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  • Public defence: 2019-10-23 10:00 FA32, Stockholm
    De Luca, Eleonora
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics.
    Nonlinear Properties of III-V Semiconductor Nanowaveguides2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Nonlinear optics (NLO) plays a major role in the modern world: nonlinear optical phenomena have been observed in a wavelength range going from the deep infrared to the extreme ultraviolet, to THz radiation. The optical nonlinearities can be found in crystals, amorphous materials, polymers, liquid crystals, liquids, organic materials, and even gases and plasmas. Nowadays, NLO is relevant for applications in quantum optics, quantum computing, ultra-cold atom physics, plasma physics, and particle accelerators. The work presented in the thesis is limited only to the semiconductors that have a second-order optical nonlinearity and includes two phenomena that use second-order nonlinearity: second-harmonic generation (SHG) and spontaneous parametric down-conversion (SPDC). Among the many options available, the investigation presented concerns gallium phosphide (GaP) and gallium indium phosphide (Ga0.51In0.49P), two semiconductors of the group III-V with the ¯43m crystal symmetry.

    However, some of the results found can be generalized for other materials with ¯43m crystal symmetry.

    In the thesis, the fabrication of GaP nanowaveguides with dimensions from 0.03 μm and an aspect ratio above 20 using focused ion beam (FIB) milling is discussed. The problem of the formation of gallium droplets on the surface is solved by using a pulsed laser to oxidize the excess surface gallium locally on the FIB-milled nanowaveguides. SHG is used to evaluate the optical quality of the fabricated GaP nanowaveguides. Additionally, a theoretical and experimental way to enhance SHG in nanowaveguides is introduced. This process uses the overlap of interacting fields defined by the fundamental mode of the pump and the second-order mode of the SHG, which is enhanced by the longitudinal component of the nonlinear polarization density. Through this method, it was possible to obtain a maximum efficiency of 10−4, which corresponds to 50 W−1cm−2. The method can be generalized for any material with a ¯43m crystal symmetry. Furthermore, SHG is used to characterize the nonlinear properties of a nanostructure exposed for a long time to a CW laser at 405 nm to reduce the photoluminescence (PL) of Ga0.51In0.49P. The PL was reduced by -34 dB without causing any damage to the nanostructures or modifying the nonlinear properties. The fabrication process for obtaining the nanowaveguide is interesting as well, since the fabricated waveguide in Ga0.51In0.49P, whose sizes are 200 nm thick, 11 μm wide and 1.5 mm long, was transferred on silicon dioxide (SiO2). This type of nanowaveguide is interesting for SPDC, since it satisfies the long interaction length necessary for an efficient SPDC. Finally, a configuration consisting of illuminating the top surface of a nanowaveguide with a pump beam to generate signal and idler by SPDC is presented. These fabricated nanostructures open a way to the generation of counter-propagating idler and signal with orthogonal polarization. By using a different cut of the crystal, i.e. [110], it makes possible to obtain degenerate wavelength generation, and in certain conditions to obtain polarization-entangled photons or squeezed states.

  • Public defence: 2019-10-24 10:00 sal F3, Stockholm
    Josefsson, Leila
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH).
    Bioanalysis using capillary electrophoresis and mass spectrometry: Applied on proteins, protein nanofibrils and polyvinyl alcohol microbubbles2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The sequencing of the genome of various species, including the human species, have led to increased understanding about how a protein structure is generated, and how specific structures are related to the proteins’ functionality. In paper I and II of this thesis, the folding of proteins in vitro to form hierarchical nanostructures, which in vivo often have a pathological effect, have been studied. Protein isolates from soybean and potato, that are byproducts from oil and starch production, respectively, were used as a starting material for protein nanofibril (PNF) formation, and mass spectrometry was used to identify the building blocks that are included in the formed PNF. The five peptides identified in soybean PNF and the six peptides identified in potato PNF originated from the major seed storage proteins for the respective crop.

    The use of ionic liquids has increased for improvement of the performance of different separation techniques due to their adjustable properties, and good solvating ability. In paper III, an ionic liquid and water mixture was used as background electrolyte in capillary electrophoresis for protein separation. The system showed high reproducibility at basic conditions, and could potentially be used for routine control analysis.

    Many diseases and injuries require clinical diagnosis techniques e.g. ultrasound imaging, to be detected, and for the physician to be able to decide the correct therapy. To increase the resolution of such imaging techniques, contrast agents can be used. In paper IV-VI, a newly developed contrast agent consisting of air-filled microbubbles stabilized with a shell of polyvinyl alcohol (PVA-MBs) was studied. Development of a capillary electrophoretic method for analysis of the PVA-MBs with the intentions to be used for clinical diagnosis is performed, where different detectors such as a UV detector, a UV area imaging detector and an in-house constructed microscope are used to increase the sensitivity of detection for the PVA-MBs. The developed method could be used for quantification of the contrast agent, since individual PVA-MBs were visible using the imaging detectors. Findings regarding the mobility of the PVA-MBs in human blood plasma and in water implies that a protein corona was formed around the MBs.

  • Public defence: 2019-10-24 10:00 Kollegiesalen, Stockholm
    Ruggieri, Federica
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Industrial Biotechnology.
    Transaminase Biocatalysis: Applications and Fundamental Studies2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Biocatalysis is the branch of science at the intersection between chemistry and biology and specifcally dedicated to the application of natural evolvable catalysts, i.e. enzymes, in human-designed chemical processes. Among the array of promising biocatalysts, transaminases (EC 2.6.1.x) are possibly one of the enzyme classes with the largest unrealized potential. Fast inactivation, poor acceptance towards unnatural substrates and limited tolerance to cosolvents are some of the main factors hampering their implementation in chemical synthesis. In the present thesis work advances in both transaminase application and molecular understanding are presented. Indeed, these two topics are deeply interconnected, as a better molecular understanding is expected to ease the generation of novel enzyme variants suitable for new desired applications.

    From the application perspective, the design of an effective one-pot transaminase-based racemization system offers new possibilities for the design of fully biocatalytic dynamic kinetic resolutions of valuable chiral amines. Similarly, the successful structure-guided redesign of the small substrate binding pocket of the Chromobacterium violaceum (S)-selective transaminase (Cv-TA) granted access to a new enzyme variant active on semi-preparative scale towards the unnatural substrate 1,2-diphenylethylamine.

    From the molecular understanding perspective, the combination of crystallographic and computational techniques led to the formulation of a dimer dissociation model valid for Cv-TA and possibly for other enzymes belonging to the same fold type. This model, which aided the improvement of the Cv-TA stability by structure-based engineering, will hopefully enable similar results in other structurally related enzymes.

  • Public defence: 2019-10-25 09:00 Atrium, solna
    Mahdessian, Diana
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Cellular and Clinical Proteomics.
    Spatiotemporal characterization of the human proteome2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Characterizing the molecular components of the basic unit of life; the cell, is crucial for a complete understanding of human biology. The cell is divided into compartments to create a suitable environment for the resident proteins to fulfill their functions. Therefore, spatial mapping of the human proteome is essential to understand protein function in health and disease.


    Spatial proteomics is most commonly investigated using mass spectrometry or imaging, combined with machine learning for the data analysis. Until now, studies have been limited to high abundant proteins and relied on the purification of organelle fractions from a bulk of cells. Within the scope of this thesis, we were able to systematically localize proteins in their native cellular environment using antibody-based imaging techniques, and to investigate protein subcellular localization and dynamics on a single cell level, introducing a major advance within the field of spatial proteomics.


    Paper I of this thesis presents a subcellular map of the human proteome, where the spatial distribution of 12,003 human proteins was mapped into 30 subcellular structures, half of which were not previously localized. Besides providing a valuable dataset for cell biology, this study is the first to reveal the spatial complexity of human cells with proteins localizing to multiple compartments and pronounced single cell variations. Paper II reports on the systematic temporal dissection of these single cell variations and the identification of cell cycle correlated variations. We identified 258 novel cell cycle regulated proteins and showed that several of these proteins may be connected to proliferative diseases. A key finding of Paper II is that proteins showing non-cell cycle dependent variations are significantly enriched in mitochondria, whereas cell cycle dependent proteins are enriched in nucleoli. In Paper III and IV, we spatiotemporally characterized the proteomes of these two organelles, mitochondria and nucleoli, in greater detail.

    In Paper III, we expanded the mitochondrial proteome with 560 novel proteins. As many as 20% of the mitochondrial proteome showed variations in their expression pattern at the single cell level, most often independent of the cell cycle. Paper IV provides a complete characterization of the nucleolar proteome. Nucleoli are not only important for ribosome synthesis and assembly, but are also crucial for cell cycle regulation through the recruitment of its proteins to the chromosomal periphery during cell division. Here, we presented the first proteome-wide spatiotemporal analysis of the nucleolus with its sub-compartments, and identified 69 nucleolar proteins that relocated to the chromosomes periphery during mitosis.


    In conclusion, this thesis unravels the spatiotemporal proteome organization of the human cell over the course of a cell cycle and offers a valuable starting point for a better understanding of human cell biology in health and disease.

  • Public defence: 2019-10-25 10:00 F3, Stockholm
    Wei, Xin-Feng
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology.
    Ageing behavior of plastics used in automotive fuel systems2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The increase in service temperature and the use of biobased fuels, such as biodiesel, have raised concerns on the short/long-term performance of plastic components used in automotive fuel systems.

    In this work the ageing behavior of unreinforced and glass-fibre reinforced polyamide 12 (PA12), exposed to three different fuels (petroleum diesel, biodiesel, and a mixture of these (80/20)) at high temperature, was investigated. The interactions between the polymer and the fuel, and the associated polymer ageing mechanisms (fuel uptake, extraction of monomer and oligomers, annealing and oxidation), were found to be “generic” in the sense that they occurred, although to various extent, for all fuels. In the glass-fibre reinforced polyamides, the ageing occurred mainly in the polyamide matrix and not in the matrix-fibre interface. The semi-aromatic polyamide showed better performance when exposed to fuels than the aliphatic PA12.  

    At a component level, multilayer polyamide-based pipes, with polyamide or fluoropolymer as inner layer, were aged under “in-vehicle” conditions where the pipes were exposed to fuel on the inside and to the air on the outside. All pipes stiffened during ageing but embrittlement occurred only for the pipes with polyamide being the inner layer. Compared to polyamide, the fluoropolymer inner layer showed significantly better barrier properties towards the fuel and no material was extracted into the fuel. The plasticizer loss from the PA12 outer layers into air was diffusion controlled and its diffusivity followed a linear Arrhenius behavior in the high temperature region. Relationships between plasticizer loss and the changes in mechanical properties were established.

    The polyamides experienced diffusion-limited oxidation when exposed to air and/or fuel, involving the formation of a thin oxidized surface layer which was responsible for a significant decrease in strain-at-break. 

    The fracture behavior of PA 6 in air at high temperature, found to involve three distinct stages, were systematically studied and linked to underlying mechanisms responsible for the reduction in strain-at-break.

  • Public defence: 2019-10-25 10:00 Ångdomen, Stockholm
    Ottonello Briano, Floria
    KTH, School of Electrical Engineering and Computer Science (EECS), Micro and Nanosystems.
    Mid-infrared photonic devices for on-chip optical gas sensing2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Gas detection is crucial in a wide range of fields and applications, such as safety and process control in the industry, atmospheric sciences, and breath diagnostics. Optical gas sensing offers some key advantages, compared to other sensing methods such as electrochemical and semiconductor sensing: high specificity, fast response, and minimal drift.

    Wavelengths between 3 and 10 μm are of particular interest for gas sensing. This spectral range, called the mid-infrared (mid-IR), is also known as the fingerprint region, because several gas species can be identified by their sharp absorption lines in this region. The most relevant mid-IR-active gases are the trace gases carbon dioxide (CO2), methane (CH4), carbon monoxide (CO), ammonia (NH3), and nitrous oxide (N2O). They are greenhouse gases, contributing to global warming. They are waste products of human activities and widely used in agriculture and industry. Therefore, it is crucial to accurately and extensively monitor them. However, traditional optical gas sensors with a free-space optical path configuration, are too bulky, power-hungry, and expensive to be widely adopted.

    This thesis presents mid-IR integrated photonic devices that enable the on-chip integration of optical gas sensors, with a focus on CO2 sensing. The reported technologies address the fundamental sensor functionalities: light-gas interaction, infrared light generation, and infrared light detection. The thesis introduces a novel mid-IR silicon photonic waveguide that allows a light path as long as tens of centimeters to fit in a volume smaller than a few cubic millimeters. Mid-IR CO2 spectroscopy demonstrates the high sensing performance of the waveguide. The thesis also explores the refractive index sensing of CO2 with a mid-IR silicon photonic micro-ring resonator.

    Furthermore, the thesis proposes platinum nanowires as low-cost infrared light sources and detectors that can be easily integrated on photonic waveguides. Finally, the thesis presents a large-area infrared emitter fabricated by highs-peed wire bonding and integrated in a non-dispersive infrared sensor for the detection of alcohol in breath.

    The technologies presented in this thesis are suited for cost-effective mass production and large-scale adoption. Miniaturized integrated optical gas sensors have the potential to become the main choice for an increasingly broad range of existing and new applications, such as portable, distributed, and networked environmental monitoring, and high-volume medical and consumer applications.

  • Public defence: 2019-10-25 14:00 F3, STOCKHOLM
    Bakyayita, Grace Kizito
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Water and Environmental Engineering. Makerere University, Kyambogo University.
    Batch Sorption Studies of Aqueous Cadmium and Lead from Contaminated Water onto Selected Biosorbents2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Groundwater, wastewater, surface runoff and surface water samples from Lake Victoria basin, Uganda was assessed for trace metals contamination. Untreated, base-treated and peroxide-treated biosorbents from Albizia coriaria, Coffea canephora, Cyperus papyrus, Erythrina abyssinica and Musa spp were investigated for removal of selected trace metals from contaminated water in batch studies. The assessed shallow groundwater and surface water was contaminated with iron and manganese. Selected speciation studies using Visual MINTEQ showed that in leachates from Municipal dumpsites 74% of the metal ions were bound to DOM, 13% were free ions and 13% were in inorganic forms moreover for urban streams 37% of the metal ions were bound to DOM, 44% were free ions and 19% were in inorganic forms. The metal levels in surface water, landfill leachate and surface runoff showed elevated levels and revealed increased risks to environmental health. Risk analysis based on the Swedish EPA showed that varied risks of negative effects in 30% – 76% of the sample sites ranging from high to increased risk in surface water whereas the results from Bio-met tool showed potential risk to toxicity effects of Cu2+, Ni2+, Zn2+ and Pb2+ in 15.3% - 30.8% surface water samples and 8.3% - 62.5% groundwater samples. Batch sorption studies revealed that the optimal conditions for Cd2+ and Pb2+ ions uptake were; pH 3.5 – 5.0 for contact time 3.0 – 3.5 hours and biosorbent dosage 10 – 12.5 g/L. Base-treated biosorbents showed 10 – 17 % sorption enhancement for Cd2+ ions and 1.6 – 2.3 % uptake reduction for Pb2+ ions. The biomass negative potential for binding base cations was in the order; Musa spp. > A. coriaria > E. abyssinica and base treatment reduced DOC leaching from biosorbents in the order; E. abyssinica > A. coriaria > Musa spp. Speciation studies showed that more ions were complexed to DOC in solutions at various pH levels. The maximum sorption intensities for both Cd2+ and Pb2+ ions uptake onto biomass occurred for low initial metal concentration; 5 mg/L. Freundlich model best fitted data for Pb2+ ions ions uptake whereas Temkin model fitted the sorption data for Cd2+ ions onto both treated and untreated biomass. For peroxide treated biomass, the maximum sorption efficiencies for both Cd2+ and Pb2+ ions were between 95.2 – 98.7% for C.canephora, 79.9 – 92.2% for Musa spp. and 42.0 – 91.3% for C.papyrus in non-competitive media and 90.8 – 98.0% for C.canephora, 56.4 – 89.3% for Musa spp. and 19.5 – 90.4% for C.papyrus in competitive media. The Langmiur model fitted non-competitive sorption data with 0.769 ≤ R2 ≥ 0.999 and the Freundlich model fitted competitive sorption data with 0.867 ≤ R2 ≥ 0.989. The pseudo second order kinetic model fitted the sorption data for Cd2+ and Pb2+ ions for untreated, peroxide treated and base treated biomass with 0.917 ≤ R2 ≥ 1.000. The sorption of trace metals was a complex potentially monolayer chemisorption with heterogeneous surface properties exhibited. In competitive sorption, sorption suppression effects observed were greater for Cd2+ than Pb2+ ions. The comparative studies on sorption performance presented agreement and no significant difference between the untreated and base treated biosorbents. 

  • Public defence: 2019-10-28 14:00 F3, Stockholm
    Pechsiri, Joseph
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering.
    Nutrient Recovery as an Added Benefit to Harvests of Photosynthetic Marine Biomass: A Holistic Systems Perspective on Harvesting Marine Microalgae, Cyanobacteria, and Macroalgae2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    As a result of increasing environmental burdens from anthropogenic activities andresource scarcity, interest for the development of solutions utilizing photosyntheticmarine biomass has also been increasing in both academia and industries. Medium tolarge scale production and harvest of photosynthetic marine biomass have beenpracticed to achieve numerous services, including improving tourism industries,production of biofuels, and production of food/feed. However, few studies haveevaluated the potential for nutrient recovery as an added benefit to the aforementionedservices and the potential environmental burdens of such solutions from a holisticsystems perspective. This thesis, therefore, sought to determine the nutrient recoverypotential of harvesting photosynthetic marine biomass at industrial scales whileassessing the environmental burdens from a holistic systems perspective. Techniquesinvolving life cycle inventory and analysis, input-output analysis, growth modellingand experimentation, energy analysis, and assessment of greenhouse gas emissionsfrom a life cycle perspective were used to assess the potential environmental burdensof large scale harvest of photosynthetic marine biomass.This study employed five real world case studies of five different photosynthetic marinebiomass species at various geographical locations across the globe. Each case wasassessed to determine the potential to recover nutrients while evaluating the potentialenvironmental burdens from an energy and greenhouse gas perspective. Each casecontains unique specific details and therefore methods applied were case specific.Results showed that nutrient recovery potential existed in most cases with the exceptionof one case. Cases evaluated for their potential environmental burdens showed thatlarge scale harvest of photosynthetic marine biomass is resource intensive regardless ofspecies but showed mixed results from an energy perspective. The key findings of thisthesis were that a) the potential for nutrient recovery was estimated in both large scalecultivation and large scale wild harvest of photosynthetic marine biomass, b) from anenergy and biomass harvesting perspective, the viability of industrial harvests ofphotosynthetic marine biomass were found for both large scale cultivations and wildharvesting of biomass blooms, and c) scale of operations is an important factor towardsevaluating the environmental performance of photosynthetic marine biomassproduction systems.

  • Public defence: 2019-10-31 14:00 F3, Stockholm
    Adler, Jonas
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Mathematics (Div.).
    Data-driven Methods in Inverse Problems2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In this thesis on data-driven methods in inverse problems we introduce several new methods to solve inverse problems using recent advancements in machine learning and specifically deep learning. The main goal has been to develop practically applicable methods, scalable to medical applications and with the ability to handle all the complexities associated with them.

    In total, the thesis contains six papers. Some of them are focused on more theoretical questions such as characterizing the optimal solutions of reconstruction schemes or extending current methods to new domains, while others have focused on practical applicability. A significant portion of the papers also aim to bringing knowledge from the machine learning community into the imaging community, with considerable effort spent on translating many of the concepts. The papers have been published in a range of venues: machine learning, medical imaging and inverse problems.

    The first two papers contribute to a class of methods now called learned iterative reconstruction where we introduce two ways of combining classical model driven reconstruction methods with deep neural networks. The next two papers look forward, aiming to address the question of "what do we want?" by proposing two very different but novel loss functions for training neural networks in inverse problems. The final papers dwelve into the statistical side, one gives a generalization of a class of deep generative models to Banach spaces while the next introduces two ways in which such methods can be used to perform Bayesian inversion at scale.

  • Public defence: 2019-11-04 10:00 F3, Stockholm
    Paulraj, Thomas
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Polymeric Materials.
    Plant cell-inspiredmicrocontainers: Fabrication, Characterization and Applications2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Biomimetic materials have been inspiring mankind since a longtime for applications in a variety of fields. In particular, the production of lipidbasedvesicles have aided in our understanding of a variety of functions in animalcells, and also served as e.g. drug delivery systems and bioreactors. On thecontrary, the preparation of synthetic plant cells is limited, which is mainly due tothe challenges of building the complex plant primary cell wall fencing the lipidplasma membrane in real plant cells.The present thesis focuses on the bottom-up fabrication ofbiomimetic microcontainers that can serve as simple model systems for plant cells.In the first part, the interactions of plant cell wall polysaccharides, cellulosenanofibers (CNFs), pectin and xyloglucan, are examined. The knowledge is used inthe fabrication of microcapsules and the permeability properties were assessed.The results show that the polysaccharides must be assembled in a specific order inthe capsule wall to incorporate all the three polysaccharides. Additionally, thestructural stability and permeability highly depend on the capsule wallcomposition. The permeability also depends on the composition of thesurrounding media.The second part deals with the fabrication of more advancedbiomimetic microcapsules, with a lipid layer beneath the polysaccharide capsulewall. These capsules are semi-permeable and the phase behavior of the lipids isexploited to grow tubular structures (long filamentous structures) through thecapsule wall, as well as create a vesicle-crowded interior. Real plant cells usetubular structure (Plasmodesmata) for intercellular communications.In the third part, application-oriented aspects of the fabricatedmicrocapsules are discussed. The LbL-derived microcapsules (from the first part)were loaded with active glucose oxidase enzyme, thereby allowing their use as aglucose sensor. The capsule wall acts like a sieve, only allowing small molecules toeffectively pass through. Finally, cell culture experiments demonstrate theirbiocompatibility, paving way for tissue culture applications.

    The full text will be freely available from 2020-10-01 11:00
  • Public defence: 2019-11-05 10:00 F3, Stockholm
    Eriksson, Björn
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemical Engineering, Applied Electrochemistry.
    Electrochemical evaluation of new materials in polymer electrolyte fuel cells2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Polymer electrolyte fuel cells (PEFC) convert the chemical energy in hydrogen to electrical energy and heat, with the only exhaust being water. Fuel cells are considered key in achieving a sustainable energy sector. The main obstacles to wide scale commercialization are cost and durability. The aim of this thesis is to evaluate new materials for PEFC to potentially lower cost and increase durability. To lower the amount of expensive platinum catalyst in the fuel cell, the activities of Pt-rare earth metal (REM) alloy catalysts have been tested. To improve the lifetime of the carbon support, the carbon corrosion properties of multi walled carbon nanotubes have been evaluated. To reduce the overall cost of fuel cell stacks, carbon coated and metal coated bipolar plates have been tested. To increase the performance and lifetime of anion exchange membranes, the water transport has been studied.

    The results show that the Pt-REM catalysts had at least two times higher specific activity than pure platinum, and even higher activities should be obtainable if the surface structures are further refined.

    Multi-walled carbon nanotubes had lower carbon corrosion than conventional carbon Vulcan XC-72. However, once severely corroded their porous structure collapsed, causing major performance losses.

    The carbon coated metallic bipolar plates showed no significant increase of internal contact resistance (ICR) by cycling, suggesting that these coatings are stable in fuel cells. The NiMo- and NiMoP coated bipolar plates showed low ICR, however, presence of the coated bipolar plates caused secondary harmful effects on the polymer membrane and ionomer.

    Considering the water transport through anion exchange membranes it was found that most membranes showed very similar water transport properties, with more water detected at both the anode and cathode when a current was applied. The most significant factor governing the water transport properties was the membrane thickness, with thicker membranes reducing the backflow of water from anode to cathode.

    The results indicate that all of the new tested materials have the capability to improve the lifetime and reduce cost and thereby improve the overall performance of PEFC.

  • Public defence: 2019-11-05 12:00
    Jovanovic, Nenad
    KTH, School of Electrical Engineering and Computer Science (EECS). Research Technology Institute, Comillas Pontifical University, Spain; Delft University of Technology, the Netherlands..
    Electricity markets operation planning with risk-averse agents: stochastic decomposition and equilibium2019Doctoral thesis, monograph (Other academic)
    Abstract [en]

    The growing penetration of renewable energy sources in electricity systems requires adapting operation models to face the inherent variability and uncertainty of wind or solar generation. In addition, the volatility of fuel prices (such as natural gas) or the uncertainty of the hydraulic natural inflows requires to take into account all these sources of uncertainty within the operation planning of the generation system. Thus, stochastic optimization techniques have been widely used in this context. From the point of view of the system operation, the introduction of wind and solar generation in the mix has forced conventional generators to be subject to more demanding schedules from the technical point of view, increasing for example the number of start-up and shutdown decisions during the week, or having to face more pronounced ramps. From the point of view of the market, all these technical issues are transferred to the market prices that are subject to greater volatility. This thesis focuses on the problem of risk management using the Conditional Value at Risk (CVaR) as a coherent risk measure. The thesis presents a novel iterative method that can be used by a market agent to optimize its operating decisions in the short term when the uncertainty is characterized by a set of random variable scenarios. The thesis analyses how it is possible to decompose the problem of risk management by means of Lagrangian Relaxation techniques and Benders decomposition, and shows that the proposed iterative algorithm (Iterative-CVaR) converges to the same solution as under the direct optimization setting. The algorithm is applied to two typical problems faced by agents: 1) optimization of the operation of a combined cycle power plant (CCGT) that has to cope with the volatility in the spot market price to build the supply curve for the futures market, and 2) strategic unit-commitment model. In a second part of the thesis the problem of market equilibrium is studied to model the interaction between several generating companies with mixed generation portfolios (thermal, hydraulic and renewable). The thesis analyses how the Nash equilibrium solution is modified at different risk-aversion level of the risk of the agents. In particular, the thesis studies how the management of hydroelectric reservoirs ismodified along the annual horizon when agents are risk-averse, and it is compared with the risk-neutral solution that coincides with a centralized planning when the objective is the minimization expected operational cost.

  • Public defence: 2019-11-06 10:00 Kollegiesalen, Stockholm
    Song, Meng
    KTH, School of Electrical Engineering and Computer Science (EECS), Electric Power and Energy Systems.
    Planning and Operation of Demand-Side Flexibility2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Power systems are changing with growing penetration of non-dispatchable renewable generation and increased demand of electric energy. More generation, transmission or distribution capacities are needed to balance the varying production and higher consumption. Demand-side flexibility is a potential solutionto tackle those challenges. By shifting the consumption time and temporarily increase or decrease the power demand, the demand-side flexibility can help to integrate more wind and solar energy in the system, alleviate network congestion and postpone the investment for grid reinforcement. Therefore, technical and regulatory measures are undergoing in many countries to encourage demand response and engage customers.

    On the other hand, unlocking the flexibility will introduce more complexityand uncertainty on demand side. This would result in difficulties for different actors in power systems and power markets to make optimal decisionsin their planning and operation. The thesis addresses the problem by proposing methods to support the decision making of actors on demand side. Firstly, it develops models to facilitate residential customers and commercial electric vehicle fleet operators scheduling their shiftable appliances for reducing electricity cost. The willingness of households for responding to time-varying price is taken into account. Results from Stockholm Royal Seaport project are analysed to demonstrate such willingness. Secondly, the thesis develops models for the short-term planning of retailers and balance responsible players. Different approaches are deployed under price-taker and price-maker assumptions respectively. The planning concerns the price sensitivityof end customers and the risk related with certain bidding strategies.Thirdly, the thesis proposes models to coordinate and aggregate the flexible charging power of electric vehicles to provide regulation service on the balancing market. The models encompass the decision process from day-aheadplanning to real-time operation management. The proposed models in the thesis are based on the rules of Nordic electricity market and could be further developed for adapting to other market frameworks. Stochastic programmingis applied to address the uncertainties about consumption and market behaviours.In addition, the thesis discusses the impacts of demand response interms of generation cost, system reliability and market price. It shows that a widely implemented demand response can reduce the total generation cost, improve the reliability of supply and decrease the market price.

  • Public defence: 2019-11-07 10:00 Kollegiesalen, Stockholm
    Stigsson, Martin
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering.
    Structural Uncertainties of Rock Fractures and their Effect on Flow and Tracer Transport2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    A clear understanding of solute flow and transport through the network of fractures in the rock mass is essential for accurate long-term safety assessments of geological storage of hazardous waste. In a discrete fracture network (DFN) model, flow and transport of solutes are described by chains of flow paths through single fractures, each of which contributes to the total flow and transport properties of the rock mass. Hence, knowledge of the flow and transport properties of each single fracture is essential for accurate safety assessment.The void space that forms a fracture is a derivative of the roughness of the bounding surfaces and the normal force acting on the fracture and is hence dependent on accurate measurement of these properties. As all measurements are associated with uncertainties stemming from e.g. instrument imprecision, external disturbances and human factors, the measured value of the properties will not be single values, but probability distributions. Depending on the set of values drawn from these distributions, interpretations of flow and transport properties of sheared fractures in crystalline hard rock will vary.This thesis examines how flow and transport properties through single fractures are affected by uncertainties in fracture orientation and in roughness. By inferring the orientation and its uncertainty from the fracture intercepts in boreholes, a probability space for the orientation of the fracture is obtained. For a given stress state, this uncertainty in orientation will result in a distribution of normal stresses acting on the fracture. The roughness of the fracture and its uncertainty can be inferred from the small intersecting surfaces of the rock core, if the resolution is sufficient and the surface is representative of the fracture. The inferred roughness affects the correlation structure of the void between the two surfaces defining the fracture and, together with the distribution of normal stresses, produces different flow paths and hence different properties of flow and transport of solutes. Depending on the parameter combinations, the median and variance of the aperture field will change, as will the correlation structure of apertures. Since the flow and transport properties depend on the geometrical framework, the uncertainty will affect path length, travel time, transport resistance and flow-wetted surface. Higher normal stress acting on the fracture will typically result in longer travel times, longer travel lengths, higher transport resistance and larger flow-wetted surface. A rougher fracture will typically result in shorter travel times, longer travel lengths, lower transport resistance and smaller flow-wetted surface. The conclusion is, hence, that uncertainties in the geometric framework will affect flow and tracer transport properties.

  • Public defence: 2019-11-07 13:00 F3, Stockholm
    Åsberg, Per
    KTH, School of Industrial Engineering and Management (ITM), Industrial Economics and Management (Dept.).
    Brand Architecture from Above: Understanding the Customer Disconnect2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Global business is transforming. Information technology in general, and the Internet specifically, has globalized business and empowered the consumer with more information and choice than ever before. Consequently, academic research into brand portfolios and brand architecture is faced with new challenges to reflect this changing reality.

    Traditional research into brand portfolio management and its structural embodiment using brand architecture has approached these concepts from the perceptive of the brand owner/company. For instance, the portfolio has been mapped based on legal ownership of brands, which has been criticized as being a too narrow approach that exclude key contributors of the portfolio’s collective brand equity. Even in the cases where partner brands are acknowledged as part of the portfolio, their inclusion is often based on the revenue stream they represent or their link in the distribution chain instead of association. Brand architecture research has therefor focused on structural representations based on hierarchical trees created within the walls of the company itself, without necessarily investigating if the intended structure works as expected.

    The missing ingredient in this halting logic is the perceptions of the market in which the portfolio and its architecture operates. Associations and transfer of brand equity is dependent on a concept’s mental perception in the minds of consumers. An endorsement that does not get noticed by the target market is a mirage in the minds of marketing managers, and an historical collaboration that was cancelled years ago may still influence the brand portfolio today by means of association in consumer memory.

    The research presented in this thesis extends current theory in brand portfolio management and brand architecture to directly include the consumer perspective. This thesis re-classifies the portfolio and architecture concept as perceptual constructs whose efficiency is determined by the mental alignment between company representatives as the creators of the intended meaning and customers as the interpreters, or even co-creators, of the same. Study results presented indicate significant misalignment not only between stakeholder groups as a collective, but also between individuals within each group – even for brand managers working together on the same portfolio day after day. Current hierarchical models for representing brand architecture are extended using the perceptual dimension as well as a layer accounting for the openness of the portfolio, and a new brand portfolio model segregating brands based on the degree of perceptual inclusion in the portfolio is presented.

    This introduction of the perceptual dimension into both brand portfolio management and brand architecture represents a new way to view these abstract concepts, a conceptual idea that has ripple effects into areas such as brand equity transfer, brand alliances, and portfolio risk management.

  • Public defence: 2019-11-11 10:00 T2, Huddinge
    Meng, Shiyang
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Biomedical Engineering and Health Systems, Neuronic Engineering.
    Towards improved motorcycle helmet test methods for head impact protection: Using experimental and numerical methods2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Head injury is the leading cause of death and major trauma for users of powered two-wheelers (PTWs). Helmet use can prevent and reduce head injuries when a crash is inevitable. However, today’s motorcycle helmets do not protect equally against all types of head injuries. All helmets available on the market today are designed, manufactured and tested to meet certain standards. Current test standards evaluate helmet performance by dropping a helmeted headform perpendicular to an impact surface, and passing or failing a helmet based on the peak linear acceleration between 250-400G. Yet, real-world head impacts, being either linear (perpendicular) or oblique, impart both linear and angular head acceleration. Oblique impacts, which are known to be more common than linear impacts from in-depth analysis of motorcycle accidents, can transmit the tangential impulse to the head and hence cause the head to rotate. Head rotation has been hypothesised to be the main cause of traumatic brain injury (TBI) ranging from mild injuries such as concussions to more severe injuries such as acute subdural haematomas and diffuse axonal injuries. Therefore, there is a great need to develop test methods that replicate real-world accidents and reproduce realistic head impact responses. A number of potential test methods that subject the head to rotational insults are available today. However, there are still several questions that need to be answered: At what speed and angle should the helmet be tested? How boundary conditions of the head in the test methods, i.e. free, partially constrained or a surrogate neck, affect the kinematics of the head?

    To answer these research questions, both experimental and numerical methods, such as finite element (FE) methods were used. Experimental tests for the helmet were performed using multiple test methods, providing a comparison between the test methods and data for subsequent validation of the FE helmet model coupled with anthropomorphic test devices (ATDs). FE Human body models (HBMs) with accurate anatomical structures and material properties were employed to evaluate the biofidelity of current test methods. Brain tissue strain of a head model resulting from direct impacts or inertial loadings were used to provide a direct causal link between the mechanical insult and the brain injury.

    The first study in the thesis showed that both the US and European helmet standards lacked consideration for head rotation in linear impact tests. The US helmet standards use a partially constrained headform, which does not permit head rotation and hence not rotation induced TBI. European standards, on the other hand, adopt a free headform but the head rotation is not measured or assessed. The brain tissue strain resulting from the European standard tests at which rotation is allowed was up to 6.3 times higher than that in the US standards. In the second study, 300 simulations of possible motorcycle accidents were performed to understand the effect of impact velocity angle on impact severity. The results indicated that a 30o or 45o impact angle produced greater brain tissue strain than other impact angles, i.e., 15o, 60o and 75o. In the third study, it was found that when the helmeted head impacted the ground from low to high tangential velocities, i.e., 0-216 km/h, the motion of the helmet exhibited rolling and sliding phenomena. Since the helmet rolling and sliding phenomena govern impulses transmitted to the head-helmet system, and consequently the brain tissue strain, it is desirable to test helmets at speeds covering both the rolling and sliding regime. The tangential velocity at which motion transitioned from rolling to sliding was identified to be 10.8 m/s (38.9 km/h), given that the normal velocity is 5.66 m/s (20.4 km/h) and the coefficient of friction between the helmet outer shell and the impact surface is 0.45. In the final study, simulations with and without the experimental neck (Hybrid III) were compared to the HBMs. The results showed that the Hybrid III head-neck ATD used in the laboratory setting proved to correlate less with the head responses of the HBMs than the free headform. In particular, the Hybrid III head-neck ATD correlated poorly with the HBMs in axial (inferior-superior) acceleration and over-predicted the maximum angular velocity by up to 75%. However, the free headform was also limited in replicating the chin-neck and helmet-torso interactions. The need for a more biofidelic surrogate neck, especially under axial compression, is evident.

    In summary, this thesis demonstrates methodologies for a reason and objective based decision making process and provides important information in the design of future helmet test methods and standards. Some of the major findings in this thesis, despite focusing on motorcycle helmets, can also be applied to other types of helmets.

  • Public defence: 2019-11-13 10:00 FB54, Stockholm
    Hagrot, Erika
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Industrial Biotechnology.
    Macroscopic models of Chinese hamster ovary cell cultures2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Biopharmaceuticals treat a range of diseases, and is a growing sector within the pharmaceutical industry. A majority of these complex molecules are produced by genetically modified mammalian cells in large-scale cell cultures. Biopharmaceutical process development is costly and labor intensive, and has often been based on time-consuming empirical methods and trial-and-error. Mathematical modeling has great potential to speed up this work. A central question however, engaging researchers from various fields, is how to translate these complex biological systems into feasible and useful models.

    For biopharmaceutical production, macroscopic kinetic flux modeling has been proposed. This model type is derived from typical data obtained in the industry, and has been able to simulate cell growth and the uptake/secretion of important metabolites. Often, however, their scope is limited to specific culture conditions due to e.g. the lack of information on reaction kinetics, limited data sets, and simplifications to achieve calculability.

    In this thesis, the macroscopic kinetic model type is the starting point, but the goal is to capture a variety of culture conditions, as will be necessary for future applications in process optimization. The effects of varied availability of amino acids in the culture medium on cell growth, uptake/secretion of metabolites, and product secretion were studied in cell cultures.

    In Paper I, the established methodology of Metatool was tested: (i) a simplified metabolic network of approx. 30 reactions was defined; (ii) all possible so-called elementary flux modes (EFMs) through the network were identified using an established mathematical algorithm; and (iii) the effect on each flux was modelled by a simplified generalized kinetic equation. A limitation was identified; the Metatool algorithm could only handle simple networks, and therefore several reactions had to be discarded. In this paper, a new strategy for the kinetics was developed. A pool of alternative kinetic equations was created, from which a smaller set could be given higher weight as determined via data-fitting. This improved the simulations.

    The identification of EFMs was further studied in papers II–IV. In Paper II, a new algorithm was developed based on the column generation optimization technique, that in addition to the network also accounts for the data from one of the parallel cultures. The method identifies a subset of the EFMs that can optimally fit the data, even in more complex metabolic networks.

    In Paper III, a kinetic model based on EFM subsets in a 100 reaction network was generated, which further improved the simulations. Finally, in Paper IV, the algorithm was extended to EFM identification in a genome-scale network. Despite the high complexity, small subsets of EFMs relevant to the experimental data could be e ciently identified.

  • Public defence: 2019-11-20 10:00 Kollegiesalen, Stockholm
    Bakas, Panagiotis
    KTH, School of Electrical Engineering and Computer Science (EECS), Electric Power and Energy Systems.
    Hybrid Converters for HVDC Transmission2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The line-commutated converter (LCC) and the voltage-source converter (VSC) are the two main converter technologies utilized in high-voltage direct current (HVDC) transmission applications. Depending on the application requirements, one technology might be more advantageous than the other. On the one hand, the LCC features technological maturity, high efficiency, and high power-transfer capability, but it lacks the ability to independently control active and reactive power and to ride through ac faults. On the other hand, the VSC overcomes the shortcomings of the LCC and offers more functionality, as it features the ability to independently control active and reactive power, ac-fault ride through capability, black-start capability, and superior harmonic performance. Yet, it is less mature, less efficient, and has lower power-transfer capability than the LCC. Thus, the combination of the LCC and the VSC topologies could yield hybrid converters that leverage the complementary characteristics of both technologies and thus are optimized for HVDC applications. Therefore, the main objective of this thesis is to investigate existing and derive new hybrid converters that combine the complementary characteristics of the LCC and VSC technologies.

    The hybrid converters investigated in this thesis are divided in two main categories, namely: (a) current-source; and (b) voltage-source hybrid converters. The former category includes hybrid converters that are based on the LCC structure and utilize a VSC part either for compensating the reactive power consumed by the LCC, or for active filtering of the LCC current harmonics, or for independently controlling active and reactive power, or for achieving a combination of these functionalities. Four different current-source hybrid converters have been investigated and compared in terms of functionality, conduction losses, and semiconductor requirements.

    The second category includes more complex circuits that combine thyristors and modular VSC elements in ways that enable these hybrid converters to operate as VSCs and to achieve high active-power capability. Two new voltage-source hybrid converters are analyzed and compared in terms of active-power capability, semiconductor requirements, and controllability. This study reveals that the hybrid alternate-common-arm converter (HACC) is the most interesting circuit; thus, an in-depth analysis is performed for this converter. The theoretical analysis shows that, under certain operating conditions, the HACC can transfer twice the active power of the full-bridge modular multilevel converter (FB-MMC) with lower semiconductor rating per unit of active power. Yet, if the total commutation time of the thyristors and/or the power angle are increased beyond certain values, the active-power capability of the HACC is reduced. Finally, simulation and experimental results are provided in order to verify the theoretical analysis and prove the feasibility of the HACC.

  • Public defence: 2019-11-22 10:00 M3, Stockholm
    He, Yunjuan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Surface and Corrosion Science.
    Corrosion protection and nanomechanical properties of waterborne acrylate-based coating with and without nanocellulose on carbon steel2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Corrosion protection is commonly achieved by applying a thin polymer coating on metal surfaces. In this doctoral thesis, a waterborne hydroxyacrylate-melamine copolymer coating was used for this purpose. The first step was to find the optimal curing conditions. To this end the effect of curing time at 180 °C on the conversion of the cross-linking reaction, surface topography, nanomechanical and nanowear properties were investigated using atomic force microscopy, AFM. The results demonstrated that optimal performance required 10 min curing at 180 °C. This resulted in 80% conversion of the cross-linking reaction, as well as good barrier performance with polarization resistance of the order of 109Ω·cm2during 35 days in 0.1 M NaCl solution as determined by Electrochemical Impedance Spectroscopy (EIS). It also resulted in minor surface roughness and high surface elastic modulus in the order of GPa. 


    This waterborne coating and its nanocomposite containing 0.5 wt.% cellulose nanocrystals (CNC) were systematically studied, focusing on their corrosion protection performance and the effect of environment and localized wear on the properties of the top surface. The results show that both coatings have high polarization resistance, Rp. For the matrix coating the polarization resistance displays a slightly decreasing trend with time, as expected for a barrier coating. In contrast, the CNC nanocomposite coating exhibits an unusual and unexpected increase in polarization resistance with time. The difference in the time dependence of Rp can be attributed to the reinforcement effect of CNC, which form strong hydrogen bonding interactions with the matrix coating. Further, the appearance of a second time constant in the corresponding EIS spectra implies formation of a more protective second layer at the metal-coating interface. The presence of this compact layer also contributes to the corrosion protection offered by the CNC nanocomposite coating. In addition, both coatings show only limited water-uptake during long term exposure to 0.1 M NaCl. The water up-take is too small to measurably change the coating capacitance, as studied by EIS. However, AFM studies of surface nanomechanical properties show that for the CNC nanocomposite some water penetration occurs, which irreversibly renders the surface softer.


    Inspired by the CNC nanocomposite coating and its favorable corrosion protective properties, 0.5 wt.% cellulose nanofibrils, CNF, nanocomposite coatings were also studied using the same methodologies. The results revealed that the CNF nanocomposite coating cannot provide efficient corrosion protection performance even over a period of 24 h. The measured polarization resistance decreases rapidly over time, and consistently water uptake is readily observed by analyzing coating capacitance using EIS technique. The substantial difference in corrosion protective properties of the CNC nanocomposite and the CNF nanocomposite are explained mainly from the perspective of microstructure, matrix-CNC or matrix-CNF interactions by using scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR). The results show the presence of defects on the surface and in the bulk and absence of strong hydrogen bonding interactions between matrix and CNF. These are two reasons for why the CNC nanocomposite performs well in terms of corrosion protection, whereas the CNF nanocomposite does not. 


    In real applications good barrier coatings may also fail due to external forces such as erosion by wind and water, impact of solid particles or sliding motions against other objects, which may destroy the coating integrity. This motivated further studies of the matrix and the CNC nanocomposite, by focusing on their nanomechanical and nano-wear properties using local measurements by means of AFM. The effect of applied normal load, ranging from 50 – 400 nN, scanning speed, ranging from 1 – 20 µm/s, operating environment including air and water, as well as exposure to corrosive 0.1 M NaCl solution, were systematically studied and discussed.

  • Public defence: 2019-11-22 13:00 Kollegiesalen, Stockholm
    Johansson, Stefan
    KTH, School of Electrical Engineering and Computer Science (EECS), Media Technology and Interaction Design, MID.
    Design for Participation and Inclusion will Follow: Disabled People and the Digital Society2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Digitalization is rapidly taking over all aspects of society, but still there are parts of the population who have to struggle for access to, and to be able to use, the digital resources. Design processes and outcomes in the form of artefacts, that takes accessibility into account, is key to participation. This gives the designer a central role in providing for a more equal participation of all, in the digital society. The work in this thesis contributes to a better understanding of the prerequisites for participation in the digital society, and in the design processes to accomplish this, by presenting research done together with three communities: people with cognitive impairments, people with mental health issues and homeless people.

    The overall question has been How can participation in the digital society be understood? We have investigated the nature of difficulties or enabling factors for people with impairments, people with mental health issues and homeless people, when using the internet. We have also investigated possible digital divides within the groups, and how they can be explained.

    Ontologically, the work is based on an assumption that knowledge is to be found in a dialectic interplay between the material world and how we interpret what is going on in this world. The underlying epistemological assumption is that data has to be empiric, and critically interpreted in dialogue between members of the communities, which are being researched, and other stakeholders. This work draws on the idea of emancipation and that research can be liberating.

    The work also takes on a pragmatic stance. We have used adapted versions of Emancipatory Participatory Research, and of Participatory and Value Sensitive Design, thus making them accessible to people with cognitive impairments, people with mental health issues or homeless people. We have tested and adapted methods for sampling of rare populations, to enhance the quality of quantitative studies of how people with impairments and people with mental health issues have access to, and are using, the internet.

    In our research, we have found fourteen prerequisites, all of which need to be in place to provide for participation. To promote participation, we need a toolbox of methods and accessible tools. Finally, to analyse what is going on we need an analytical model which allows for analysis on multiple levels and from multiple perspectives.

    As a result, I here propose, define and position a framework for researching and understanding participation in the digital society, based on three parts: Guidelines, Ethics and Statistics. Guidelines can be understood as the theories, the regulations, the standards, etc. that inform our thinking. Ethics guide us in the right direction. Statistics make progress or lack of progress visible.

    The conclusion is: if we plan for participation - by improved statistic survey sampling methods, a participatory approach to collaborative research and in using research methods in an accessible and emancipatory way – inclusion will follow.

  • Public defence: 2019-12-03 10:00 Kollegiesalen, Stockholm
    Ahmed, Laeeq
    KTH, School of Electrical Engineering and Computer Science (EECS), Computational Science and Technology (CST).
    Scalable Analysis of Large Datasets in Life Sciences2019Doctoral thesis, monograph (Other academic)
    Abstract [en]

    We are experiencing a deluge of data in all fields of scientific and business research, particularly in the life sciences, due to the development of better instrumentation and the rapid advancements that have occurred in information technology in recent times. There are major challenges when it comes to handling such large amounts of data. These range from the practicalities of managing these large volumes of data, to understanding the meaning and practical implications of the data.

    In this thesis, I present parallel methods to efficiently manage, process, analyse and visualize large sets of data from several life sciences fields at a rapid rate, while building and utilizing various machine learning techniques in a novel way. Most of the work is centred on applying the latest Big Data Analytics frameworks for creating efficient virtual screening strategies while working with large datasets. Virtual screening is a method in cheminformatics used for Drug discovery by searching large libraries of molecule structures. I also present a method for the analysis of large Electroencephalography data in real time. Electroencephalography is one of the main techniques used to measure the brain electrical activity.

    First, I evaluate the suitability of Spark, a parallel framework for large datasets, for performing parallel ligand-based virtual screening. As a case study, I classify molecular library using prebuilt classification models to filter out the active molecules. I also demonstrate a strategy to create cloud-ready pipelines for structure-based virtual screening. The major advantages of this strategy are increased productivity and high throughput. In this work, I show that Spark can be applied to virtual screening, and that it is, in general, an appropriate solution for large-scale parallel pipelining. Moreover, I illustrate how Big Data analytics are valuable in working with life sciences datasets.

    Secondly, I present a method to further reduce the overall time of the structured-based virtual screening strategy using machine learning and a conformal-prediction-based iterative modelling strategy. The idea is to only dock those molecules that have a better than average chance of being an inhibitor when searching for molecules that could potentially be used as drugs. Using machine learning models from this work, I built a web service to predict the target profile of multiple compounds against ready-made models for a list of targets where 3D structures are available. These target predictions can be used to understand off-target effects, for example in the early stages of drug discovery projects.

    Thirdly, I present a method to detect seizures in long term Electroencephalography readings - this method works in real time taking the ongoing readings in as live data streams. The method involves tackling the challenges of real-time decision-making, storing large datasets in memory and updating the prediction model with newly produced data at a rapid rate. The resulting algorithm not only classifies seizures in real time, it also learns the threshold in real time. I also present a new feature "top-k amplitude measure" for classifying which parts of the data correspond to seizures. Furthermore, this feature helps to reduce the amount of data that needs to be processed in the subsequent steps.