| 1. |
- Eriksson, Martin
(författare)
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Photoluminescence Characteristics of III-Nitride Quantum Dots and Films
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- III-Nitride semiconductors are very promising in both electronics and optical devices. The ability of the III-Nitride semiconductors as light emitters to span the electromagnetic spectrum from deep ultraviolet light, through the entire visible region, and into the infrared part of the spectrum, is a very important feature, making this material very important in the field of light emitting devices. In fact, the blue emission from Indium Gallium Nitride (InGaN), which was awarded the 2014 Nobel Prize in Physics, is the basis of the common and important white light emitting diode (LED).Quantum dots (QDs) have properties that make them very interesting for light emitting devices for a range of different applications, such as the possibility of increasing device efficiency. The spectrally well-defined emission from QDs also allows accurate color reproduction and high-performance communication devices. The small size of QDs, combined with selective area growth allows for an improved display resolution. By control of the polarization direction of QDs, they can be used in more efficient displays as well as in traditional communication devices. The possibility of sending out entangled photon pairs is another QD property of importance for quantum key distribution used for secure communication.QDs can hold different exciton complexes, such as the neutral single exciton, consisting of one electron and one hole, and the biexciton, consisting of two excitons. The integrated PL intensity of the biexciton exhibits a quadratic dependence with respect to the excitation power, as compared to the linear power dependence of the neutral single exciton. The lifetime of the neutral exciton is 880 ps, whereas the biexciton, consisting of twice the number of charge carriers and lacks a dark state, has a considerably shorter lifetime of only 500 ps. The ratio of the lifetimes is an indication that the size of the QD is in the order of the exciton Bohr radius of the InGaN crystal making up these QDs in the InGaN QW.A large part of the studies of this thesis has been focused on InGaN QDs on top of hexagonal Gallium Nitride (GaN) pyramids, selectively grown by Metal Organic Chemical Vapor Deposition (MOCVD). On top of the GaN pyramids, an InGaN layer and a GaN capping layer were grown. From structural and optical investigations, InGaN QDs have been characterized as growing on (0001) facets on truncated GaN pyramids. These QDs exhibit both narrow photoluminescence linewidths and are linearly polarized in directions following the symmetry of the pyramids.In this work, the neutral single exciton, and the more rare negatively charged exciton, have been investigated. At low excitation power, the integrated intensity of the PL peak of the neutral exciton increases linearly with the excitation power. The negatively charged exciton, on the other hand, exhibits a quadratic power dependence, just like that of the biexciton. Upon increasing the temperature, the power dependence of the negatively charged exciton changes to linear, just like the neutral exciton. This change in power dependence is explained in terms of electrons in potential traps close to the QD escaping by thermal excitation, leading to a surplus of electrons in the vicinity of the QD. Consequently, only a single exciton needs to be created by photoexcitation in order to form a negatively charged exciton, while the extra electron is supplied to the QD by thermal excitation.Upon a close inspection of the PL of the neutral exciton, a splitting of the peak of just below 0.4 meV is revealed. There is an observed competition in the integrated intensity between these two peaks, similar to that between an exciton and a biexciton. The high energy peak of this split exciton emission is explained in terms of a remotely charged exciton. This exciton state consists of a neutral single exciton in the QD with an extra electron or hole in close vicinity of the QD, which screens the built-in field in the QD.The InGaN QDs are very small; estimated to be on the order of the exciton Bohr radius of the InGaN crystal, or even smaller. The lifetimes of the neutral exciton and the negatively charged exciton are approximately 320 ps and 130 ps, respectively. The ratio of the lifetimes supports the claim of the QD size being on the order of the exciton Bohr radius or smaller, as is further supported by power dependence results. Under the assumption of a spherical QD, theoretical calculations predict an emission energy shift of 0.7 meV, for a peak at 3.09 eV, due to the built-in field for a QD with a diameter of 1.3 nm, in agreement with the experimental observations.Studying the InGaN QD PL from neutral and charged excitons at elevated temperatures (4 K to 166 K) has revealed that the QDs are surrounded by potential fluctuations that trap charge carriers with an energy of around 20 meV, to be compared with the exciton trapping energy in the QDs of approximately 50 meV. The confinement of electrons close to the QD is predicted to be smaller than for holes, which accounts for the negative charge of the charged exciton, and for the higher probability of capturing free electrons. We have estimated the lifetimes of free electrons and holes in the GaN barrier to be 45 ps and 60 ps, in consistence with excitons forming quickly in the barrier upon photoexcitation and that free electrons and holes get trapped quickly in local potential traps close to the QDs. This analysis also indicates that there is a probability of 35 % to have an electron in the QD between the photoexcitation pulses, in agreement with a lower than quadratic power dependence of the negatively charged exciton.InN is an attractive material due to its infrared emission, for applications such as light emitters for communication purposes, but it is more difficult to grow with high quality and low doping concentration as compared to GaN. QDs with a higher In-composition or even pure InN is an interesting prospect as being a route towards increased quantum confinement and room temperature device operation. For all optical devices, p-type doping is needed. Even nominally undoped InN samples tend to be heavily n-type doped, causing problems to make pn-junctions as needed for LEDs. In our work, we present Mg-doped p-type InN films, which when further increasing the Mg-concentration revert to n-type conductivity. We have focused on the effect of the Mg-doping on the light emission properties of these films. The low Mg doped InN film is inhomogeneous and is observed to contain areas with n-type conductivity, so called n-type pockets in the otherwise p-type InN film. A higher concentration of Mg results in a higher crystalline quality and the disappearance of the n-type pockets. The high crystalline quality has enabled us to determine the binding energy of the Mg dopants to 64 meV. Upon further increase of the Mg concentration, the film reverts to ntype conductivity. The highly Mg doped sample also exhibits a red-shifted emission with features that are interpreted as originating from Zinc-Blende inclusions in the Wurtzite InN crystal, acting as quantum wells. The Mg doping is an important factor in controlling the conductivity of InN, as well as its light emission properties, and ultimately construct InN-based devices.In summary, in this thesis, both pyramidal InGaN QDs and InGaN QDs in a QW have been investigated. Novel discoveries of exciton complexes in these QD systems have been reported. Knowledge has also been gained about the challenging material InN, including a study of the effect of the Mg-doping concentration on the semiconductor crystalline quality and its light emission properties. The outcome of this thesis enriches the knowledge of the III-Nitride semiconductor community, with the long-term objective to improve the device performance of III-Nitride based light emitting devices.
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| 2. |
- Kurujyibwami, Celestin
(författare)
-
Admissible transformations and the group classification of Schrödinger equations
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- We study admissible transformations and solve group classification problems for various classes of linear and nonlinear Schrödinger equations with an arbitrary number n of space variables.The aim of the thesis is twofold. The first is the construction of the new theory of uniform seminormalized classes of differential equations and its application to solving group classification problems for these classes. Point transformations connecting two equations (source and target) from the class under study may have special properties of semi-normalization. This makes the group classification of that class using the algebraic method more involved. To extend this method we introduce the new notion of uniformly semi-normalized classes. Various types of uniform semi-normalization are studied: with respect to the corresponding equivalence group, with respect to a proper subgroup of the equivalence group as well as the corresponding types of weak uniform semi-normalization. An important kind of uniform semi-normalization is given by classes of homogeneous linear differential equations, which we call uniform semi-normalization with respect to linear superposition of solutions.The class of linear Schrödinger equations with complex potentials is of this type and its group classification can be effectively carried out within the framework of the uniform semi-normalization. Computing the equivalence groupoid and the equivalence group of this class, we show that it is uniformly seminormalized with respect to linear superposition of solutions. This allow us to apply the version of the algebraic method for uniformly semi-normalized classes and to reduce the group classification of this class to the classification of appropriate subalgebras of its equivalence algebra. To single out the classification cases, integers that are invariant under equivalence transformations are introduced. The complete group classification of linear Schrödinger equations is carried out for the cases n = 1 and n = 2.The second aim is to study group classification problem for classes of generalized nonlinear Schrödinger equations which are not uniformly semi-normalized. We find their equivalence groupoids and their equivalence groups and then conclude whether these classes are normalized or not. The most appealing classes are the class of nonlinear Schrödinger equations with potentials and modular nonlinearities and the class of generalized Schrödinger equations with complex-valued and, in general, coefficients of Laplacian term. Both these classes are not normalized. The first is partitioned into an infinite number of disjoint normalized subclasses of three kinds: logarithmic nonlinearity, power nonlinearity and general modular nonlinearity. The properties of the Lie invariance algebras of equations from each subclass are studied for arbitrary space dimension n, and the complete group classification is carried out for each subclass in dimension (1+2). The second class is successively reduced into subclasses until we reach the subclass of (1+1)-dimensional linear Schrödinger equations with variable mass, which also turns out to be non-normalized. We prove that this class is mapped by a family of point transformations to the class of (1+1)-dimensional linear Schrödinger equations with unique constant mass.
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| 3. |
- Liu, Yuan
(författare)
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Theoretical Studies of Natural Gas Hydrates and H-bonded Clusters and Crystals
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In this thesis H-bonded systems (natural gas hydrates, water clusters, and crystal ice) are studied by density functional theory (DFT) computations.Natural gas hydrates (NGHs) play an important role in energy and environmental fields: NGHs are considered as a promising backup energy resource in the near-future due to their tremendous carbon content; improper exploration of NGHs could induce geological disasters and aggravate the greenhouse effect. In addition, many technologies based on gas hydrates are being applied and developed. The thermodynamic stabilities of various water cavities in different clathrate crystalline phases occupied by hydrocarbon gas molecules are studied by dispersion-corrected hybrid functionals. The Raman spectra of C-C and C-H stretching vibrations of hydrocarbon molecules in various water cavities in the solid state are derived. The trends of C-H stretching vibrational frequencies are found to follow the prediction by the “loose cage ─| tight cage” model. In addition, the trends and origins of 13C NMR chemical shifts of hydrocarbon molecules in various NGHs are presented. These theoretical results will enlarge the database of C-C and C-H stretching vibrational frequencies and 13C NMR parameters of hydrocarbon molecules in NGHs, and provide valuable information to help identify the types of clathrate phases and varieties of guest molecules included in NGHs samples taken from natural sites.The behavior of water clusters may help to understand the properties of its liquid and solid states. The thermodynamic stabilities and IR spectra of a small-, medium-, and large-sized water cluster are studied in this work. After full optimization of (H2O)20,54,100 using the hybrid functional B3LYP, the electronic energies, zero-point energies, internal energies, enthalpies, entropies, and Gibbs free energies of the water clusters are computed. The OH stretching vibrational IR spectra of (H2O)20,54,100 are also presented and split into sub-spectra for different H-bond types based on the specific contributions from each group. It is found that the OH stretching vibrational frequencies of water are sensitive to the conformations of the H-bonds and the vibrations of the H-bonds belonging to different types are located in separated regions in the IR spectra. Thus, the spectroscopic fingerprints will reflect the H-bond topology of the water molecules in a water cluster.Ice XI has been suggested to be involved in the process of planetary formation as a considerable electric field might be formed from the ferroelectric ice XI in space. IR and Raman spectroscopic technology can be directly used to identify the occurrence of ferroelectric ice XI in laboratory or extraterrestrial settings. Due to the difficulty for DFT to describe non-covalent systems, the performance of 16 different DFT methods applied on the ice Ih, VIII, IX, and XI crystal phases are assessed. Based on the computational accuracy and cost, the IR and Raman spectra of ice Ih and XI are derived and compared. The librational vibrations are found to be the identifier which can be used to distinguish ice Ih and ice XI in the universe. In addition, the existence only one kind of H-bond in ice Ih is demonstrated from the overlapping sub-spectra for different types of H-bonded pair configurations in 16 isomers of ice Ih.The region of water under negative pressure is an exotic land in lack of exploitation. Guest free clathrate hydrate (clathrate ice) of sII type has been recently confirmed experimentally at negative pressure. Does any other clathrate ice phase exist at negative pressure region? Since clathrate hydrate are isostructural with silica clathrate minerals and semiconductor clathrates, and crystal structure prediction by analogy with known structures and first-principles computations is an effective way to find new crystalline phases of solid materials, we are motived to look for new clathrate ice phases from silica or semiconductor clathrate materials based on first-principles computations. Borrowing the idea new clathrate frameworks of ZnO and SiC can be constructed by connecting their bubble clusters in different ways, new clathrate ice phases (sL, sL_I, sL_II, and sL_III) are generated by connecting the water bubble clusters according to different rules. Using the non-local dispersion-corrected vdW-DF2 functional, clathrate ice sL with ultralow density (0.6 g/cm3) is predicted by first-principles phase diagram computations to be stable under larger negative pressures than the sII phase. The phase diagram of water is thus extended into the lower negative pressure region.
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| 4. |
- Zhang, Xin, 1990-
(författare)
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Tailoring Fluorescent Probes for Organelle-Specific Imaging and Sensing
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Exploring and visualizing biological and pathological processes in living cells are useful for both fundamental research and applications. An understanding on the molecular level for these processes with focus on tracking biomarkers, collecting information about their surroundings, and uncovering essential molecular pathways and functions in live cells are of vital interest for cell biological study and clinical diagnosis application. Fluorescent imaging technologies have become essential tools in cell biology studies, providing dynamic information about the localization and quantity of the analytes in living systems that we can not see by our naked eyes. Since the discovery of organic fluorescent dyes, unremitting efforts have been made to visualize the behaviors of specific targets by using these fluorophores as labels. Today, a variety of probes and nanoprobes have been developed for specific targeting and sensing. However, the current probes and nanoprobes still show some inherent deficiencies, such as poor specificity, strong photobleaching, high toxicity, low signal-to-noise ratio, poor cell membrane penetration, etc. To conquer these limitations, this thesis will focus on developing fluorescent platforms for bioimaging and biosensing with improved sensitivity, selectivity, specificity, and stability.A red-emitting fluorescent probe is first proposed that not only tracks the dynamic changes in real-time, during migration and fusion of lipid droplets but also monitors starvation-induced lipophagy (Paper I). In addition to organic fluorophores, hybrid fluorescent silica nanoparticles (SiNPs) are very promising for bioimaging/sensing owing to the advantages of low toxicity, high biocompatibility, multifunctionality, hydrophilicity and accessible surface functionality. Nonetheless, to apply SiNPs for such purposes, it is mandatory to address common problems of poor cell penetration and lack of specificity. Therefore, in this thesis, an efficient membrane-penetration SiNP is tailored with the intention to enable subcellular imaging/sensing. The proposed SiNPs are characterized by rapid cellular uptake (˂ 30 min) and specific subcellular targeting capabilities with surface modification. Finally, real-time tracking of dynamic changes in mitochondria and lysosomes during autophagy process is successfully performed (Paper II). Through the rational design of new functionalities on the established SiNPs, mitochondria- and lysosome-specific pH nanoprobes are further tailored for real-time monitoring of pH variations under various stimuli (Paper III and IV). Another ratiometric nanoprobe is developed for quantitative indication of lysosomal adenosine 5'-triphosphate (ATP) levels in living cells. The nanoprobe enables a deeper understanding of the interplay between energy metabolism and autophagy (Paper V).In conclusion, throughout the studies in this thesis, the fabrication and utilization of fluorescent molecular probes and SiNP-based nanoprobes for cellular probing have been investigated and analyzed. The strategies and the fabricated SiNPs can facilitate our deeper understanding of cellular pathological processes and provide basic knowledge for the development of other functional materials for life science applications.
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| 5. |
- Fashandi, Hossein, 1984-
(författare)
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Novel Layered and 2D Materials for Functionality Enhancement of Contacts and Gas Sensors
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Chemical gas sensors are widely-used electronic devices for detecting or measuring the density levels of desired gas species. In this study, materials with established or potential applications for gas sensors are treated. For the case of high-temperature applications (≈ 600 °C), semiconductor-based gas sensors suffer from rapid oxidation of the metallic ohmic contacts, the same cause-of-failure as for the general case of high-temperature semiconductor electronics. 4H-SiC is an ideal semiconductor for high-temperature applications. Ti3SiC2 is a known ohmic contact to 4H-SiC with the known two-step synthesis process of post-annealing of pre-deposited Ti/Al multilayers or sputter-deposition of Ti3SiC2 films at > 900 °C. Here, sputter-deposition of Ti on 4H-SiC at > 900 °C is presented as a novel single-step method for the synthesis of Ti3SiC2 ohmic contacts, based on a concurrent reaction between sputter-deposited Ti and 4HSiC. Ti3SiC2, similar to any other known ohmic contact, degrade rapidly in high-temperature oxidizing ambient. To try to overcome this obstacle, noble metal diffusion into Ti3SiC2 has been s studied with the goal to retain ohmic properties of Ti3SiC2 and harnessing oxidation resistivity of noble metals. A novel exchange intercalation between Ti3SiC2 and Au is discovered which results in the almost complete exchange of Si with Au giving rise to novel Ti3AuC2 and Ti3Au2C2. Ti3IrC2 is also synthesized through exchange intercalation of Ir into Ti3Au2C2. All the aforementioned phases showed ohmic properties to 4H-SiC. This technique is also studied based on Ti2AlC and Ti3AlC2 resulting in the synthesis of novel Ti2Au2C and Ti3Au2C2, respectively. Using Ti3AuC2 and an Au/IrOx capping layer, an ohmic contact was manufactured, which maintained ohmic properties and showed no structural defects after 1000 h of aging at 600 °C air.Ti3SiC2 is a member of a large family of materials known as Mn+1AXn phases. While exchange reactions of Si (or Al) planes in Ti3SiC2 (Ti2AlC and Ti3AlC2) is presented here, a world-wide research already exists on chemical removal of the same atomic planes from different Mn+1AXn phases and the synthesis of Mn+1Xn sheets known as MXenes. I performed a theoretical study regarding simulation of electronic and structural properties of more than120 different possible MXene phases. The results show that some MXene phases, when terminated by particular gas species, turn into Dirac materials. That is, they possess massless Dirac fermions with different properties compared to graphene such as higher number of Dirac points at the Fermi level, giant spin orbit splitting, and preserved 2D-type electronic properties by extending the dimensionality. The general substantial change of the electronic properties of MXenes under different gas adsorption configurations stands out and can thus be harnessed for sensing applications.Growth of monolayer iron oxide on porous Pt sensing layers is another novel approach used in this study for applying the unique properties of 2D materials for gas sensors. A low temperature shift in CO oxidation characteristics is presented. The approach is similar to that previously reported using bulk single crystal Pt substrate, the latter being an unrealistic model for sensors and catalysts. Monolayer-coated Pt sensing layers were fabricated as the metal component of a metal oxide semiconductor (MOS) capacitor device, whereby the electrical response of the MOS device could be used to map out the catalytic properties of the sensing layer. The monolayer-coated Pt surface showed to be stable with retained improved catalytic properties for > 200 h. The MOS device measurements are here utilized as a handy method for in-situ monitoring of the surface chemical properties of the monolayer-coated Pt and the approach is highly functional for use and characterization of monolayer coatings of widely used sensingor catalytic layers.
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| 6. |
- Sani, Negar
(författare)
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Addressability and GHz Operation in Flexible Electronics
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The discovery of conductive polymers in 1977 opened up a whole new path for flexible electronics. Conducting polymers and organic semiconductors are carbon rich compounds that are able to conduct charges while flexed and are compatible with low-cost and large-scale processes including printing and coating techniques. The conducting polymer has aided the rapidly expanding field of flexible electronics, leading to many new applications such as electronic skin, RFID tags, smart labels, flexible displays, implantable medical devices, and flexible sensors.However, there are several remaining challenges in the production and implementation of flexible electronic materials and devices. The conductivity of organic conductors and semiconductors is still orders of magnitude lower compared to their inorganic counterparts. In addition, non-flexible inorganic semiconductors still remain the materials of choice for high frequency applications; since the charge carrier mobility and thus operational speed of the organic materials are limited. Therefore, there remains a high demand to combine the high frequency operation of inorganic semiconductors with the flexible fabrication methods of organic systems for future electronics.In addition to the challenges in the choice of materials in flexible electronics, the upscaling of the flexible devices and implementing them in circuits can also be complicated. Lack of non-linearity is an issue that arises when flexible devices with linear behavior need to be incorporated in an array or matrix form. Non-linearity is important for applications such as displays and memory arrays, where the devices are arranged as matrix cells addressed by their row and column number. If the behavior of cells in the matrix is linear, addressing each cell affects the adjacent cells. Therefore, inducing non-linearity and, consequently, addressability in such linear devices is the first step before scaling up into matrix schemes.In this work, non-linear organic/inorganic hybrid devices are produced to overcome the limitations mentioned above and leverage the advantages of both organic and inorganic materials. Two novel methods are developed to incorporate non-flexible inorganic semiconductors into ultra-high frequency (UHF) flexible devices. In the first method, Si is ground into a powder with micrometer-sized particles and printed through standard screen printing. For the first time, allprinted flexible diodes operating in the GHz range are produced. The energy harvesting application of the printed diodes is demonstrated in a flexible circuit coupling an antenna and the display to the diode.A second and simpler room-temperature method based on lamination was later developed, which further improves device performance and operational frequency. For the first time, a flexible semiconducting composite film consisting of Si micro-particles, glycerol, and nano-fibrillated cellulose is produced and used as the semiconducting layer of the UHF diode.The diodes fabricated through both mentioned processes are demonstrated in energy harvesting applications in the GHz range; however, they can also serve as rectifiers or non-linear elements in any other flexible and UHF circuit.Furthermore, a new approach is developed to induce non-linearity and hence addressability in linear devices in order to make their implementation in flexible matrix form feasible. This is accomplished by depositing a ferroelectric layer on a device electrode and thus controlling charge transfer through the electrode. The electrode current becomes limited to the charge displacement current established in the ferroelectric layer during polarization. Thus, the current does not follow the voltage linearly and non-linearity is induced in the device. The polarization voltage is dictated by the thickness of the ferroelectric layer. Therefore, the switching voltage of the device can be tuned by adjusting the ferroelectric layer thickness. In this work, the organic ferroelectric poly(vinylidene fluoride-co-trifluoroethylene) (P(VDF-TrFE)) is used due to its distinctive properties such as stability, high polarizability and simple processability. The polarization of P(VDF-TrFE) through an electrolyte and an electrophoretic liquid is investigated. In addition, a simple model is presented in order to understand the field and potential distribution, and the ferroelectric polarization, in the P(VDF-TrFE)-electrolyte contact. The induction of non-linearity through P(VDF-TrFE) is successfully demonstrated in novel addressable and bistable devices and memory elements such as non-linear electrophoretic display cells, organic ferroelectrochromic displays (FeOECDs), and ferroelectrochemical organic transistors (FeOECTs).
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| 7. |
- Speda, Jutta
(författare)
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Methods development for metaproteomics-guided bioprospecting of novel enzymes
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Industrial biotechnology has been announced by several organizations and governments as a key enabling technology for the enhanced economic growth in a low-carbon and knowledge-based bioeconomy. An important goal to promote an environment friendly and sustainable industrial biotechnology is the discovery of new enzymes.To date, almost all enzymes used in industry have been discovered by pure culturing of microorganisms, however, it is known that less than 1% of all microorganisms can be obtained in pure cultures. The remaining majority of microorganisms is only viable by close biological interactions provided in microbial communities and is not available for enzyme discovery using the classical pure culture approaches. The investigation of microbial communities, which can be viewed as metaorganisms, has been enabled during the last two decades by refining established methods for the analysis of genes, mRNA or proteins and are called metagenomics, metatranscriptomics and metaproteomics, respectively. To date, these techniques have mostly been used in the field of microbial ecology for the understanding of the composition, function and metabolism of microbial communities but not for the purpose of bioprospecting for novel enzymes. Identification of genes that code for possible enzyme candidates is hindered, due to the fact that 30-40% of the sequenced metagenomes contain genes coding for unidentified proteins. Additionally, the -omics techniques generate large amounts of data that need to be analyzed and the outcome of the analysis does not necessarily lead to the discovery of novel applicable enzymes.The work presented in this thesis describes the establishment of the necessary conditions for a metaproteomics-based method that allows for a straightforward and targeted identification of novel enzymes with desired activity from microbial communities. The approach provides a valuable alternative to the incomplete and inefficient analysis of non-targeting data and laborious workflow, which is typically generated by the established meta-omics techniques. In developing the methods presented in this thesis, microbial communities in constructed environments were established, which allowed for the controlled expression of extracellular hydrolytic enzymes under defined conditions. By combination and modulation of advanced metaproteomics and metagenomics techniques, we were able to directly identify the enzymes and the corresponding gene sequences of several cellulolytic enzymes as a first example for the feasibility of this approach.
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| 8. |
- Tengdelius, Mattias, 1984-
(författare)
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Fucoidan-Mimetic Glycopolymers : Synthesis and Biomedical Applications
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The marine polysaccharide fucoidan has demonstrated several interesting biological properties, for instance being antiviral, anticoagulant, anti-inflammatory, anticancer, and platelet activating. Many of these properties are desirable for various biomedical applications. Yet, there are few reports on fucoidan being used in such applications. The reasons for this are primarily the heterogeneity and low structural reproducibility of fucoidan.This thesis describes the synthesis of polymers with pendant saccharides bearing the key structural features of fucoidan. These glycopolymers were synthesized via different radical polymerization techniques yielding polymers of different chain lengths and dispersity. These glycopolymers showed antiviral and platelet activating properties similar to those of natural fucoidan, thus making them fucoidan-mimetic glycopolymers. However, compared to fucoidan from natural sources, the fucoidan-mimetic glycopolymers had homogeneous and reproducible structures making them suitable for biomedical applications.Further studies demonstrated that platelet activation, caused by these glycopolymers, showed dose-response curves almost identical to fucoidan. The platelet activation was induced via intracellular signaling and caused platelet surface changes similar to those of fucoidan. Fucoidan-mimetic glycopolymers can therefore be used as unique biomolecular tools for studying the molecular and cellular responses of human platelets.Fucoidan-mimetic glycopolymers generally assert their antiviral activity by blocking viral entry to host cells, thus inhibiting spreading of the viral infection but not acting virucidal, i.e. not killing the viruses. Introduction of hydrophobic groups to the polymer’s chain ends improved the antiviral properties significantly and is an important step towards yielding glycopolymers with virucidal properties.The fucoidan-mimetic glycopolymers were also applied as capping agents when synthesizing gold nanoparticles. These fucoidan-mimetic glycopolymer coated gold nanoparticles showed improved colloidal stability compared to uncapped gold nanoparticles. Furthermore, the nanoparticles also demonstrated selective cytotoxicity against a human colon cancer cell line over fibroblast cells.
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| 9. |
- Aronsson, Christopher
(författare)
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Tunable and modular assembly of polypeptides and polypeptide-hybrid biomaterials
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Biomaterials are materials that are specifically designed to be in contact with biological systems and have for a long time been used in medicine. Examples of biomaterials range from sophisticated prostheses used for replacing outworn body parts to ordinary contact lenses. Currently it is possible to create biomaterials that can e.g. specifically interact with cells or respond to certain stimuli. Peptides, the shorter version of proteins, are excellent molecules for fabrication of such biomaterials. By following and developing design rules it is possible to obtain peptides that can self-assemble into well-defined nanostructures and biomaterials.The aim of this thesis is to create ”smart” and tunable biomaterials by molecular self-assembly using dimerizing –helical polypeptides. Two different, but structurally related, polypeptide-systems have been used in this thesis. The EKIV-polypeptide system was developed in this thesis and consists of four 28-residue polypeptides that can be mixed-and-matched to self-assemble into four different coiled coil heterodimers. The dissociation constant of the different heterodimers range from μM to < nM. Due to the large difference in affinities, the polypeptides are prone to thermodynamic social self-sorting. The JR-polypeptide system, on the other hand, consists of several 42-residue de novo designed helix-loop-helix polypeptides that can dimerize into four-helix bundles. In this work, primarily the glutamic acid-rich polypeptide JR2E has been explored as a component in supramolecular materials. Dimerization was induced by exposing the polypeptide to either Zn2+, acidic conditions or the complementary polypeptide JR2K.By conjugating JR2E to hyaluronic acid and the EKIV-polypeptides to star-shaped poly(ethylene glycol), respectively, highly tunable hydrogels that can be self-assembled in a modular fashion have been created. In addition, self-assembly of spherical superstructures has been investigated and were obtained by linking two thiol-modified JR2E polypeptides via a disulfide bridge in the loop region. ŒThe thesis also demonstrates that the polypeptides and the polypeptide-hybrids can be used for encapsulation and release of molecules and nanoparticles. In addition, some of the hydrogels have been explored for 3D cell culture. By using supramolecular interactions combined with bio-orthogonal covalent crosslinking reactions, hydrogels were obtained that enabled facile encapsulation of cells that retained high viability.The results of the work presented in this thesis show that dimerizing α–helical polypeptides can be used to create modular biomaterials with properties that can be tuned by specific molecular interactions. The modularity and the tunable properties of these smart biomaterials are conceptually very interesting andmake them useful in many emerging biomedical applications, such as 3D cell culture, cell therapy, and drug delivery.
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| 10. |
- Bélteky, Johan
(författare)
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Chicken domestication : Effects of tameness on brain gene expression and DNA methylation
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Domestication greatly increases phenotypic variation in a short time span, with selection for a single phenotype and a plethora of associated phenotypic changes as an outcome of the process. The domestication process influences the underlying genomic architecture of a species, and the success and speed of the process is likely influenced by it. The main aims of my thesis was to study how domestication affects the brain of chickens: specifically changes in morphology, gene expression, and DNA methylation. Differences in gene expression and DNA methylation between White Leghorn and Red Junglefowl chickens were mapped, and inheritance of these patterns were quantified, indicating a faithful transmission of breed-specific epigenetic markers. Selection on the behavioral trait fearfulness, generated high and low fearful lines of Red Junglefowl. Both the parental population and the fifth selected generation were used for the analyses in this thesis. One experiment studied morphological changes in the brain and other vital organs, and found that relative total brain size increased in high fearful birds, as a consequence of an increase in cerebral hemisphere size in high fearful birds and not in low fearful birds. Also, the relative heart, liver, spleen and testis size increased in high fearful birds, indicating correlated morphological changes with selection for fearfulness. Two additional experiments examined differential gene expression in the hypothalamus and the anterior cerebral hemisphere. The hypothalamus differed in expression of genes with reproductive and immunological functions, whilst the cerebral hemisphere differed in expression of genes related to social behaviors and neurological functions especially those upregulated in low fearful birds. These results indicate the occurrence of tissue- and species-specific changes in gene expression as overlap with other domestication events were nearly nonexistent. A fourth experiment sought to associate the change in fear levels and gene expression differences with DNA methylation. Chromosomal regions with differential DNA methylation between high and low fearful birds were identified, and genes in these regions had annotated functions relevant to phenotypic differences between the selection lines. This thesis is the first to study the genetic alterations of domestication using the wild ancestor of an already domesticated species to repeat the domestication process selecting against fear of humans. The findings corroborate results from previous comparisons of wild and domestic animals, and further support the theory that rigorous selection for a behavioral trait can cause a cascade of genetic and epigenetic changes facilitating the domestication of a population.
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