the Arctic are able to adjust to environmental variability is essential in order to predict the impact of future climate change. In this context, the flexibility og two Acrtic-breeding seabirds, the little Auk (Alle alle) and the kittiwake (Rissa tridactyla), in foraging behavior and energy expenditure in response to environmental variability. Analysis of the foraging behavior of little auks revealed the during chick-rearing this species adopts a bimodal foraging strategy in which they alternate single foraging trips of long duration with several trips of short length. This stereotyped pattern was found to be highly flexivle and adjusted to psatial and temporal variation in foraging conditions. However, behavioral modifications led to reduced chick feeding rates and lower reproductive success, indicating the adjustments did not allow birds to fully compensate for costs incurred by unfavorable conditions. Adjustment and limitation of energy expenditure differed remarkably between the two study species. Metabolic rate in little auks was flexible and adjusted in response to variation in food availability. Birds increased energy expenditure when food was abundant. Elevated metabolism was associated with increased chick provisioning, resulting in enhanced chick surival, and increased resource allocation to self-maintenance, associated with higher body mass and a higher return rate of individuals the subsquent season. In contrast, kittiwakes did not adjust their metabolic rate in response to environmental variability. In this species, metabolic rate was similar across five study years despite large variation in foraging conditions. Instead, kittiwakes seemed to operate close to an energetic ceiling which seemed independent of extrinsic factors. This study suggested a limited ability of Arctic seabirds to compensate for large variation to environmental conditions.
Description:	Papers number 1, 2 and 3 of the thesis are not available in Munin due to publishers' restrictions. Papers 4 and 5 are manuscripts, and not available in Munin. 1. Jorg Welcker, Ann M. A. Harding, Nina J. Karnovsky, Harald Steen, Hallvard Strøm and Geir W. Gabrielsen: "Flexibility in the bimodal foraging strategy of a high Arctic alcid, the little auk Alle alle." Journal of Avian Biology 2009; 40(4): 388-399 (Wiley). Available at http://dx.doi.org/10.1111/j.1600-048X.2008.04620.x 2. Jorg Welcker, Harald Steen, Ann M. A. Harding and Geir W. Gabrielsen: "Sex-specific provisioning behaviour in a monomorphic seabird with a bimodal foraging strategy." Ibis 2009; 151(3): 502-513 (Wiley). Available at http://dx.doi.org/10.1111/j.1474-919X.2009.00931.x 3. Jorg Welcker, Ann M. A. Harding, Alexander S.Kitaysky, John R. Speakman and Geir W. Gabrielsen: "Daily energy expenditure increases in response to low nutritional stress in an Arctic-breeding seabird with no effect on mortality." Functional Ecology 2009; 23(6): 1081-1090 (Wiley). Available at http://dx.doi.org/10.1111/j.1365-2435.2009.01585.x 4. Jorg Welcker, Børge Moe, Claus Bech, Jannik Schultner, John R. Speakmana and Geir W. Gabrielsen: "Evidence for an energetic ceilinf in free-ranging kittiwakes (Rissa tridactyla)". Manuscript 5. Jannic Schultner, Jorg Welcker, John R. Speakman, Erling S. Nordøy and Geir W. Gabrielsen: "Application of the two-sample doubly-lebeled water method alters behavior and affects estimates of energy expenditure in black-legged kittiwakes". Manuscript
URI:	http://hdl.handle.net/10037/2598

File(s) in this item: 1

thesis.pdf (3.297Mb)

Arctic Ocean warmings from the last glaciation to the present : implementing and assessing the reliability of planktic foraminiferal paleoreconstructions

Zamelczyk, Katarzyna Agnieszka (Doctoral thesis; Doktorgradsavhandling, 11-May-2012)

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Abstract:	The aim of the PhD study was to use planktic foraminifera to elucidate paleoceanographic variability and the preservation state of calcium carbonate in the eastern Fram Strait throughout the last 30,000 years. Sediment cores were studied using a multiproxy approach which included analyzing planktic and benthic foraminiferal fauna distribution patterns, measurements of stable isotopes (δ18O, δ13C), grain size analysis, IRD counts, and chemical analysis of bulk sediment. In addition, mean shell weight records combined with fragmentation indices were applied. Three time periods representing important oceanographic changes in the Fram Strait were investigated with a high temporal resolution. The results show that the Atlantic water inflow governed the oceanographic development and had an important influence on the preservation state of calcium carbonate in the Fram Strait. The best preserved planktic foraminifera assemblages during the last 30,000 years were found during the Last Glaciation Maximum. Some minor dissolution events occurred during the Last Glacial Maximum as response to seasonally changing physical oceanographic parameters, sea ice formation, increased surface productivity, and melt water pulses. During the deglaciation and the Holocene, the preservation state of carbonates generally deteriorated. This trend was interrupted at 10,800-8000 BP, where the preservation of planktic foraminifera markedly improved. Changes in preservation are related to the extent and influence of the Arctic water and the marginal ice zone (MIZ) and its associated high organic productivity in the surface waters. During the last century, the preservation of small subpolar species improved. This coincided with distinctly increased sedimentation rates in the eastern and central Fram Strait. This study of planktic foraminifera preservation has shown that carbonate dissolution is a common phenomenon in the Fram Strait and should be considered in paleoreconstructions based on planktic foraminifera fauna.
Description:	The papers of this thesis are not available in Munin: 1. Zamelczyk, K., Rasmussen, T.L, Husum, K., Haflidason, H., de Vernal, A., Ravna, E.K., Hald, M. and Hillaire-Marcel, C.: 'Between two oceanic fronts : Paleoceanographic changes and calcium carbonate dissolution in the central Fram Strait during the last 20,000 years' (manuscript in revision for Quaternary Research). 2. Zamelczyk, K., Rasmussen, T.L., Husum, K. and Hald, M.: 'Marine calcium carbonate preservation vs. climate change over the last two millennia in the Fram Strait : implications for planktic foraminiferal paleostudies' (manuscript submitted to Marine Micropaleontology). 3. Zamelczyk, K., Husum, K., Rasmussen, T.L., Godtliebsen, F. and Hald, H.: 'Surface water conditions and calcium carbonate preservation in the Fram Strait during the late Weichselian 29,000-16,000 years BP', (manuscript to be submitted to Paleooceangraphy). 4. Spielhagen, R. F.,Werner, K., Aagaard-Sørensen, S., Zamelczyk, K., Kandiano,E., Budeus, G., Husum, K., Marchitto, T., and Hald, M.: 'Enhanced modern heat transfer to the Arctic by warm Atlantic Water', Science (2011), vol. 331 no. 6016:450-453. Available at http://dx.doi.org/10.1126/science.1197397 5. Werner, K., Spielhagen, R.F., Bauch, D., Hass, H.Ch., Kandiano, E. and Zamelczyk, K.: 'Atlantic Water advection to the eastern Fram Strait- Multiproxy evidence for late Holocene variability', Palaeogeography, Palaeoclimatology, Palaeoecology (2011), vol. 308 no. 3-4:264-276. Available at http://dx.doi.org/10.1016/j.palaeo.2011.05.030
URI:	http://hdl.handle.net/10037/4148

File(s) in this item: 1

thesis.pdf (948.6Kb)

Complexity in plasma and geospace systems

Živkovic, Tatjana (Doctoral thesis; Doktorgradsavhandling, 10-May-2011)

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Abstract:	The subject of this thesis is self-organization, chaos and stochastic dynamics in laboratory plasmas, the magnetosphere, and in the Earth's climate system. For each of these systems we pose the question whether the global dynamics can be described by a set of a few variables governed by the same small number of deterministic equations. This problem is not trivial, because low-dimensional deterministic systems may exhibit chaotic dynamics where the solutions are sensitive to the initial conditions, and in most respects are indistinguishable from stochastic, noise-like dynamics. A number of data analysis methods for time series are employed and adapted to the problems at hand. Among these methods are time-delay phase space reconstruction, correlation-dimension estimation of strange attractors, recurrence plots, empirical mode decomposition, wavelet decomposition, estimation of predictability and long-range memory, estimation of low-dimensional determinism of the dynamics, and principal value decomposition. The analysis is complemented by numerical simulations of simple dynamic-stochastic model systems. Some of these have solutions with known properties, some low-dimensional and chaotic, and some are realizations of well-known stochastic processes. These are used to benchmark the analysis methods. Other models are designed to provide solutions with statistical properties very similar to those of the observational signals, and hence can be considered as minimal models for the phenomenon at hand. The thesis consists of an introductory part and four journal papers. The former briefly reviews the basics of low-dimensional dynamical systems and the reconstruction of the phase-space attractor from experimental time series, long-memory stochastic processes, and critical phenomena with emphasis on self-organized critical dynamics. We also review the data analysis methods employed in this work, and finally we give an introduction to, and some examples from, the particular plasma laboratory and geospace systems which are studied in more detail in the papers. This part ends with a section where some of the analysis methods are employed to climate data. This section has been included because climate dynamics appears to be a promising field for application of these concepts and methods, although this author has not published or submittet journal papers on this application yet. Paper 1 and Paper 2 deal with the detection of low-dimensional chaotic dynamics on time scales longer than those of the turbulent plasma dynamics in the laboratory Helimak configuration, and estimation of the largest Lyapunov exponent and the fractal dimension of the phase-space attractor. These estimates give us the degree of unpredictability and indicate how many equations we need to describe the chaotic dynamics. In Paper 3 and Paper 4 we estimate the degree of predictability and the organization of a deterministic component in the global magnetosphere during magnetic storms and substorms, respectively. These are accompanied by simultaneous estimations of solar wind parameters which are known to influence magnetospheric dynamics. From these results one may draw conclusions about the causal relationship between perturbations in the solar wind and in the magnetosphere, and infer that the organization of the magnetosphere during these events are internal processes and not imposed by an organization of the solar wind.
Description:	Paper 1 in the thesis is not available in Munin: 1. T. Živković and K. Rypdal:'Evidence of low-dimensional chaos in magnetized plasma turbulence', Eur. Phys. J. Special Topics 164, 157–164 (2008). Available at http://dx.doi.org/10.1140/epjst/e2008-00841-5
URI:	http://hdl.handle.net/10037/3231

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thesis.pdf (4.529Mb)

The few touch digital diabetes diary : user-involved design of mobile self-help tools for peoplewith diabetes

Årsand, Eirik (Doctoral thesis; Doktorgradsavhandling, 10-Dec-2009)

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Abstract:	Paradoxically, the technological revolution that has created a vast health problem due to a drastic change in lifestyle also holds great potential for individuals to take better care of their own health. The first consequence is not addressed in this dissertation, but the second represents the focus of the work presented, namely utilizing ICT to support self-management of individual health challenges. As long as only 35% of the patients in Norway achieve the International Diabetes Federation‟s goal for blood glucose (HbA1c), actions and activities to improve blood glucose control and related factors are needed. The presented work focuses on the development and integration of alternative sensor systems for blood glucose and physical activity, and a fast and effortless method for recording food habits. Various user-interface concepts running on a mobile terminal constitute a digital diabetes diary, and the total concept is referred to as the “Few Touch application”. The overall aim of this PhD project is to generate knowledge about how a mobile tool can be designed for supporting lifestyle changes among people with diabetes. Applying technologies and methods from the informatics field has contributed to improved insight into this issue. Conversely, addressing the concrete use cases for people with diabetes has resulted in the achievement of ICT designs that have been appreciated by the cohorts involved. Cooperation with three different groups of patients with diabetes over several years and various methods and theories founded in computer science, medical informatics, and telemedicine have been combined in design and research on patient-oriented aids. The blood glucose Bluetooth adapter, the step counter, and the nutrition habit registration system that have been developed were all novel and to my knowledge unique designs at the time they were first tested, and this still applies to the latter two. Whether it can be claimed that the total concept presented, the Few Touch application, will increase quality of life, is up to future research and large-scale tests of the system to answer. However, results from the Type 2 diabetes half-year study showed that several of the participants did adjust their medication, food habits and/or physical activity due to use of the application.
Description:	Paper number 2, 4, 5 and 7 are not available in Munin, due to publishers' restrictions: 2. Årsand E, and Demiris G.: "User-Centered Methods for Designing Patient-Centric Self-Help Tools", Informatics for Health and Social Care, 2008 Vol. 33, No. 3, Pages 158-169 (Informa Healthcare). Available at http://dx.doi.org/10.1080/17538150802457562 4. Årsand E, Olsen OA, Varmedal R, Mortensen W, and Hartvigsen G.: "A System for Monitoring Physical Activity Data Among People with Type 2 Diabetes", pages 173-178 in S.K. Andersen, et.al. (eds.) "eHealth Beyond the Horizon - Get IT There", Proceedings of MIE2008, Studies in Health Technology and Informatics, Volume 136, May 2008, ISBN: 978-1-58603-864-9 5. Årsand E, Tufano JT, Ralston J, and Hjortdahl P.: "Designing Mobile Dietary Management Support Technologies for People with Diabetes", Journal of Telemedicine and Telecare, 2008 Volume 14, Number 7, Pp. 329-332 (Royal Society of Medicine Press). Available at http://dx.doi.org/10.1258/jtt.2008.007001 7. Årsand E, Walseth OA, Andersson N, Fernando R, Granberg O, Bellika JG, and Hartvigsen G.: "Using Blood Glucose Data as an Indicator for Epidemic Disease Outbreaks", pages 199-204 in R. Engelbrecht et.al. (eds.): "Connecting Medical Informatics and Bio-Informatics", Proceedings of MIE2005, Studies in Health Technology and Informatics, Volume 116, August 2005, ISBN: 978-1-58603-549-5. Check availability
URI:	http://hdl.handle.net/10037/2762

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