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• 20351.
Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, The Institute of Technology. Division of Sensor and Electronic Warfare, Swedish Defence Research Agency (FOI), Linköping, Sweden .
Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, The Institute of Technology. Division of Sensor and Electronic Warfare, Swedish Defence Research Agency (FOI), Linköping, Sweden . Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology. Division of Defence and Security, Systems and Technology, Swedish Defence Research Agency (FOI), Sweden. Division of Sensor and Electronic Warfare, Swedish Defence Research Agency (FOI), Linköping, Sweden . Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, The Institute of Technology.
Scattering and Polarization Properties of the Scarab Beetle Cyphochilus insulanus cuticle2015In: Applied Optics, ISSN 1559-128X, E-ISSN 2155-3165, Vol. 54, no 19Article in journal (Refereed)

Optical properties of natural photonic structures can inspire material developments in diversified areas, such as the spectral design of surfaces for camouflage. Here, reflectance, scattering, and polarization properties of the cuticle of the scarab beetle Cyphochilus insulanus are studied with spectral directional hemispherical reflectance, bidirectional reflection distribution function (BRDF) measurements, and Mueller-matrix spectroscopic ellipsometry (MMSE). At normal incidence, a reflectance (0.6–0.75) is found in the spectral range of 400–1600 nm and a weaker reflectance <0.2  in the UV range as well as for wavelengths >1600  nm  . A whiteness of 𝑊=42  is observed for mainly the elytra of the beetle. Chitin is a major constituent of the insect cuticle which is verified by the close similarity of the measured IR spectrum to that of 𝛼  -chitin. The BRDF signal shows close-to-Lambertian properties of the beetle for visible light at small angles of incidence. From the MMSE measurement it is found that the beetles appear as dielectric reflectors reflecting linearly polarized light at oblique incidence with low gloss and a low degree of polarization. The measured beetle properties are properties that can be beneficial in a camouflage material.

fulltext
• 20352.
Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, The Institute of Technology.
Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, The Institute of Technology. Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, The Institute of Technology. Dept of Sensor systems FOI Swedish Defence Research Agency. Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, The Institute of Technology.
Optical properties and switching of a rose bengal derivative studied by spectroscopic ellipsometry2008In: European Optical Society Meeting 2008, 2008, p. 34-Conference paper (Other academic)
• 20353.
Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, Faculty of Science & Engineering. Swedish Defence Research Agency (FOI), Linköping .
Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, The Institute of Technology. Linköpings universitet. Swedish Defence Research Agency (FOI), Linköping . Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, The Institute of Technology.
Optical Properties and Switching of a Rose Bengal Derivativ2009Conference paper (Refereed)
• 20354.
Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering. FOI, Linköping, Sweden.
Evaluation criteria for spectral design of camouflage2015In: Proc. SPIE 9653, Target and Background Signatures / [ed] Karin U. Stein; Ric H. M. A. Schleijpen, SPIE - International Society for Optical Engineering, 2015, Vol. 9653, p. Art.no: 9653-2-Conference paper (Refereed)

In development of visual (VIS) and infrared (IR) camouflage for signature management, the aim is the design of surface properties of an object to spectrally match or adapt to a background and thereby minimizing the contrast perceived by a threatening sensor. The so called 'ladder model" relates the requirements for task measure of effectiveness with surface structure properties through the steps signature effectiveness and object signature. It is intended to link materials properties via platform signature to military utility and vice versa. Spectral design of a surface intends to give it a desired wavelength dependent optical response to fit a specific application of interest. Six evaluation criteria were stated, with the aim to aid the process to put requirement on camouflage and for evaluation. The six criteria correspond to properties such as reflectance, gloss, emissivity, and degree of polarization as well as dynamic properties, and broadband or multispectral properties. These criteria have previously been exemplified on different kinds of materials and investigated separately. Anderson and Åkerlind further point out that the six criteria rarely were considered or described all together in one and same publication previously. The specific level of requirement of the different properties must be specified individually for each specific situation and environment to minimize the contrast between target and a background. The criteria or properties are not totally independent of one another. How they are correlated is part of the theme of this paper. However, prioritization has been made due to the limit of space. Therefore all of the interconnections between the six criteria will not be considered in the work of this report. The ladder step previous to digging into the different material composition possibilities and choice of suitable materials and structures (not covered here), includes the object signature and decision of what the spectral response should be, when intended for a specific environment. The chosen spectral response should give a low detection probability (DP). How detection probability connects to image analysis tools and implementation of the six criteria is part of this work.

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• 20355.
Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, The Institute of Technology. Department of Sensor Technology, Swedish Defense Research Agency, Linköping, Sweden.
Department of Sensor Technology, Swedish Defense Research Agency, Linköping, Sweden. Department of Sensor Technology, Swedish Defense Research Agency, Linköping, Sweden. Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, The Institute of Technology.
Spectroscopic ellipsometry and vector network analysis for determination of the electromagnetic response in two wavelength regions2008In: Physica Status Solidi. C: Current Topics in Solid State Physics, ISSN 1862-6351, Vol. 5, no 5, p. 1089-1092Article in journal (Refereed)

In this work, spectroscopic ellipsometry and vector network analysis are used to determine the electromagnetic response of three samples, an epoxy polymer, a sample with ferrit-based nanoparticles in a polymer matrix and silicon, in the wavelength ranges 0.4-30 μm and 0.75-7.59 cm. Both methods measure amplitude and phase changes due to interaction with a sample and can be used to measure the full complex-valued dielectric response to electromagnetic radiation. The data from the two methods show similar levels of the response at the two ends of the spectral gap between the ranges of the two methods.

• 20356.
Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, The Institute of Technology. FOI Swedish Defence Research Agency, Sweden.
FOI Swedish Defence Research Agency, Sweden. FOI Swedish Defence Research Agency, Sweden.
Polymer based devices with adaptable infrared reflection and transmission2006In: "Organic optoelectronics and photonics II : 3-6 April, 2006, Strasbourg, France" / [ed] Paul L. Heremans; Michele Muccini and Eric A. Meulenkamp, SPIE - International Society for Optical Engineering, 2006, Vol. 6192Conference paper (Refereed)

In the present work the infrared-transmission of PEDOT:PSS (poly(3,4-ethylenedioxythiophene):poly(styrensulfonat)) is being investigated using three different kind of electrochromic devises. PEDOT:PSS is an electrochromic conducting polymer able to change its optical properties when it is doped and undoped. The doping is achieved by a voltage applied across the cell. The optical properties are reversible if the polarity of the voltage is changed. We report here, to our knowledge, the first cell with adaptive transmission in the infrared wavelength range. The issue for this type of cell is that all the layers in the device must be transmissive in the whole relevant wavelength range. The results were further verified by construction of similar cells with different configuration giving adaptable reflectivity.

• 20357.
Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
Kommunikation i Norrköpings kommun - En fallstudie av krisen under Bråvalla Festival 20142017Independent thesis Basic level (degree of Bachelor), 10,5 credits / 16 HE creditsStudent thesis

Idag lever vi i ett digitalt samhälle där det tidvis uppdagas kriser av olika slag. På grund av att medborgare jämt och ständigt kan bevaka, sprida och dela information med varandra, har allt fler kommuner valt att arbeta med sociala medier vid kris. Denna studie syftar därför till att kartlägga hur en svensk kommun arbetar med Facebook i sitt kriskommunikationsarbete. Studien visar att en kommuns syfte med att i kristider finnas på Facebook kan vara att snabbt nå ut till intressenter med krisinformation. En kommun måste inte nödvändigtvis kommunicera med en specifikt uttalad målgrupp via kanalen utan kan istället där försöka nå så många intressenter som möjligt. Före en kris kan en kommun publicera Facebookinlägg som är av varnande och uppmanande karaktär. En kommun kan också arbeta aktivt med att förebygga kriser. Under en kris kan en kommun publicera Facebookinlägg av instruerande karaktär för att lugna intressenter. En kommun kan under en kris också försöka förhindra ryktesspridning genom att själv se till att vara aktiv och ständigt gå ut med trovärdig information. Efter en kris kan en kommun publicera Facebookinlägg för att ge så kallad övrig information till intressenter. En kommun kan också dra flera lärdomar av en avklarad kris. Ett exempel på en sådan är att sociala medier öppnar upp för så snabb kriskommunikation att de interna riktlinjerna inte alltid räcker till. Avslutningsvis finner studien flera fördelar och nackdelar med att som kommun arbeta med kriskommunikation på Facebook.

Communication before, during and after a crisis in Norrköping municipality - A case study of the crisis in Bråvalla Festival 201
• 20358.
Linköping University, Department of Computer and Information Science, Human-Centered systems.
Guided reflection in Simulator-Based Crisis Management Training: Examining the possibility to implement After Action Reviews in the CCRAAAFFFTING project2019Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis

Reflection is an important team learning activity, allowing team members to process feedback and to learn from experiences. Debriefing methods such as the After Action Review (AAR), proved to increase learning, can be used to guide teams through the process of reflection. This thesis, commissioned by the Creating Collaborative Resilience Awareness, Analysis and Action for Finance, Food and Fuel Systems in INteractive Games (CCRAAAFFFTING) project, aims to investigating how current post-exercise discussions within the CCRAAAFFFTING project support reflection and whether or not AAR could be implemented. This study used an explorative, semi-experimental research design, containing two conditions - the current post-exercise discussions (condition 1) and AAR’s (condition 2). Data was collected through observations and questionnaires. Due to issues regarding validity, data from questionnaires given to participants, as well as comparisons of participants' subjective experiences between the two conditions, could not be used to provide any support for choosing one post-exercise discussion over the other. However, observations showed that the current post-exercise discussion did not support reflection, thus, making it beneficial to implement AAR. Proper implementation of AAR could not only support team learning, but also organizational learning by facilitating the transference of knowledge back to participants home organizations. This transferred knowledge, if used right by the organizations, could help increased resilience. However, AAR cannot simply be implemented, and this thesis concludes with a list of identified recommendations.

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• 20359.
Linköping University, Department of Computer and Information Science.
Utveckling av Verktyg för generering av Stubb- och Mockobjekt för C2008Independent thesis Basic level (professional degree), 20 points / 30 hpStudent thesis

Testdriven utveckling samt användning av enhetstestning är ett växande område. Vid användning av dessa tekniker är det önskvärt att kunna använda stubb- och mockobjekt för att ersätta en DOC(Dependent on Component).

I dagsläget finns det ett verktyg hos Enea som genererar stubbar för C++-källkod. Examensarbetet består av att vidareutveckla detta verktyg i flera avseenden. Stöd för C-kod adderas till verktyget. För C-kod adderas även möjligheten att generera stubb- och mockobjekt. Testning av verktyget görs mot ett befintligt kundprojekt hos Enea med goda resultat.

FULLTEXT01
• 20360.
Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
Alternativ modell för miljöundervisning i dagens gymnasieskola - modellekosystem2011Independent thesis Advanced level (professional degree), 10 credits / 15 HE creditsStudent thesis

Studies show that today's students are worried about the future and the increasing climate change. A survey made by the Swedish National Agency for Education about environmental education shows that approximately half of the surveyed secondary school teachers are not engaged in teaching in the field. This study describes an alternative model for teaching environmental issues. Students are by the modeling of ecosystem given an opportunity to deepen their understanding of climate change associated with the exploitation of top predators. This is a realistic problem, numerous studies show that today's ecosystems are exposed to a variety of stressors, with the origin of climate change, and the exploitation of top predators can lead to serious consequences with extinction as a result. The model used in this study is a generalized Lotka-Volterra model which works as an analytical tool. The Swedish National Agency for Education emphasizes the role of mathematics as interdisciplinary tools and model ecosystem gives students the opportunity to use math skills in a real scenario. The study also investigated how much exploitation top predators can be exposed to in line with increased climate change. The research sites include three-and four-species system of marine and terrestrial environments. The results show that the exploitation must be reduced in line with increased climate-caused changes in all cases, except terrestrial three-species system exposed to changes in interaction strengths.

Exjobb-modellekosystem
• 20361.
Linköping University, Department of Computer and Information Science, PELAB - Programming Environment Laboratory. Linköping University, The Institute of Technology.
An LLVM Back-end for REPLICA: Code Generation for a Multi-core VLIWProcessor with Chaining2012Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis

REPLICA is a PRAM-NUMA hybrid architecture, with support for instructionlevel parallelism as a VLIW architecture. REPLICA can also chain instructionsso that the output from an earlier instruction can be used as input to a laterinstruction in the same execution step.

There are plans in the REPLICA project to develop a new C-based program-ming language, compilers and libraries to speed up development of parallel pro-grams. We have developed a LLVM back-end as a part of the REPLICA projectthat can be used to generate code for the REPLICA architecture. We have alsocreated a simple optimization algorithm to make better use of REPLICAs supportfor instruction level parallelism. Some changes to Clang, LLVMs front-end forC/C++/Objective-C, was also necessary so that we could use assembler in-liningin our REPLICA programs.

Using Clang to compile C-code to LLVMs internal representation and LLVMwith our REPLICA back-end to transform LLVMs internal representation intoMBTAC1 assembler.

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• 20362.
Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics.
Robust Community Predictions of Hubs in Gene Regulatory Networks2018Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis

Many diseases, such as cardiovascular diseases, cancer and diabetes, originate from several malfunctions in biological systems. The human body is regulated by a wide range of biological systems, composed of biological entities interacting in complex networks, responsible for carrying out specific functions. Some parts of the networks, such as hubs serving as master regulators, are more important for maintaining a function. To find the cause of diseases, where hubs are possible disease regulators, it is critical to know the structure of these biological systems. Such structures can be reverse engineered from high-throughput data with measured levels of biological entities. However, the complexity of biological systems makes inferring their structure a complicated task, demanding the use of computational methods, called network inference methods. Today, many network inference methods have been developed, that predicts the interactions of biological networks, with varying degree of success. In the DREAM5 challenge 35 network inference methods were evaluated on how well interactions in gene regulatory networks (GRNs) were predicted. Herein, in contrast to the DREAM5 challenge, we have evaluated network inference methods’ ability to predict hubs in GRNs. In accordance with the DREAM5 challenge, different methods performed the best on different data sets. Moreover, we discovered that network inference methods were not able to identify hubs from groups of similarly expressed genes. Also, we noticed that hubs in GRNs had a distinct expression in the data, leading to the development of a new method (the PCA method) for the prediction of hubs. Furthermore, the DREAM5 challenge showed that community predictions, combining the predictions from many network inference methods, resulted in more robust predictions of interactions. Herein, the community approach was applied on predicting hubs, with the conclusion that community predictions is the more robust approach. However, we also concluded that it was enough to combine 6-7 network inference methods to achieve robust predictions of hubs.

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• 20363.
Linköping University, Department of Physics, Chemistry and Biology.
Analys av tanniner: från granbarksextrakt2009Independent thesis Basic level (university diploma), 10 credits / 15 HE creditsStudent thesis

The objective for this master’s thesis was to test and evaluate two methods for determining the content of tannin in a pinebarkextract. The methods used at Södra for this previously have not been specific enough, only the amount of polyphenolics have been measured. One of these methods is a test based on the Stiasny test and it determines the extracts ability to form a gel with formaldehyde. When this test was carried out it showed that the extract did not contain much tannin. The other method used at Södra measures the amount of polyphenolic substances with a spectrophotometer. The result from this method showed that the content were 50 %.

One of the two new methods that were evaluated determines the amount tannin present in the extract because of tannins ability to form a complex with proteins. According to this method, the amount tannin in the extract were 42,5 %, and 19,4 % of this in the form of tannic acid. These results are credible on basis of previous information about the extract.

The other method uses a RP- HPLC where ellagic and gallic acid were used as standards. The amount ellagic acid in the extract was determined to 0,06 %, but the result from gallic acid was inconclusive. Further analysis is necessary to evaluate the obtained results and the methods reliability.

If the metods is to be used on a regular basis, my recommendation would be to start evaluating the protein-binding method because this would be easier and less time-consuming than modifying the HPLC- method. The HPLC- method could on the other hand provide useful information about the extract, not only the amount tannin could be measured, but also which kind of tannin could be investigated.

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• 20364.
Linköping University, Department of Computer and Information Science, Statistics.
Linköping University, Department of Computer and Information Science, Statistics.
Klassificering av köp på betalda sökannonser2016Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis

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• 20365.
Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
Molecular Dynamics of the Adsorption of Organic Molecules on Organic Substrates2013Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis

A great interest has been shown for self-assembled organic nano-structures that can be used in a variety of optoelectronic applications, from element detection to home electronics. It is known from experimental research that sexiphenyl (6P) grown on muscovite mica substrate form uniaxially self-assembled nanofibers which together with sexithiophene (6T) deposited on top gives the possibility to tune their polarized emission. A key to continue develop and explore the full potential of this technique is to understand the mechanisms behind the growth. This thesis investigate the initial growth of 6P and 6T on a 6P$\left(11 \bar{1} \right)$ nanofiber substrate through Molecular Dynamics (MD) simulations. The adsorption of the molecules has been simulated with Simulated Annealing (SA) where 6P align perfectly with the substrate for all coverage while 6T starts to align after a certain amount of coverage. Both molecules show a monotonic increase in the adsorption energy per molecule with an increasing coverage. The surface diffusion of the molecules has been studied and shows a higher movement for both in the direction of the longmolecular axis.

Masters Thesis Patrik Åkesson
• 20366.
Linköping University, Department of Computer and Information Science.
A Skeleton library for Cell Broadband Engine2008Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis

The Cell Broadband Engine processor is a powerful processor capable of over 220 GFLOPS. It is highly specialized and can be controlled in detail by the programmer. The Cell is significantly more complicated to program than a standard homogeneous multi core processor such as the Intel Core2 Duo and Quad. This thesis explores the possibility to abstract some of the complexities of Cell programming while maintaining high performance. The abstraction is achieved through a library of parallel skeletons implemented in the bulk synchronous parallel programming environment NestStep. The library includes constructs for user defined SIMD optimized data parallel skeletons such as map, reduce and more. The evaluation of the library includes porting of a vector based scientific computation program from sequential C code to the Cell using the library and the NestStep environment. The ported program shows good performance when compared to the sequential original code run on a high-end x86 processor. The evaluation also shows that a dot product implemented with the skeleton library is faster than the dot product in the IBM BLAS library for the Cell processor with more than two slave processors.

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• 20367.
Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, PELAB - Programming Environment Laboratory. Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, PELAB - Programming Environment Laboratory.
BlockLib: A Skeleton Library for Cell Broadband Engine2008In: Proceedings - International Conference on Software Engineering, New York, USA: ACM , 2008, p. 7-14Conference paper (Refereed)

Cell Broadband Engine is a heterogeneous multicore processor for high-performance computing and gaming. Its architecture allows for an impressive peak performance but, at the same time, makes it very hard to write efficient code. The need to simultaneously exploit SIMD instructions, coordinate parallel execution of the slave processors, overlap DMA memory traffic with computation, keep data properly aligned in memory, and explicitly manage the very small on-chip memory buffers of the slave processors, leads to very complex code. In this work, we adopt the skeleton programming approach to abstract from much of the complexity of Cell programming while maintaining high performance. The abstraction is achieved through a library of parallel generic building blocks, called BlockLib. Macro-based generative programming is used to reduce the overhead of genericity in skeleton functions and control code size expansion. We demonstrate the library usage with a parallel ODE solver application. Our experimental results show that BlockLib code achieves performance close to hand-written code and even outperforms the native IBM BLAS library in cases where several slave processors are used.

• 20368.
Linköping University, Department of Mathematics, Computational Mathematics. Linköping University, Faculty of Science & Engineering.
Department of Mechanical Engineering and Institute for Computational Mathematical Engineering, Stanford University, Stanford, California, USA. Linköping University, Department of Mathematics, Computational Mathematics. Linköping University, Faculty of Science & Engineering.

Artificial neural networks together with associated computational libraries provide a powerful framework for constructing both classification and regression algorithms. In this paper we use neural networks to design linear and non-linear discrete differential operators. We show that neural network based operators can be used to construct stable discretizations of initial boundary-value problems by ensuring that the operators satisfy a discrete analogue of integration-byparts known as summation-by-parts. Furthermore we demonstrate the benefits of building the summation-by-parts property into the network by weight restriction, rather than enforcing it through a regularizer. We conclude that, if possible, known structural elements of an operation are best implemented as innate—rather than learned—properties of the network. The strategy developed in this work also opens the door for constructing stable differential operators on general meshes.

Learning to Differentiate
• 20369.
Linköping University, Department of Mathematics, Computational Mathematics. Linköping University, Faculty of Science & Engineering.
Linköping University, Department of Mathematics, Computational Mathematics. Linköping University, Faculty of Science & Engineering.
A provably stable, non-iterative domain decomposition technique for the advection-diffusion equation2016Report (Other academic)

We describe an efficient, non-iterative domain decomposition approach for the onedimensional advection–diffusion equation based on the Summation-by-Parts technique in both time and space. A fully discrete multidomain analogue of the continuous equation is formulated and a linear system consisting only of the solution components involved in the coupling between the subdomain interfaces is isolated. Once the coupling system is solved, the full solution is found by computing linear combinations of known vectors, weighted by the coupling components. Both stability and invertibility of the discrete scheme is proved using standard Summation-by-Parts procedures.

In a numerical study we show that perfunctory implementations of monodomain Summation-by-Parts based time integration can be improved upon significantly. Using our proposed method we are able to reduce execution time and memory footprint by up to 80% and 95% respectively. Similar improvements in execution time is shown also when compared against explicit Runge–Kutta time integration.

Provably Stable, Non-iterative Domain Decomposition Technique for the Advection-Diffusion Equation
• 20370.
Linköping University, Department of Mathematics, Computational Mathematics. Linköping University, Faculty of Science & Engineering.
Linköping University, Department of Mathematics, Computational Mathematics. Linköping University, Faculty of Science & Engineering.
A Stable Domain Decomposition Technique for Advection–Diffusion Problems2018In: Journal of Scientific Computing, ISSN 0885-7474, E-ISSN 1573-7691, Vol. 77, no 2, p. 755-774Article in journal (Refereed)

The use of implicit methods for numerical time integration typically generates very large systems of equations, often too large to fit in memory. To address this it is necessary to investigate ways to reduce the sizes of the involved linear systems. We describe a domain decomposition approach for the advection–diffusion equation, based on the Summation-by-Parts technique in both time and space. The domain is partitioned into non-overlapping subdomains. A linear system consisting only of interface components is isolated by solving independent subdomain-sized problems. The full solution is then computed in terms of the interface components. The Summation-by-Parts technique provides a solid theoretical framework in which we can mimic the continuous energy method, allowing us to prove both stability and invertibility of the scheme. In a numerical study we show that single-domain implementations of Summation-by-Parts based time integration can be improved upon significantly. Using our proposed method we are able to compute solutions for grid resolutions that cannot be handled efficiently using a single-domain formulation. An order of magnitude speed-up is observed, both compared to a single-domain formulation and to explicit Runge–Kutta time integration.

fulltext
• 20371.
Linköping University, Department of Mathematics, Computational Mathematics. Linköping University, Faculty of Science & Engineering.
Linköping University, Department of Mathematics, Computational Mathematics. Linköping University, Faculty of Science & Engineering.
A stable, high order accurate and efficient hybrid method for flow calculations in complex geometries2018In: 2018 AIAA Aerospace Sciences Meeting, AIAA SciTech Forum, (AIAA 2018-1096), American Institute of Aeronautics and Astronautics, 2018, no 210059, p. 1-9Conference paper (Refereed)

The suitability of a discretization method is highly dependent on the shape of the domain. Finite difference schemes are typically efficient, but struggle with complex geometry, while finite element methods are expensive but well suited for complex geometries. In this paper we propose a provably stable hybrid method for a 2D advection–diffusion problem, using a class of inner product compatible projection operators to couple the non-conforming grids that arise due to varying the discretization method throughout the domain.

A stable, high order accurate and efficient hybrid method for flow calculations in complex geometries
• 20372.
Linköping University, Department of Mathematics, Computational Mathematics. Linköping University, Faculty of Science & Engineering.
Linköping University, Department of Mathematics, Computational Mathematics. Linköping University, Faculty of Science & Engineering.
Encapsulated high order difference operators on curvilinear non-conforming grids2019In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 385, p. 209-224Article in journal (Refereed)

Constructing stable difference schemes on complex geometries is an arduous task. Even fairly simple partial differential equations end up very convoluted in their discretized form, making them difficult to implement and manage. Spatial discretizations using so called summation-by-parts operators have mitigated this issue to some extent, particularly on rectangular domains, making it possible to formulate stable discretizations in a compact and understandable manner. However, the simplicity of these formulations is lost for curvilinear grids, where the standard procedure is to transform the grid to a rectangular one, and change the structure of the original equation. In this paper we reinterpret the grid transformation as a transformation of the summation-by-parts operators. This results in operators acting directly on the curvilinear grid. Together with previous developments in the field of nonconforming grid couplings we can formulate simple, implementable, and provably stable schemes on general nonconforming curvilinear grids. The theory is applicable to methods on summation-by-parts form, including finite differences, discontinuous Galerkin spectral element, finite volume, and flux reconstruction methods. Time dependent advection–diffusion simulations corroborate the theoretical development.

The full text will be freely available from 2021-02-26 12:23
• 20373.
Linköping University, Department of Physics, Chemistry and Biology.
Klimatinducerade fenologiförändringar och dess effekter i näringsväven2011Independent thesis Basic level (degree of Bachelor), 10,5 credits / 16 HE creditsStudent thesis

The climate affects animal populations through several processes. These processes includereproduction, phenology and the success of hunting. By influencing the phenology of species theclimate also affects the way species interact. If a climate-induced phenology change promotes abasal species to bud earlier in the spring for example, this will affect the links to other species inthe food web due to a time lag in the tropic levels above. This dependence, that a predator has tobeing synchronous to its prey, is called the match/mismatch hypothesis (MMH). Studies haveindicated that species higher up in the food web adapt slower than species lower in the food webwith shorter generation times (which creates a temporal mismatch).A climate-induced phenology change in basal species could therefore be expected to affect thedensities and extinction rates of species higher up in the food web.In this study a declining conversion efficiency for predators was used to model the effects ofclimate change on triangular food webs with three trophic levels. This was done by using ageneralized Lotka-Volterra model. The results indicate that, in a food web with three trophiclevels, the densities of herbivores and carnivores drops in response to an increased change ofclimate. The extinction rates of carnivores also increase rapidly in response to an increasedclimate change.

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• 20374.
Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
Univ Exeter Penryn Campus, England. Oviedo Univ Campus Mieres, Spain. Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering. Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
Conditions for successful range shifts under climate change: The role of species dispersal and landscape configuration2018In: Diversity & distributions: A journal of biological invasions and biodiversity, ISSN 1366-9516, E-ISSN 1472-4642, Vol. 24, no 11, p. 1598-1611Article in journal (Refereed)

Aim: Ongoing climate change is currently modifying the geographical location of areas that are climatically suitable for species. Understanding a species ability to successfully shift its geographical range would allow us to assess extinction risks and predict future community compositions. We investigate how habitat configuration impedes or promotes climate-driven range shifts, given different speeds of climate change and dispersal abilities. Location: Theoretical, but illustrated with European examples. Methods: We model how a species ability to track a directional shift in climatic conditions is affected by (a) species dispersal abilities; (b) speed of climatic shift; and (c) spatial arrangement of the habitat. Our modelling framework includes within-and between-patch population dynamics and uses ecologically realistic habitat distributions and dispersal scenarios (verified with data from a set of European mammal species) and, as such, is an improvement of classical range shift models. Result: In landscapes with a homogeneous distribution of suitable habitats, all but the least dispersive species will be able to range shift. However, species with high dispersal ability will have lower population densities after range shift. In heterogeneous landscapes species ability to range shift is far more variable and heavily dependent on the habitat configuration. This means that landscape configuration in combination with the speed of climate change and species dispersal abilities give rise to nonlinear effects on population sizes and survival after a climatic shift. Main conclusions: Our analyses point out the importance of accounting for the interplay of species dispersal and the landscape configuration when estimating future climate impact on species. These results link ecologically important attributes of both species and their landscapes to outcomes of species range shift, and thereby long-term persistence of ecological communities.

• 20375.
Linköping University, The Tema Institute, The Department of Gender Studies.
Hultman, MartinLinköping University, The Tema Institute, Technology and Social Change.Lee, FrancisLinköping University, The Tema Institute, Technology and Social Change.
Posthumanistiska nyckelstexter2012Collection (editor) (Refereed)

Den här boken introducerar några viktiga författare på samtidsaktuella teoriområden. Donna Haraway, Karen Barad, Rosi Braidotti, Michel Callon, Gilles Deleuze, Félix Guattari, Michel Serres och Annemarie Mol presenteras i boken, som också innehåller översatta texter av dessa namn. Boken ger en bakgrund till och en överblick över ett område i intensiv teoriutveckling. Här presenteras den så kallade materiella, posthumana eller ontologiska vändningen. Här kartläggs grunderna för olika posthumanistiska förhållningssätt till de både mänskliga och icke-mänskliga (djur, miljö, teknik) krafterna i vår värld så som de begreppsliggjorts inom filosofi, feministisk teori, kulturstudier och samhällsvetenskapliga studier av naturvetenskap, medicin och teknik. Genom lästips och en omfattande litteraturlista öppnar boken för fortsatta studier och vidare diskussioner. Avslutningsvis finns också en omfattande ordlista med viktiga nyckelbegrepp som i sig ger en introduktion till ett heterogent forskningsfält. Boken riktar sig till studenter, doktorander och andra nyfikna forskare inom olika tvärvetenskapliga eller disciplinära former av humaniora och samhällsvetenskap.

POSTHUMANISTISKA NYCKELTEXTER ger i de inledande kapitlen en överblick och en introduktion till posthumanistiska studier och till materiell-semiotik. Här behandlas tankeströmningar som rör det humanas natur, humanismens etik och humanvetenskapernas framtid. Boken ger en introduktion till det som inom genusvetenskap och tekniksociologi kommit att kallas den ontologiska vändningen mot de materiaaliteter och världsliga relationer som både gör och förgör oss. Här kartläggs grunderna för posthumanistiska förhållningssätt till de både mänskliga och icke-mänskliga (djur, miljö, teknik) dimensionerna av vår värld så som de begreppsliggjorts inom filosofi, feministisk teori, kulturstudier och sociala studier av vetenskap och teknik.

POSTHUMANISTISKA NYCKELTEXTER erbjuder introduktioner till viktiga författare och översättningar av nyckeltexter skrivna av Donna Haraway, Karen Barad, Rosi Braidotti, Michel Callon, Gilles Deleuze med Felix Guattari, Michel Serres och Annemarie Mol. Boken innehåller även en omfattande ordlista med viktiga nyckelbegrepp som i sig ger en introduktion till ett mångfaldigt forskningsfält.

• 20376.
Linköping University, Department of Computer and Information Science.
Jämförelse av Oracle och MySQL med fokus på användning i laborationer för universitetsutbildning2008Independent thesis Basic level (professional degree), 10 points / 15 hpStudent thesis

Syftet med arbetet som beskrivs i denna rapport var att undersöka om den Oracle-baserade laborationsmiljö som användes hos ADIT gick att överföra till MySQL. Oracle är ett komplext system som är krävande att administrera, något som ADIT ansvarat för med egen personal och egen hårdvara och detta var inte idealiskt. I kombination med ett stort intresse från studenter att använda just MySQL vid laborationer hos ADIT beslutades det att man skulle undersöka om MySQL nu var moget att axla den roll som Oracle tidigare haft. Utifrån detta går rapporten igenom vad som behövde göras med det befintliga laborationsmaterialet. En introduktion till relations¬modellen och SQL samt förklaringar av skillnader i features mellan Oracle och MySQL som hade betydelse för laborationerna återfinns också. Det visade sig att överföringen var enkel att göra och sist i rapporten sammanställs våra erfarenheter.

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• 20377.
Linköping University, The Institute of Technology. Linköping University, Department of Computer and Information Science, Database and information techniques.
Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
Bioinformatics: From Disparate Web Services to Semantics and Interoperability2010In: International Journal of Advances in Software, ISSN 1942-2628, Vol. 3, no 3-4, p. 396-406Article in journal (Refereed)

In the field of bioinformatics, there exists a large number of web service providers and many competing standards regarding how data should be represented and interfaced. However, these web services are often hard to use for a non-programmer and it can be especially hard to understand how different services can be used together to create scientific workflows. In this paper we have performed a literature study to identify problems involved in developing interoperable webservices for the bioinformatics community and steps taken by other projects to address them. We have also conducted a case study by developing our own bioinformatic web service to further investigate these problems. Based on our case study we have identified a number of design issues important to consider when designing web services. The paper is concluded by discussing current approaches aimed at making web services easier to use and by presenting our own proposal of an easy-to-use solution for integrating information from web services.

• 20378.
Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, The Institute of Technology.
Hydrogels of conjugated polyelectrolytes for biosensor and biochip applications2005Doctoral thesis, comprehensive summary (Other academic)

This thesis describes the use of conjugated polyelectrolytes (CPEs) in biosensor devices. The method is based on non-covalent assembly of the biomolecule of interest and the CPE functioning as the reporter, in one case as a transducer, of biomolecular events. Devices of these assemblies on solid supports that can operate in liquid solutions have been the focus. Polythiophenes, both semiconducting and conducting, is the class of materials that has been used in this work. The semiconducting polythiophenes have ionic side chains which makes them water soluble. This ionic side chain is capable of both forming electrostatic and hydrogen bonds, and when paired with the hydrophobic backbone of the polymer a great number of interactions with biomolecules are possible. The highly conducting polythiophene derivative PEDOT -PSS, (PEDOT) doped with ionic and water soluble PSS polyelectrolyte, was used as the conducting material in 3D-electrode. Both the semiconducting and conducting polymers described above forms hydrogels on solid supports if crosslinked with the appropriate ion, biomolecule or polymer. Evaluation of the CPEs, both with and without biomolecules, was performed in liquid, solid and hydrogel state using a number of techniques. This was done to understand how the CPEs behave when exposed to different buffer systems and various biomolecules.

Hydrogels of conjugated polyelectrolytes combined with biomolecules are attractive as biosensors. The advantage with the hydrogel format is the high water content, the porous structure and the large capacity of binding molecules. High water content is important to preserve the biomolecules by providing the correct buffered environment. In this thesis we demonstrated a hydrogel of the highly conducting PEDOT -PSS polymer that was crosslinked on a solid support together with horseradish peroxidase (HRP) enzyme, forming an enzyme-enhanced electrode. Further studies of hydrogels were done using in situ quartz crystal microbalance with dissipation (QCM-D). POWT is a CPE withproperties well suited for biochip applications and readily forms hydrogels when exposed to water-based buffer solutions or biomolecule solutions. Detection ofcomplementary DNA and rejection of non-complementary DNA in a POWT hydrogel was demonstrated. The interaction between POWT and DNAoligonucleotides was also evaluated using fluorescence resonance energy transfer (FRET) in solution. Labeled DNA oligonucleotides with energy accepting or donating fluorophores allowed us to determine distance and binding stoichiometry in the non-covalent POWT-DNA complex.

Patterning and anchoring of biomolecules and non-covalent assembled CPE-biomolecule complexes to a chip surface was studied; in the adsorbed state these complexes are hydrogels. Our novel method is based on the modification of the surface energy of a hydrophilic substrate surface using hydrophobic poly(dimethylsiloxane) (PDMS) elastomer stamp containing a relief pattern. Different conformations in biomolecules could be detected using fluorescence microscopy, where the CPEs acts as reporters and the PDMS modified substrates as discriminator. Also, excellent enzyme activity in patterned CPE/Horseradish peroxidase (HRP) enzyme was shown.

Distances between the individual molecules in solid state devices of conjugated polymers can be small. In luminescence devices, such as light emitting diodes or fluorescence biosensors, there is a chance of interaction between conjugated molecules especially if more than one type of molecule is present. Quenching of the light and fluorescence energy transfer can occur and a simple approach to study this was developed.

1. Hydrogels of a conducting conjugated polymer as 3-D enzyme electrode
Open this publication in new window or tab >>Hydrogels of a conducting conjugated polymer as 3-D enzyme electrode
2003 (English)In: Biosensors & bioelectronics, ISSN 0956-5663, E-ISSN 1873-4235, Vol. 19, no 3, p. 199-207Article in journal (Refereed) Published
Abstract [en]

We have utilized the highly conducting poly(3,4-ethylenedioxythiophene)/poly(styrenesulfonate) aqueous dispersion (PEDOT/PSS) to build a conducting hydrogel matrix. Together with appropriate biomolecules this constitutes a hydrogel bio-electrode. The open hydrogel structure makes diffusion of analytes surrounding the cells into the matrix electrode easier. If enzymes are utilized, osmium is used as mediator between the prosthetic group of the enzyme and the conducting polymer matrix. Osmium also functions as a crosslink point to poly-4-vinylpyridine, which together with the magnesium crosslinked PEDOT/PSS gives a rigid hydrogel. The enzyme Horseradish peroxidase (HRP) was used as a model enzyme to evaluate the enzyme-enhanced electrode. We evaluated the electrode at pH 7, which is the pH choice for many biological systems. From cyclic voltammetry (CV) measurements we deduced that a very low reduction potential was needed to reduce the prosthetic group. Constant potential amperometry were performed to demonstrate the biosensor capabilities. A differential sensitivity of 0.13 A M−1 cm−2 through the 0–30 μM concentration range was achieved. Both the biostability and the influence on conductivity, important aspects when for example making nerve- or cell-electrodes, were investigated.

Keywords
Biomolecule electrode, Conjugated polymer, Horseradish peroxidase, Hydrogel, Osmium, PEDOT/PSS
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-46422 (URN)10.1016/S0956-5663(03)00220-3 (DOI)
Available from: 2009-10-11 Created: 2009-10-11 Last updated: 2017-12-13
2. Hydrogels from a water-soluble Zwitterionic polythiophene: dynamics under pH change and biomolecular interactions observed using quartz crystal microbalance with dissipation monitoring
Open this publication in new window or tab >>Hydrogels from a water-soluble Zwitterionic polythiophene: dynamics under pH change and biomolecular interactions observed using quartz crystal microbalance with dissipation monitoring
2005 (English)In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 21, no 16, p. 7292-7298Article in journal (Refereed) Published
Abstract [en]

The water-soluble zwitterionic polythiophene, poly(3-((S)-5-amino-5- carboxyl-3-oxapentyl)-2,5-thiophene) hydrochloride (POWT), is a conjugated polyelectrolyte (CPE) with properties well suited for biochip applications. CPEs readily form hydrogels when exposed to water-based buffer solutions or biomolecule solutions. In this work, we used in situ quartz crystal microbalance with dissipation (QCM-D) monitoring to collect information on the interaction between POWT films exposed to buffers with different pH and POWT/DNA chains. Our data show that POWT swells significantly when exposed to low-pH buffers, such as pH 4 acetate, this is seen as an increase in thickness and decrease in viscosity obtained via a Voight-based modeling of combined f and D QCM-D measurements. The magnitude of thickness and viscosity change upon changing from a pH 10 carbonate buffer to pH 4 acetate is 100% increase in thickness and 50% decrease in viscosity. The response of the hydrogel under pH change is well correlated with fluorescence data from POWT films on glass. The state of the hydrogel is important during interaction with biomolecules; illustrated by the observation that a swollen CPE hydrogel adsorbs a higher amount of DNA than a compacted one. In agreement with previous results, the QCM-D data confirmed that the POWT/DNA hydrogel sense complementary DNA specifically and with negligible binding of noncomplementary DNA. These results are important for efficient constructions of biochips in water environments using this class of materials.

National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-12726 (URN)10.1021/la050479e (DOI)
Available from: 2007-12-07 Created: 2007-12-07 Last updated: 2017-12-14
3. Interactions between a zwitterionic polythiophene derivative and oligonucleotides as resolved by fluorescence resonance energy transfer
Open this publication in new window or tab >>Interactions between a zwitterionic polythiophene derivative and oligonucleotides as resolved by fluorescence resonance energy transfer
2005 (English)In: Chemistry of Materials, ISSN 0897-4756, E-ISSN 1520-5002, Vol. 17, no 16, p. 4204-4211Article in journal (Refereed) Published
Abstract [en]

The interactions between a zwitterionic polythiophene derivative, POWT, and DNA oligonucleotides in solution have been studied by FRET (fluorescence resonance energy transfer). When POWT and ssDNA are bound alone in a complex, the distance between them is at its smallest. The distance increases when adding complementary DNA, but POWT is still mainly bound to the first DNA strand. We find that two POWT chains bind to one DNA strand, and the two POWT chains seem held together in pairs, unable to separate, as they can only bind to and quench half their own amount of labeled DNA. This POWT−POWT complex appears to dissociate at lower concentrations. ssDNA attached to POWT in a complex can also be substituted by other ssDNA in solution; this occurs to 50% when the free DNA is present in 10-fold concentration compared to the ssDNA bound to POWT. Titration studies at different concentrations show positive cooperativity in the binding of POWT and ssDNA into a complex. The hybridization of complementary DNA to the same complex involves no cooperativity. These observations indicate interesting possibilities for the use of POWT as a DNA sensor.

National Category
Natural Sciences
Identifiers
urn:nbn:se:liu:diva-30356 (URN)10.1021/cm050328x (DOI)15901 (Local ID)15901 (Archive number)15901 (OAI)
Available from: 2009-10-09 Created: 2009-10-09 Last updated: 2017-12-13
4. Fluorescence quenching and excitation transfer between semiconducting and metallic organic layers
Open this publication in new window or tab >>Fluorescence quenching and excitation transfer between semiconducting and metallic organic layers
2004 (English)In: Journal of Applied Physics, ISSN 0021-8979, E-ISSN 1089-7550, Vol. 96, no 6, p. 3140-3147Article in journal (Refereed) Published
Abstract [en]

Here we present a simple approach to study the interaction of singlet excitons with polarons in conjugated polymers in organic electronic devices. Interlayer quenching constants KIL of 1.5 M−1 between a fluorescent molecule and a doped polymer in a layered sample demonstrates the importance of understanding the quenching of excited states in polymeric devices. A combination of Förster resonance energy transfer and quenching of photoluminescence between a fluorescent molecule and a conjugated polymer in its semiconducting and metallic states were studied. The polymer is a chiral 3-substituted polythiophene (POWT) and the fluorescent molecule is fluorescein bound to dextran (D-FITC). Bilayer samples with fluorescein on top of the POWT were fabricated and studied with absorption spectroscopy, fluorescence microscopy, and electrochemical doping methods. When POWT is electrochemically dedoped it is possible to enhance the photoluminescence in the polymer layer by excitation transfer from the fluorescein layer. Our results demonstrate that PL from the polythiophene disappears rapidly as soon as the layer is doped. As the doping of polymer layer increases the fluorescence from the fluorescein on top of the polymer decreases, due to excitation quenching. Models for excitation transfer and excitation quenching in POWT/FITC bilayer devices have been developed. This model predicts a linear relationship between the PL from the two molecules, in agreement with our experimental findings. These results are relevant for the development of electroluminescent devices or solar cells based on conjugated polymers.

National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-45631 (URN)10.1063/1.1774247 (DOI)
Available from: 2009-10-11 Created: 2009-10-11 Last updated: 2017-12-13
5. Surface energy modified chips for detection of conformational states and enzymatic activity in biomolecules
Open this publication in new window or tab >>Surface energy modified chips for detection of conformational states and enzymatic activity in biomolecules
2006 (English)In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 22, no 5, p. 2205-2211Article in journal (Refereed) Published
Abstract [en]

A novel patterning method for anchoring biomolecules and noncovalent assembled conjugated polyelectrolyte (CPE)/biomolecule complexes to a chip surface is presented. The surface energy of a hydrophilic substrate is modified using an elastomeric poly(dimethylsiloxane) (PDMS) stamp, containing a relief pattern. Modification takes place on the parts where the PDMS stamp is in conformal contact with the substrate and leaves low molecular weight PDMS residues on the surface resulting in a hydrophobic modification, and then biomolecules and CPE/biomolecule complexes are then adsorbed in a specific pattern. The method constitutes a discrimination system for different conformations in biomolecules using CPEs as reporters and the PDMS modified substrates as the discriminator. Detection of different conformations in two biomacromolecules, a synthetic peptide (JR2E) and a protein (calmodulin), reported by the CPE and resolved by fluorescence was demonstrated. Also, excellent enzyme activity in patterned CPE/horseradish peroxidase (HRP) enzyme was shown, demonstrating that this method can be used to pattern biomolecules with their activity retained. The method presented could be useful in various biochip applications, such as analyzing proteins and peptides in large-scale production, in making metabolic chips, and for making multi-microarrays.

National Category
Natural Sciences
Identifiers
urn:nbn:se:liu:diva-34580 (URN)10.1021/la0527902 (DOI)22009 (Local ID)22009 (Archive number)22009 (OAI)
Available from: 2009-10-10 Created: 2009-10-10 Last updated: 2017-12-13
• 20379.
Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, The Institute of Technology.
Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, The Institute of Technology.
Surface energy modified chips for detection of conformational states and enzymatic activity in biomolecules2006In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 22, no 5, p. 2205-2211Article in journal (Refereed)

A novel patterning method for anchoring biomolecules and noncovalent assembled conjugated polyelectrolyte (CPE)/biomolecule complexes to a chip surface is presented. The surface energy of a hydrophilic substrate is modified using an elastomeric poly(dimethylsiloxane) (PDMS) stamp, containing a relief pattern. Modification takes place on the parts where the PDMS stamp is in conformal contact with the substrate and leaves low molecular weight PDMS residues on the surface resulting in a hydrophobic modification, and then biomolecules and CPE/biomolecule complexes are then adsorbed in a specific pattern. The method constitutes a discrimination system for different conformations in biomolecules using CPEs as reporters and the PDMS modified substrates as the discriminator. Detection of different conformations in two biomacromolecules, a synthetic peptide (JR2E) and a protein (calmodulin), reported by the CPE and resolved by fluorescence was demonstrated. Also, excellent enzyme activity in patterned CPE/horseradish peroxidase (HRP) enzyme was shown, demonstrating that this method can be used to pattern biomolecules with their activity retained. The method presented could be useful in various biochip applications, such as analyzing proteins and peptides in large-scale production, in making metabolic chips, and for making multi-microarrays.

• 20380.
Linköping University, Department of Computer and Information Science.
Sökfrasanalys på Gula Sidorna2006Independent thesis Advanced level (degree of Magister), 20 points / 30 hpStudent thesis

Söktjänsten på Gula Sidorna innefattar sökningar på produkter, varor och tjänster och där görs tusentals sökningar varje dag. Enligt Eniro finns en del problem med söktjänsten och syftet med studien är att fastställa vilka dessa problem är och om systemet med språkteknologiska metoder kan förbättra träffarnas relevans, omfattning och rankning.

Studiens huvudsakliga frågeställning är om det är möjligt att med språkteknologiska metoder förbättra sökningen på Gula Sidorna med avseende på träffarnas relevans och täckning samt rankning av dessa träffar, och vilka språkteknologiska metoder som i så fall mest höjer systemets kvalitet utifrån användningssynpunkt, inom ramarna för företagets intressen.

Genom lingvistisk analys av en månads sökordssökningar på www.gulasidorna.eniro.se identifierades sju olika problemtyper utifrån hur väl träffarna matchade sökfrasens syntax och semantik. Med bakgrund i systemets existerande struktur och den typ av data som finns lagrad togs ett antal lösningsförslag fram utifrån teorier om språkteknologiska metoder i informationssökningssystem. Sju kortsiktiga och fem långsiktiga lösningar presenterades och dess effekter på prestationen vid en eventuell implementering diskuterades. Med nämnda förbättringsförslag som grund gavs förslag på hur rankningssystemet för Gula Sidorna skulle kunna förbättras.

Slutsatser som kan dras utifrån resultaten är att de kortsiktiga lösningarna vid implementering bör kunna lösa drygt hälften av de identifierade problemen. Dock krävs vidare studier för att säkerställa att de långsiktiga lösningarna inte orsakar fler problem än de löser.

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• 20381.
Linköping University, Department of Computer and Information Science.
Evaluation of Hierarchical Temporal Memory in algorithmic trading2010Independent thesis Advanced level (professional degree), 10 credits / 15 HE creditsStudent thesis

This thesis looks into how one could use Hierarchal Temporal Memory (HTM) networks to generate models that could be used as trading algorithms. The thesis begins with a brief introduction to algorithmic trading and commonly used concepts when developing trading algorithms. The thesis then proceeds to explain what an HTM is and how it works. To explore whether an HTM could be used to generate models that could be used as trading algorithms, the thesis conducts a series of experiments. The goal of the experiments is to iteratively optimize the settings for an HTM and try to generate a model that when used as a trading algorithm would have more profitable trades than losing trades. The setup of the experiments is to train an HTM to predict if it is a good time to buy some shares in a security and hold them for a fixed time before selling them again. A fair amount of the models generated during the experiments was profitable on data the model have never seen before, therefore the author concludes that it is possible to train an HTM so it can be used as a profitable trading algorithm.

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• 20382.
Linköping University, Department of Physics, Chemistry and Biology, Organic Chemistry. Linköping University, The Institute of Technology.
Studies of luminescent conjugated polythiophene derivatives-Enhanced spectral discrimination of protein conformational states2007In: Bioconjugate chemistry, ISSN 1043-1802, E-ISSN 1520-4812, Vol. 18, no 6, p. 1860-1868Article in journal (Refereed)

Improved probes for amyloid fibril formation are advantageous for the early detection and better understanding of this disease-associated process. Here, we report a comparative study of eight luminescent conjugated polythiophene derivates (LCPs) and their discrimination of a protein (insulin) in the native or amyloid-like fibrillar state. For two of the LCPs, the synthesis is reported. Compared to their monomer-based analogues, trimer-based LCPs showed significantly better optical signal specificity for amyloid-like fibrils, seen from increased quantum yield and spectral shift. The trimer-based LCPs alone were highly quenched and showed little interaction with native insulin, as seen from analytical ultracentrifugation and insignificant spectral differences from the trimer-based LCP in buffered and native protein solution. Hence, the trimer-based LCPs showed enhanced discrimination between the amyloid-like fibrillar state and the corresponding native protein.

• 20383.
Linköping University, Department of Physics, Chemistry and Biology, Organic Chemistry. Linköping University, The Institute of Technology.
Linköping University, Department of Physics, Chemistry and Biology, Organic Chemistry. Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Organic Chemistry. Linköping University, The Institute of Technology.
Synthesis of a pentathiophene fluorescent probe, 4’,3’’’-Bis-carboxymethyl-[2,2’;5’,2’’;5’’,2’’’;5’’’,2’’’‘]quinquethiophene-5,5’2010In: Nature Protocols, ISSN 1754-2189Article in journal (Other academic)

Poly and oligo-thiophenes have previously been used for in vitro, ex vivo and in vivo imaging of protein aggregates. The probe (p-FTAA) has been developed for the purpose of in vivo staining of protein aggregates such as amyloid deposits. It effectively passes the blood brain barrier and imaging can be performed live with two-photon imaging or ex vivo.

The straightforward synthesis of p-FTAA, including two Suzuki couplings, makes it an attractive probe for studies of most diseases involving protein aggregates.

• 20384.
Linköping University, Department of Physics, Chemistry and Biology, Organic Chemistry. Linköping University, The Institute of Technology.
Institute of Neuropathology, Department of Pathology, Universitätsspital Zürich, Schmelzbergstrasse 12, CH-8091 Zürich, Switzerland. Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering. Department of Cellular Neurology, Hertie-Institute for Clinical Brain Research, University of Tuebingen, D-72076 Tuebingen, Germany. Department of Cellular Neurology, Hertie-Institute for Clinical Brain Research, University of Tuebingen, D-72076 Tuebingen, Germany. Department of Neuroscience, Mount Sinai School of Medicine, New York, New York 10029, USA. Department of Physics, Norwegian University of Science and Technology, N-7491 Trondheim, Norway. Department of Neuropathology, Charité-Universitätsmedizin Berlin, D-13353 Berlin, Germany. Department of Physics, Norwegian University of Science and Technology, N-7491 Trondheim, Norway. Linköping University, Department of Physics, Chemistry and Biology, Organic Chemistry. Linköping University, The Institute of Technology. Department of Neurology, Alzheimer’s Disease Research Center, Washington University, St. Louis, Missouri 63110, USA. Department of Neuroscience, Mount Sinai School of Medicine, New York, New York 10029, USA. Department of Neuropathology, Charité-Universitätsmedizin Berlin, D-13353 Berlin, Germany. Alzheimer’s Disease Research Center, Mount Sinai School of Medicine, New York, New York 10029, USA. Department of Cellular Neurology, Hertie-Institute for Clinical Brain Research, University of Tuebingen, D-72076 Tuebingen, Germany. Institute of Neuropathology, Department of Pathology, Universitätsspital Zürich, Schmelzbergstrasse 12, CH-8091 Zürich, Switzerland. Linköping University, Department of Physics, Chemistry and Biology, Biochemistry. Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Organic Chemistry. Linköping University, The Institute of Technology.
Novel Pentameric Thiophene Derivatives for in Vitro and in Vivo Optical Imaging of a Plethora of Protein Aggregates in Cerebral Amyloidoses2009In: ACS CHEMICAL BIOLOGY, ISSN 1554-8929, Vol. 4, no 8, p. 673-684Article in journal (Refereed)

Molecular probes for selective Identification of protein aggregates are important to advance our understanding of the molecular pathogenesis underlying cerebral amyloidoses. Here we report the chemical design of pentameric thiophene derivatives, denoted luminescent conjugated oligothiophenes (LCOs), which could be used for real-time visualization of cerebral protein aggregates in transgenic mouse models of neurodegenerative diseases by multiphoton microscopy. One of the LCOs, p-FTAA, could be utilized for ex vivo spectral assignment of distinct prion deposits from two, mouse-adapted prion strains. p-FTAA also revealed a transient soluble pre-fibrillar non-thioflavinophilic A beta-assemblies during in vitro fibrillation of A beta peptides. In brain tissue samples, A beta deposits and neurofibrillary tangles (NFTs) were readily identified by a strong fluorescence from p-FTAA and the LCO staining showed complete co-localliation with conventional antibodies (6E10 and AT8). In addition, a patchy islet-like staining of individual A beta plaque was unveiled by the anti-oligomer A11 antibody during co-staining with p-FTAA. The major hallmarks of Alzheimers disease, namely, A beta aggregates versus NFTs, could also be distinguished because of distinct emission spectra from p-FTAA. Overall, we demonstrate that LCOs can be utilized as powerful practical research tools for studying protein aggregation diseases and facilitate the study of amyloid origin, evolution and maturation, A beta-tau interactions, and pathogenesis both ex vivo and in vivo.

• 20385.
Linköping University, The Institute of Technology. Linköping University, Department of Electrical Engineering, Vehicular Systems.
Asymptotic analysis of a mixed boundary value problem in a multi-structure2003Report (Other academic)
• 20386.
Linköping University, The Institute of Technology. Linköping University, Department of Electrical Engineering, Vehicular Systems.
Asymptotic analysis of a transmission problem in a multi-structure2003Report (Other academic)
• 20387.
Asymptotic analysis of junctions in multi-structures2002Doctoral thesis, comprehensive summary (Other academic)

A multi-structure is a compound domain that consists of several substructures such as solid bodies, thin shells and slender rods. In this thesis we consider different mixed boundary value problems in multi-structures. In the formulations of these problems a small perturbation parameter c is introduced, e.g., the thickness of a shell. The common objective of the papers in this thesis is to analyse the junctions between the substructures and to construct the asymptotics of the solution as ε tends to zero.

• 20388.
Linköping University, The Institute of Technology. Linköping University, Department of Electrical Engineering, Vehicular Systems.
• 20389.
Linköping University, Department of Electrical Engineering.
Authentication in peer-to-peer systems2002Independent thesis Basic level (professional degree)Student thesis

In the environment of the 3:rd generation Internet based on peer-to-peer architecture, well-trusted methods must exist to establish a secure environment. One main issue is the possibility to verify that a node actually is who it claims to be (authentication). Establishment of authentication between nodes in a peer-to-peer environment where nodes are exchanging information directly with each other requires more planning than in a typical client-server environment where the authentication methods are server-based. The peer-to-peer applications described in this report use authentication methods based on central authorities as well as solutions without central authorities.

Lack of standards in the way peer-to-peer systems should communicate and apply security lead to a variety of “local” communication and security solutions. These local solutions make different applications incompatible with each other, meaning that a peer using one application will not be able to communicate and exchange information with other peers using some other application.

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Linköping University, Department of Electrical Engineering, Computer Vision. Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, The Institute of Technology.
Variational Tensor-Based Models for Image Diffusion in Non-Linear Domains2015Doctoral thesis, monograph (Other academic)

Although the topic has a long history in the image processing community, researchers continuously present novel methods to obtain ever better image restoration results.

With an expanding market for individuals who wish to share their everyday life on social media, imaging techniques such as compact cameras and smart phones are important factors. Naturally, every producer of imaging equipment desires to exploit cheap camera components while supplying high quality images. One step in this pipeline is to use sophisticated imaging software including, e.g., noise reduction to reduce manufacturing costs, while maintaining image quality.

This thesis is based on traditional formulations such as isotropic and tensor-based anisotropic diffusion for image denoising. The difference from main-stream denoising methods is that this thesis explores the effects of introducing contextual information as prior knowledge for image denoising into the filtering schemes. To achieve this, the adaptive filtering theory is formulated from an energy minimization standpoint. The core contributions of this work is the introduction of a novel tensor-based functional which unifies and generalises standard diffusion methods. Additionally, the explicit Euler-Lagrange equation is derived which, if solved, yield the stationary point for the minimization problem. Several aspects of the functional are presented in detail which include, but are not limited to, tensor symmetry constraints and convexity. Also, the classical problem of finding a variational formulation to a given tensor-based partial differential equation is studied.

The presented framework is applied in problem formulation that includes non-linear domain transformation, e.g., visualization of medical images.

Additionally, the framework is also used to exploit locally estimated probability density functions or the channel representation to drive the filtering process.

Furthermore, one of the first truly tensor-based formulations of total variation is presented. The key to the formulation is the gradient energy tensor, which does not require spatial regularization of its tensor components. It is shown empirically in several computer vision applications, such as corner detection and optical flow, that the gradient energy tensor is a viable replacement for the commonly used structure tensor. Moreover, the gradient energy tensor is used in the traditional tensor-based anisotropic diffusion scheme. This approach results in significant improvements in computational speed when the scheme is implemented on a graphical processing unit compared to using the commonly used structure tensor.

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• 20391.
Heidelberg University, Germany.
Linköping University, Department of Electrical Engineering, Computer Vision. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Science and Technology, Communications and Transport Systems. Linköping University, Faculty of Science & Engineering.
Mapping-Based Image Diffusion2017In: Journal of Mathematical Imaging and Vision, ISSN 0924-9907, E-ISSN 1573-7683, Vol. 57, no 3, p. 293-323Article in journal (Refereed)

In this work, we introduce a novel tensor-based functional for targeted image enhancement and denoising. Via explicit regularization, our formulation incorporates application-dependent and contextual information using first principles. Few works in literature treat variational models that describe both application-dependent information and contextual knowledge of the denoising problem. We prove the existence of a minimizer and present results on tensor symmetry constraints, convexity, and geometric interpretation of the proposed functional. We show that our framework excels in applications where nonlinear functions are present such as in gamma correction and targeted value range filtering. We also study general denoising performance where we show comparable results to dedicated PDE-based state-of-the-art methods.

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• 20392.
Heidelberg Collaboratory for Image Processing Heidelberg University Heidelberg, Germany.
Linköping University, Department of Electrical Engineering, Computer Vision. Linköping University, Faculty of Science & Engineering. Linköping University, Center for Medical Image Science and Visualization (CMIV). BG-2: Plant Sciences Forschungszentrum Jülich 52425, Jülich, Germany.
Adaptive sharpening of multimodal distributions2015In: Colour and Visual Computing Symposium (CVCS), 2015 / [ed] Marius Pedersen and Jean-Baptiste Thomas, IEEE , 2015Conference paper (Refereed)

In this work we derive a novel framework rendering measured distributions into approximated distributions of their mean. This is achieved by exploiting constraints imposed by the Gauss-Markov theorem from estimation theory, being valid for mono-modal Gaussian distributions. It formulates the relation between the variance of measured samples and the so-called standard error, being the standard deviation of their mean. However, multi-modal distributions are present in numerous image processing scenarios, e.g. local gray value or color distributions at object edges, or orientation or displacement distributions at occlusion boundaries in motion estimation or stereo. Our method not only aims at estimating the modes of these distributions together with their standard error, but at describing the whole multi-modal distribution. We utilize the method of channel representation, a kind of soft histogram also known as population codes, to represent distributions in a non-parametric, generic fashion. Here we apply the proposed scheme to general mono- and multimodal Gaussian distributions to illustrate its effectiveness and compliance with the Gauss-Markov theorem.

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• 20393.
Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
Betydelsen av skogskontinuitet och egenskaper hos gran för förekomst av Lecanactis abietina2013Independent thesis Basic level (degree of Bachelor), 10,5 credits / 16 HE creditsStudent thesis

Skyddandet av gamla skogar med höga naturvärden är en viktig del i bevarandet av den biologiska mångfalden. För att kunna lokalisera och kvalitetsbedöma skogar med höga naturvärden används signalarter. En av dessa signalarter är Lecanactis abietina, gammelgranslav. Syftet med denna studie är att identifiera vilka faktorer som påverkar förekomst av signalarten L. abietina och täckningsgraden av apothecier. Studien utfördes i Ycke, Ullstämma och Säby Västerskog, vilka är naturreservat av olika ålder i Linköpings kommun, Östergötlands län. I de studerade områdena undersöktes samtliga granar med en diameter över 5 cm. Granarnas diameter och skuggning mättes, vid förekomst av L. abietina undersöktes förekomsten av apothecier, lavens täckningsgrad, maxhöjd och i vilka väderstreck laven förekom. Ett mindre urval av granarna borrades och ålderbestämdes. Resultatet visar att faktorerna som påverkar förekomst av L. abietina och täckningsgraden av apothecier främst är, skoglig kontinuitet i området, samt granarnas diameter och ålder. Resultaten från denna studie styrker användandet av L. abietina som lämplig indikatorart i Östergötland då lavens förekomst och spridning tydligt  speglade skogens kontinuitet (störst förekomst i de äldsta reservaten) och trädens egenskaper. Studien visar även att enbart förekomst inte räcker för att påvisa skog med höga naturvärden, utan de viktigaste faktorerna var förekomst av fertil lav, lavens täckningsgrad och frekvens på granar. Studien visar även att bevarandet av skogar med lång kontinuitet och förekomst av stora och gamla träd är viktigt för förekomsten av L. abietina.

Therese Åström
• 20394.
Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering. Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
Non-fused Phospholes as Fluorescent Probes for Imaging of Lipid Droplets in Living Cells2017In: Frontiers in Chemistry, E-ISSN 2296-2646, Vol. 5, article id 28Article in journal (Refereed)

Molecular tools for fluorescent imaging of specific compartments in cells are essential for understanding the function and activity of cells. Here, we report the synthesis of a series of pyridyl- and thienyl-substituted phospholes and the evaluation of these dyes for fluorescent imaging of cells. The thienyl-substituted phospholes proved to be successful for staining of cultured normal and malignant cells due to their fluorescent properties and low toxicity. Co-staining experiments demonstrated that these probes target lipid droplets, which are, lipid-storage organelles found in the cytosol of nearly all cell types. Our findings confirm that thienyl-substituted phospholes can be utilized as fluorescent tools for vital staining of cells, and we foresee that these fluorescent dyes might be used in studies to unravel the roles that lipid droplets play in cellular physiology and in diseases.

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• 20395.
Linköping University, The Tema Institute, Department of Water and Environmental Studies. Linköping University, Faculty of Arts and Sciences.
Local Forest Administration, Östergötland, Sweden. Linköping University, The Tema Institute, Department of Water and Environmental Studies. Linköping University, Faculty of Arts and Sciences. Linköping University, The Tema Institute, Department of Water and Environmental Studies. Linköping University, Faculty of Arts and Sciences. Department of Bioenergy, Swedish University of Agricultural Sciences, Uppsala, Sweden.
The role of organic matter bound chlorine in the chlorine cycle: a case study of the Stubbetorp catchment, Sweden2005In: Biogeochemistry, ISSN 0168-2563, Vol. 75, no 2, p. 241-269Article in journal (Refereed)

The objective of this study is to construct a balanced chlorine budget for a small forested catchment, focusing on the interaction between chloride (Clinorg) and organic-matter-bound chlorine (Clorg). Data from the actual catchment are combined with secondary data from other sites to elucidate more clearly which parts of the cycle are fairly well known and which are more or less unknown. The budget calculations show that the principal input and output fluxes of Cl in the catchment are inorganic but that the main pool is Clorg in the soil. In addition, the budget calculations suggest that a considerable portion of Clinorg in soil is transformed to Clorg and subsequently leached to deeper soil layers, that net mineralization of Clorg takes place in soil, preferably in deeper soil layers, and that degrading organic matter is a major source of Clinorg in runoff. The loss of Clorg through runoff is small to negligible in relation to other fluxes. It appears as if dry deposition of Clinorg is at risk of being underestimated if Clinorg is assumed to be conservative in soil. The pool of organic-matter-bound chlorine in soil is considerably larger than the annual flux of chloride through the system. The estimates suggest that the amount of Clorg in the upper 40 cm of the soil at the investigated site is approximately twice as large as the Clinorg. Furthermore, the amount of Clorg biomass is small in relation to the occurrence of Clorg in soil. Finally, the estimates indicate that the transport of volatile Clorg from the soil to the atmosphere may influence the chlorine cycle.

• 20396.
Linköping University, Department of Computer and Information Science, Human-Centered systems. Linköping University, The Institute of Technology.
HORN - Hank and OpenDRIVE Road Networks: An editor for creating HANK scenarios while working with OpenDRIVE2012Independent thesis Basic level (degree of Bachelor), 12 HE creditsStudent thesis

HORN is a solution to the problem of how to implement scenarios in a more efficient way than was previously possible allowing researchers who wish to create scenarios for HANK the ability to quicker implement larger scenarios than was previously possible.

OpenDRIVE is an open standard for road networks that is believed to be the way forward and Horn is an attempt at unifying OpenDRIVE scenarios with HANK - the driving simulator currently in use at Link\"{o}pings Universitet, thus futureproofing all work done to implement scenarios.

Before HORN HANK scenarios were laboriously constructed with a really bad program or by hand and HORN tries to make the process far less painful.

This thesis describes how to work with the Road Network Editor program HORN ("Hank and OpenDRIVE Road Networks") that was developed for working with HANK's scenarios as well as my experience implementing it and some of the fascinating rules for how to draw some exotic two dimensional geometries I found out about as I worked on HORN.

Horn - Hank and OpenDRIVE Road Networks
• 20397.
Linköping University, Department of Computer and Information Science.
Design av databassystem för testresultat från Tor-systemet2004Independent thesis Basic level (professional degree)Student thesis

This master’s thesis was performed at PartnerTech AB in Åtvidaberg. It addresses the problem of managing test results obtained from testing electronics manufactured by PartnerTech. PartnerTech has developed a test system, called Tor, which performs tests on manufactured boards and stores the test results in files. The Tor system consists of both hardware and software part, where the software runs on an ordinary PC with MS DOS/Windows 2000. The effects on the existing Tor system that this thesis implies are minimal.

This work focuses on a way of storing the produced test files in a database. In this work a data model has been developed, implemented, and evaluated together with a system that imports test files into the database and a graphical user interface that allows a user to easily search and browse the stored test results. It is also possible to print test reports from the Tor system. For implementing the database system Microsoft SQL Server 2000 was chosen as database server and an XML based data format was chosen to import and export data to and from the database. Two alternative graphical user interface applications were developed and compared - one server based on Microsoft IIS and one client based in Microsoft Access. For advanced data manipulation certain parts of the system were developed in Microsoft Excel.

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• 20398.
Linköping University, Department of Computer and Information Science. Linköping University, The Institute of Technology.
Middleware med Google Web Toolkit2012Independent thesis Basic level (university diploma), 10,5 credits / 16 HE creditsStudent thesis

Detta examensarbete har utförts i samarbete med företaget Systemagic AB. Systemagic är ett teknikföretag vars expertis ligger inom mjukvaruutveckling inom IPTV-teknologi. Detta innefattar bland annat utveckling av middleware till digitalboxar, också kallade Set-top-boxar.

Middleware är den mjuk- och hårdvaruinfrastruktur som sammankopplar de olika delarna av ett IPTV-system. Det är ett distribuerat operativt system som både finns på operatörens servrar samt i slutanvändarens digitalbox. Då det idag ställs allt högre krav på funktionalitet och dynamik från beställare blir utvecklingen av ett modernt middleware mycket resurskrävande. Systemagic anser att en stor bidragande orsak till den resurskrävande utvecklingsprocessen kan kopplas till användningen av scriptspråket JavaScript och är därför intresserade av alternativa metoder.

Google Web Toolkit (GWT) är ett Java-ramverk som kan användas för att på ett snabbt och smidigt sätt utveckla interaktiva webbapplikationer. Detta möjliggörs genom att all utveckling sker i Java. Slutprodukten efter kompilering är standard-kompatibel HTML och JavaScript, helt oberoende av Java.

Detta examensarbete har gått ut på att undersöka möjligheten att använda Java och GWT för att underlätta och potentiellt snabba upp utvecklingen av ett middleware. Målet var att undersöka om GWT kan användas rakt av för att ta fram den del av ett middleware som återfinns i slutanvändarens box, en så kallad portal, eller om ramverket måste anpassas för att de mest grundläggande funktionerna hos en box ska kunna implementeras. Rapporten beskriver frågeställningar, tillvägagångssätt, problem och  svårigheter som uppstod, de lösningar som använts samt en analys och diskussion av resultatet.

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• 20399.
Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
Is there a correlation between the nutrient content and variation in the HvNAM-2 gene in Hordeum vulgare?2015Independent thesis Basic level (degree of Bachelor), 10,5 credits / 16 HE creditsStudent thesis

Barley is one of the most important cereal crops in the world and a better understanding of the factors that regulates the nutrient content in the grain is of high interest. The industrial breeding during the last century has led to bigger yield but possibly a decrease in nutrient content. In wheat, the NAM-B1 gene is a well-studied gene that affects the grain protein and micronutrient content. Two orthologue genes in barley HvNAM-1 and HvNAM-2 are candidate genes to play a similar role in the barley senescence process.

I have looked for a correlation between the diversity in the HvNAM-2 gene and nutrient content in 37 Nordic barley accessions. The samples were sequenced and then aligned and analyzed for variation. I found three haplotypes which were compared in nutrient content and in micronutrient content. No significant difference between the haplotypes was found, which can be due to small sample size or that no correlation exists between the grain protein content and the HvNAM-2 gene variation. Significant correlation was however found between the nitrogen content and the micronutrient contents that indicate that the pathways of all the nutrients’ mobilizations are tightly coupled. For future research a bigger number of accessions, preferably at least 100, need to be analyzed to be able to give any conclusions. The molecular mechanisms in the cells during senescence also need further investigation.

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Linköping University, Department of Electrical Engineering, Computer Vision. Linköping University, Faculty of Science & Engineering.
Adaptive Supervision Online Learning for Vision Based Autonomous Systems2016Doctoral thesis, monograph (Other academic)

Driver assistance systems in modern cars now show clear steps towards autonomous driving and improvements are presented in a steady pace. The total number of sensors has also decreased from the vehicles of the initial DARPA challenge, more resembling a pile of sensors with a car underneath. Still, anyone driving a tele-operated toy using a video link is a demonstration that a single camera provides enough information about the surronding world.

Most lane assist systems are developed for highway use and depend on visible lane markers. However, lane markers may not be visible due to snow or wear, and there are roads without lane markers. With a slightly different approach, autonomous road following can be obtained on almost any kind of road. Using realtime online machine learning, a human driver can demonstrate driving on a road type unknown to the system and after some training, the system can seamlessly take over. The demonstrator system presented in this work has shown capability of learning to follow different types of roads as well as learning to follow a person. The system is based solely on vision, mapping camera images directly to control signals.

Such systems need the ability to handle multiple-hypothesis outputs as there may be several plausible options in similar situations. If there is an obstacle in the middle of the road, the obstacle can be avoided by going on either side. However the average action, going straight ahead, is not a viable option. Similarly, at an intersection, the system should follow one road, not the average of all roads.

To this end, an online machine learning framework is presented where inputs and outputs are represented using the channel representation. The learning system is structurally simple and computationally light, based on neuropsychological ideas presented by Donald Hebb over 60 years ago. Nonetheless the system has shown a cabability to learn advanced tasks. Furthermore, the structure of the system permits a statistical interpretation where a non-parametric representation of the joint distribution of input and output is generated. Prediction generates the conditional distribution of the output, given the input.

The statistical interpretation motivates the introduction of priors. In cases with multiple options, such as at intersections, a prior can select one mode in the multimodal distribution of possible actions. In addition to the ability to learn from demonstration, a possibility for immediate reinforcement feedback is presented. This allows for a system where the teacher can choose the most appropriate way of training the system, at any time and at her own discretion.

The theoretical contributions include a deeper analysis of the channel representation. A geometrical analysis illustrates the cause of decoding bias commonly present in neurologically inspired representations, and measures to counteract it. Confidence values are analyzed and interpreted as evidence and coherence. Further, the use of the truncated cosine basis function is motivated.

Finally, a selection of applications is presented, such as autonomous road following by online learning and head pose estimation. A method founded on the same basic principles is used for visual tracking, where the probabilistic representation of target pixel values allows for changes in target appearance.

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Supplementary files with videos
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Channel vector curves, Four channels, 3D space
Channel vector curves, Five channels, 4D space
Channel vector curves, Seven channels, 6D space
Cone, Three channels, 3D space
Cone, Four channels, 4D space
Cone, Seven channels, 7D space
Associative learning illustration
Decoding of five pixels in a sequence
Sequence with translating cameraman image
Video from UAV
Original video from the UAV
Autonomous Road Following Application, Use case demo
Autonomous Road Following Application, Demonstrator system
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