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  • 151.
    Aili, Daniel
    et al.
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics .
    Enander, Karin
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics .
    Lundström, Ingemar
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Applied Physics .
    Baltzer, Lars
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology.
    Liedberg, Bo
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics .
    Towards novel functional materials and sensors using de novo designed polypeptides on gold nanoparticles2006In: Europtrode VIII,2006, 2006Conference paper (Other academic)
    Abstract [en]

        

  • 152.
    Aili, Daniel
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Enander, Karin
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Rydberg, Johan
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Lundström, Ingemar
    Linköping University, Department of Physics, Chemistry and Biology, Applied Physics . Linköping University, The Institute of Technology.
    Baltzer, Lars
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Liedberg, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Aggregation-Induced Folding of a de novo Designed Polypeptide Immobilized on Gold Nanoparticles2006In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 128, no 7, p. 2194 -2195Article in journal (Refereed)
    Abstract [en]

    This communication reports the first steps in the construction of a novel, nanoparticle-based hybrid material for biomimetic and biosensor applications. Gold nanoparticles were modified with synthetic polypeptides to enable control of the particle aggregation state in a switchable manner, and particle aggregation was, in turn, found to induce folding of the immobilized peptides.

  • 153.
    Aili, Daniel
    et al.
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics .
    Enander, Karin
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics .
    Rydberg, Johan
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology.
    Lundström, Ingemar
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Applied Physics .
    Baltzer, Lars
    Uppsala University.
    Liedberg, Bo
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics .
    Alpha helix-inducing dimerization of synthetic polypeptide scaffolds on gold - a model system for receptor mimicking and biosensing2004In: 8th World Congress on Biosensors,2004, 2004Conference paper (Other academic)
  • 154.
    Aili, Daniel
    et al.
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics .
    Enander, Karin
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics .
    Rydberg, Johan
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology.
    Lundström, Ingemar
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Applied Physics .
    Baltzer, Lars
    Uppsala University.
    Liedberg, Bo
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics .
    Folding-induced aggregation of polypeptide-decorated gold nanoparticles - an nano-scale Lego for the construction of complex hybrid materials2004In: 5th International Conference on Biological Physics,2004, 2004Conference paper (Other academic)
  • 155.
    Aili, Daniel
    et al.
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics .
    Enander, Karin
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics .
    Rydberg, Johan
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology.
    Lundström, Ingemar
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Applied Physics .
    Baltzer, Lars
    Uppsala University.
    Liedberg, Bo
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics .
    Immobilization and heterodimerisation of helix-loop-helix polypeptides on gold surfaces - a model system for peptide-surface interactions2003In: 1st World congress on Synthetic Receptors,2003, 2003Conference paper (Other academic)
  • 156.
    Aili, Daniel
    et al.
    University of London Imperial College of Science Technology and Medicine.
    Gryko, Piotr
    University of London Imperial College of Science Technology and Medicine.
    Sepulveda, Borja
    Research Centre Nanosci and Nanotechnol CIN2 CSIC.
    Dick, John A. G.
    University of London Imperial College of Science Technology and Medicine.
    Kirby, Nigel
    Australian Synchrotron.
    Heenan, Richard
    Rutherford Appleton Lab.
    Baltzer, Lars
    Uppsala University.
    Liedberg, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics. Linköping University, The Institute of Technology.
    Ryan, Mary P.
    University of London Imperial College of Science Technology and Medicine.
    Stevens, Molly M.
    University of London Imperial College of Science Technology and Medicine.
    Polypeptide Folding-Mediated Tuning of the Optical and Structural Properties of Gold Nanoparticle Assemblies2011In: Nano letters (Print), ISSN 1530-6984, E-ISSN 1530-6992, Vol. 11, no 12, p. 5564-5573Article in journal (Refereed)
    Abstract [en]

    Responsive hybrid nanomaterials with well-defined properties are of significant interest for the development of biosensors with additional applications in tissue engineering and drug delivery. Here, we present a detailed characterization using UV-vis spectroscopy and small angle X-ray scattering of a hybrid material comprised of polypeptide-decorated gold nanoparticles with highly controllable assembly properties. The assembly is triggered by a folding-dependent bridging of the particles mediated by the heteroassociation of immobilized helix-loop-helix polypeptides and a complementary nonlinear polypeptide present in solution. The polypeptides are de novo designed to associate and fold into a heterotrimeric complex comprised of two disulfide-linked four-helix bundles. The particles form structured assemblies with a highly defined interparticle gap (4.8 +/- 0.4 nm) that correlates to the size of the folded polypeptides. Transitions in particle aggregation dynamics, mass-fractal dimensions and ordering, as a function of particle size and the concentration of the bridging polypeptide, are observed; these have significant effects on the optical properties of the assemblies. The assembly and ordering of the particles are highly complex processes that are affected by a large number of variables including the number of polypeptides bridging the particles and the particle mobility within the aggregates. A fundamental understanding of these processes is of paramount interest for the development of novel hybrid nanomaterials with tunable structural and optical properties and for the optimization of nanoparticle-based colorimetric biodetection strategies.

  • 157.
    Aili, Daniel
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering.
    Selegård, Robert
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering.
    Baltzer, Lars
    Division of Organic Chemistry, Department of Biochemistry and Organic Chemistry, BMC, Box 576, Uppsala University, SE-751 23 Uppsala, Sweden.
    Enander, Karin
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering.
    Liedberg, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering.
    Colorimetric Protein Sensing by Controlled Assembly of Gold Nanoparticles Functionalized with Synthetic Receptors2009In: Small, ISSN 1613-6810, Vol. 5, no 21, p. 2445-2452Article in journal (Refereed)
    Abstract [en]

    A strategy for colorimetric sensing of proteins, based on the induced assembly of polypeptide-functionalized gold nanoparticles, is described. Recognition was accomplished using a polypeptide sensor scaffold designed to specifically bind the model analyte, human carbonic anhydrase II (HCAII). The extent of particle aggregation, induced by the Zn2+-triggered dimerization and folding of a second polypeptide also present on the surface of the gold nanoparticle, gave a readily detectable colorimetric shift that was dependent on the concentration of the target protein. In the absence of HCAII, particle aggregation resulted in a major redshift of the plasmon peak whereas analyte binding prevented formation of dense aggregates, significantly reducing the magnitude of the redshift. The limit of detection of HCAII was estimated to be around 15 nM. The versatility of the technique was demonstrated using a second model system based on the recognition of a peptide sequence from the tobacco mosaic virus coat protein (TMVP by a recombinant antibody fragment. This strategy is proposed as a generic platform for robust and specific protein analysis that can be further developed for monitoring a wide range of target proteins.

  • 158.
    Aili, Daniel
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics. Linköping University, The Institute of Technology.
    Selegård, Robert
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering.
    Baltzer, Lars
    Uppsala University .
    Enander, Karin
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics. Linköping University, The Institute of Technology.
    Liedberg, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics. Linköping University, The Institute of Technology.
    Colorimetric sensing: Small 21/20092009In: Small, ISSN 1613-6810, E-ISSN 1613-6829, Vol. 5, no 21Article in journal (Other academic)
    Abstract [en]

    The cover picture illustrates a novel concept for colorimetric protein sensing based on the controllable assembly of polypeptide-functionalized gold nanoparticles. Recognition of the analyte is accomplished by polypeptide-based synthetic receptors immobilized on gold nanoparticles. Also present on the particle surface is a de novo-designed helix-loop-helix polypeptide that homodimerizes and folds into four-helix bundles in the presence of Zn2+, resulting in particle aggregation. Analyte binding interferes with the folding-induced aggregation, giving rise to a clearly detectable colorimetric response.

  • 159.
    Aineslahti, Emmi
    Linköping University, Department of Physics, Chemistry and Biology, Biology.
    Training of spider monkeys in a food-rewarded two-choice olfactory discrimination paradigm and assessment of olfactory learning and memory performance2019Independent thesis Advanced level (degree of Master (Two Years)), 40 credits / 60 HE creditsStudent thesis
    Abstract [en]

    There is little knowledge about olfactory learning in primates, even though primates are known to use olfaction in several behaviors including food selection and territorial defense. Therefore I assessed the olfactory learning and memory performance in five adult spider monkeys (Ateles geoffroyi) using a food-rewarded two-choice olfactory discrimination paradigm. The spider monkeys acquired the initial odor discrimination in 530-1102 trials and in a series of intramodal transfer tasks they needed 30-510 trials to reach the learning criterion. There was a significant negative correlation between the number of trials needed to reach the learning criterion and the number of transfer tasks completed. Thus, as a group, the animals displayed olfactory learning set formation. The number of trials that the spider monkeys needed in initial olfactory learning was comparable to that of other primate species tested previously but higher compared to that of other mammals such as dogs and rats. The learning speed of the spider monkeys in intramodal transfer tasks was similar to that of other mammals tested, suggesting that primates are less prepared to use olfactory cues in the initial solving of a problem but that once they learn the concept, their learning speed with novel odor discrimination problems is not generally slower than that of non-primate mammals. All spider monkeys tested reached the learning criterion in the memory tasks straight on the first testing day, that is: within 30 trials, suggesting similar long-term odor memory capabilities in spider monkeys and other mammals such as dogs, mice and rats.

    Download full text (pdf)
    Master's thesis Emmi Aineslahti
  • 160.
    Aira, Naomi
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Lactate Dehydrogenase and Citrate Synthase activity in cardiac and skeletal muscle of lowland and highland tinamous2013Independent thesis Basic level (degree of Bachelor), 10,5 credits / 16 HE creditsStudent thesis
    Abstract [en]

    Tinamous (Tinamidae) have the smallest heart in relation to body mass compared to any other flying bird today (Bishop 1997). This means that heart size is likely to restrict aerobic metabolism. Tinamous inhabit areas from sea level to 4800 m a.s.l., which means that the high altitude living species, Nothoprocta ornata (NO), is exposed to hypoxia. In this study the activity of the two metabolic enzymes Lactate Dehydrogenase (LDH) and Citrate Synthase (CS) was measured and the ratio between the enzyme activities calculated to examine if the small heart of the tinamous affects their aerobic/anaerobic metabolism. The activity of the two enzymes was measured in the heart and the gastrocnemius muscle in the three species Nothoprocta ornata (NO), Nothoprocta perdicaria (NP) and Gallus gallus (GG). CS activity was significantly higher in the heart compared to the skeletal muscle and LDH activity was significant higher in the skeletal muscle than in the heart in all three species. The LDH/CS ratio was significantly higher in NO’s skeletal muscle than in chickens but there was no significant difference between species in the heart. The higher ratio in NO´s muscle could be a sign of a higher anaerobic metabolism that is used in the muscles to compensate for the small heart NO have. In conclusion, the Tinamous

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    fulltext
  • 161.
    Ajalloueian, Fatemeh
    et al.
    Isfahan University of Technology, Iran / Uppsala University, Sweden .
    Tavanai, Hossein
    Isfahan University of Technology, Iran .
    Hilborn, Jons
    Uppsala University, Sweden .
    Donzel-Gargand, Olivier
    Uppsala University, Sweden .
    Leifer, Klaus
    Uppsala University, Sweden .
    Wickham, Abeni
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics. Linköping University, The Institute of Technology.
    Arpanaei, Ayyoob
    National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.
    Emulsion Electrospinning as an Approach to Fabricate PLGA/Chitosan Nanofibers for Biomedical Applications2014In: BioMed Research International, ISSN 2314-6133, no 475280Article in journal (Refereed)
    Abstract [en]

    Novel nanofibers from blends of polylactic-co-glycolic acid (PLGA) and chitosan have been produced through an emulsion electrospinning process. The spinning solution employed polyvinyl alcohol (PVA) as the emulsifier. PVA was extracted from the electrospun nanofibers, resulting in a final scaffold consisting of a blend of PLGA and chitosan. The fraction of chitosan in the final electrospun mat was adjusted from 0 to 33%. Analyses by scanning and transmission electron microscopy show uniform nanofibers with homogenous distribution of PLGA and chitosan in their cross section. Infrared spectroscopy verifies that electrospun mats contain both PLGA and chitosan. Moreover, contact angle measurements show that the electrospun PLGA/chitosanmats are more hydrophilic than electrospun mats of pure PLGA. Tensile strengths of 4.94 MPa and 4.21 MPa for PLGA/chitosan in dry and wet conditions, respectively, illustrate that the polyblend mats of PLGA/chitosan are strong enough for many biomedical applications. Cell culture studies suggest that PLGA/chitosan nanofibers promote fibroblast attachment and proliferation compared to PLGA membranes. It can be assumed that the nanofibrous composite scaffold of PLGA/chitosan could be potentially used for skin tissue reconstruction.

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    fulltext
  • 162.
    Ajjan, Fátima
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Ambrogi, Martina
    Max Planck Institute Colloids and Interfaces, Germany.
    Ayalneh Tiruye, Girum
    IMDEA Energy Institute, Spain.
    Cordella, Daniela
    University of Liege ULg, Belgium.
    Fernandes, Ana M.
    POLYMAT University of Basque Country UPV EHU, Spain.
    Grygiel, Konrad
    Max Planck Institute Colloids and Interfaces, Germany.
    Isik, Mehmet
    POLYMAT University of Basque Country UPV EHU, Spain.
    Patil, Nagaraj
    University of Liege ULg, Belgium.
    Porcarelli, Luca
    POLYMAT University of Basque Country UPV EHU, Spain.
    Rocasalbas, Gillem
    KIOMedPharma, Belgium.
    Vendramientto, Giordano
    University of Bordeaux, France.
    Zeglio, Erica
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Antonietti, Markus
    Max Planck Institute Colloids and Interfaces, Germany.
    Detrembleur, Cristophe
    University of Liege ULg, Belgium.
    Inganäs, Olle
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Jerome, Christine
    University of Liege ULg, Belgium.
    Marcilla, Rebeca
    IMDEA Energy Institute, Spain.
    Mecerreyes, David
    POLYMAT University of Basque Country UPV EHU, Spain; Basque Fdn Science, Spain.
    Moreno, Monica
    POLYMAT University of Basque Country UPV EHU, Spain.
    Taton, Daniel
    University of Bordeaux, France.
    Solin, Niclas
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Yuan, Jiayin
    Max Planck Institute Colloids and Interfaces, Germany.
    Innovative polyelectrolytes/poly(ionic liquid)s for energy and the environment2017In: Polymer international, ISSN 0959-8103, E-ISSN 1097-0126, Vol. 66, no 8, p. 1119-1128Article, review/survey (Refereed)
    Abstract [en]

    This paper presents the work carried out within the European project RENAISSANCE-ITN, which was dedicated to the development of innovative polyelectrolytes for energy and environmental applications. Within the project different types of innovative polyelectrolytes were synthesized such as poly(ionic liquid)s coming from renewable or natural ions, thiazolium cations, catechol functionalities or from a new generation of cheap deep eutectic monomers. Further, macromolecular architectures such as new poly(ionic liquid) block copolymers and new (semi)conducting polymer/polyelectrolyte complexes were also developed. As the final goal, the application of these innovative polymers in energy and the environment was investigated. Important advances in energy storage technologies included the development of new carbonaceous materials, new lignin/conducting polymer biopolymer electrodes, new iongels and single-ion conducting polymer electrolytes for supercapacitors and batteries and new poly(ionic liquid) binders for batteries. On the other hand, the use of innovative polyelectrolytes in sustainable environmental technologies led to the development of new liquid and dry water, new materials for water cleaning technologies such as flocculants, oil absorbers, new recyclable organocatalyst platforms and new multifunctional polymer coatings with antifouling and antimicrobial properties. All in all this paper demonstrates the potential of poly(ionic liquid)s for high-value applications in energy and enviromental areas. (c) 2017 Society of Chemical Industry

  • 163.
    Ajjan, Fátima
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Casado, N.
    University of Basque Country, Spain.
    Rebis, Tomasz
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Elfwing, Anders
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Solin, Niclas
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Mecerreyes, D.
    University of Basque Country, Spain; Ikerbasque, Spain.
    Inganäs, Olle
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    High performance PEDOT/lignin biopolymer composites for electrochemical supercapacitors2016In: Journal of Materials Chemistry A, ISSN 2050-7488, Vol. 4, no 5, p. 1838-1847Article in journal (Refereed)
    Abstract [en]

    Developing sustainable organic electrode materials for energy storage applications is an urgent task. We present a promising candidate based on the use of lignin, the second most abundant biopolymer in nature. This polymer is combined with a conducting polymer, where lignin as a polyanion can behave both as a dopant and surfactant. The synthesis of PEDOT/Lig biocomposites by both oxidative chemical and electrochemical polymerization of EDOT in the presence of lignin sulfonate is presented. The characterization of PEDOT/Lig was performed by UV-Vis-NIR spectroscopy, FTIR infrared spectroscopy, thermogravimetric analysis, scanning electron microscopy, cyclic voltammetry and galvanostatic charge-discharge. PEDOT doped with lignin doubles the specific capacitance (170.4 F g(-1)) compared to reference PEDOT electrodes (80.4 F g(-1)). The enhanced energy storage performance is a consequence of the additional pseudocapacitance generated by the quinone moieties in lignin, which give rise to faradaic reactions. Furthermore PEDOT/Lig is a highly stable biocomposite, retaining about 83% of its electroactivity after 1000 charge/discharge cycles. These results illustrate that the redox doping strategy is a facile and straightforward approach to improve the electroactive performance of PEDOT.

  • 164.
    Ajjan, Fátima
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Javad Jafari, Mohammad
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering.
    Rebis, T.
    Poznan University of Tech, Poland.
    Ederth, Thomas
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering.
    Inganäs, Olle
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Spectroelectrochemical investigation of redox states in a polypyrrole/lignin composite electrode material2015In: Journal of Materials Chemistry A, ISSN 2050-7488, Vol. 3, no 24, p. 12927-12937Article in journal (Refereed)
    Abstract [en]

    We report spectroelectrochemical studies to investigate the charge storage mechanism of composite polypyrrole/lignin electrodes. Renewable bioorganic electrode materials were produced by electropolymerization of pyrrole in the presence of a water-soluble lignin derivative acting as a dopant. The resulting composite exhibited enhanced charge storage abilities due to a lignin-based faradaic process, which was expressed after repeated electrochemical redox of the material. The in situ FTIR spectroelectrochemistry results show the formation of quinone groups, and reversible oxidation-reduction of these groups during charge-discharge experiments in the electrode materials. The most significant IR bands include carbonyl absorption near 1705 cm(-1), which is attributed to the creation of quinone moieties during oxidation, and absorption at 1045 cm(-1) which is due to hydroquinone moieties.

  • 165.
    Ajjan, Fátima
    et al.
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Mecerreyes, David
    Univ Basque Country UPV EHU, Spain.
    Inganäs, Olle
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Enhancing Energy Storage Devices with Biomacromolecules in Hybrid Electrodes2019In: Biotechnology Journal, ISSN 1860-6768, E-ISSN 1860-7314, article id 1900062Article, review/survey (Refereed)
    Abstract [en]

    The development of energy storage devices with higher energy and power outputs, and long cycling stability is urgently required in the pursuit of the expanding challenges of electrical energy storage. The utilization of biologically renewable redox compounds holds a great potential in designing sustainable energy storage systems and contributes in reducing the dependence on fossil fuels for energy materials. Quinones are the principal redox centers in natural organic materials and play a key role as charge storage electrode materials because of their abundance, multiple forms and integration into the materials flow through the biosphere. Electrical energy storage devices and systems can be significantly improved by the combination of scalable quinone-based biomaterials with good electronic conductors. This review uses recent examples to show how biopolymers are providing new directions in the development of renewable biohybrid electrodes for energy storage devices.

  • 166.
    Ajjan Godoy, Fátima Nadia
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Biohybrid Polymer Electrodes for Renewable Energy Storage2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Daily and seasonally fluctuating energy supply and demand requires adequate energy storage solutions. In recent years electrochemical supercapacitors have attracted considerable attention due to their ability to both store and deliver electrical energy efficiently. Our efforts are focused on developing and optimizing sustainable organic electrode materials for supercapacitors based on renewable bioorganic materials, offering a cheap, environmentally friendly and scalable alternative to store energy. In particular, we are using the second most abundant biopolymer in nature, lignin (Lig), which is an insulating material. However, when used in combination with electroactive and conducting polymers such as polypyrrole (PPy) and poly(3,4-ethylenedioxythiophene) (PEDOT), the biohybrid electrodes PPy/Lig and PEDOT/Lig display significantly enhanced energy storage performance as compared to the pristine conducting polymers without the lignin. Redox cyclic voltammetry and galvanostatic charge/discharge measurements indicate that the enhanced performance is due to the additional pseudocapacitance generated by the quinone moieties in lignin. Moreover, a conjugated redoxpolymer poly(aminoanthraquinone) PAAQ, with intrinsic quinone functions and excellentstability, has been combined with lignin and PEDOT resulting in a trihybrid bioelectrode. PEDOT compensates the low conductivity of PAAQ and provides electrical pathways to the quinone groups. The electrochemically generated quinones undergo a two electron, two protonredox process within the biohybrid electrodes as revealed by FTIR spectroelectrochemistry.These remarkable features reveal the exciting potential of a full organic energy storage device with long cycle life. Therefore, supercapacitor devices were designed in symmetric or asymmetric two electrode configuration. The best electrochemical performance was achieved by the asymmetric supercapacitor based on PEDOT+Lignin/PAAQ as the positive electrode and PEDOT/PAAQ as the negative electrode. This device exhibits superior electrochemical performance and outstanding stability after 10000 charge/discharge cycles due to the synergistic effect of the two electrodes. Finally, we have characterized the response of this supercapacitor device when charged with the intermittent power supply from an organic photovoltaic module. We have designed charging/discharging conditions such that reserve power was available in the storage device at all times. This work has resulted in an inexpensive fully organic system witht he dual function of energy conversion and storage.

    List of papers
    1. Biopolymer hybrid electrodes for scalable electricity storage
    Open this publication in new window or tab >>Biopolymer hybrid electrodes for scalable electricity storage
    2016 (English)In: Materials Horizons, ISSN 2051-6347, E-ISSN 2051-6355, Vol. 3, no 3, p. 174-185Article, review/survey (Refereed) Published
    Abstract [en]

    Powering the future, while maintaining a cleaner environment and a strong socioeconomic growth, is going to be one of the biggest challenges faced by mankind in the 21st century. The first step in overcoming the challenge for a sustainable future is to use energy more efficiently so that the demand for fossil fuels can be reduced drastically. The second step is a transition from the use of fossil fuels to renewable energy sources. In this sense, organic electrode materials are becoming increasingly attractive compared to inorganic electrode materials which have reached a plateau regarding performance and have severe drawbacks in terms of cost, safety and environmental friendliness. Using organic composites based on conducting polymers, such as polypyrrole, and abundant, cheap and naturally occurring biopolymers rich in quinones, such as lignin, has recently emerged as an interesting alternative. These materials, which exhibit electronic and ionic conductivity, provide challenging opportunities in the development of new charge storage materials. This review presents an overview of recent developments in organic biopolymer composite electrodes as renewable electroactive materials towards sustainable, cheap and scalable energy storage devices.

    Place, publisher, year, edition, pages
    ROYAL SOC CHEMISTRY, 2016
    National Category
    Other Environmental Engineering
    Identifiers
    urn:nbn:se:liu:diva-128741 (URN)10.1039/c5mh00261c (DOI)000375296600002 ()
    Note

    Funding Agencies|Knut and Alice Wallenberg Foundation; Wallenberg Scholar grant

    Available from: 2016-05-31 Created: 2016-05-30 Last updated: 2017-11-30
    2. Spectroelectrochemical investigation of redox states in a polypyrrole/lignin composite electrode material
    Open this publication in new window or tab >>Spectroelectrochemical investigation of redox states in a polypyrrole/lignin composite electrode material
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    2015 (English)In: Journal of Materials Chemistry A, ISSN 2050-7488, Vol. 3, no 24, p. 12927-12937Article in journal (Refereed) Published
    Abstract [en]

    We report spectroelectrochemical studies to investigate the charge storage mechanism of composite polypyrrole/lignin electrodes. Renewable bioorganic electrode materials were produced by electropolymerization of pyrrole in the presence of a water-soluble lignin derivative acting as a dopant. The resulting composite exhibited enhanced charge storage abilities due to a lignin-based faradaic process, which was expressed after repeated electrochemical redox of the material. The in situ FTIR spectroelectrochemistry results show the formation of quinone groups, and reversible oxidation-reduction of these groups during charge-discharge experiments in the electrode materials. The most significant IR bands include carbonyl absorption near 1705 cm(-1), which is attributed to the creation of quinone moieties during oxidation, and absorption at 1045 cm(-1) which is due to hydroquinone moieties.

    Place, publisher, year, edition, pages
    ROYAL SOC CHEMISTRY, 2015
    National Category
    Materials Chemistry
    Identifiers
    urn:nbn:se:liu:diva-120069 (URN)10.1039/c5ta00788g (DOI)000356022800044 ()
    Note

    Funding Agencies|Knut and Alice Wallenberg foundation; Marie Curie network Renaissance; Swedish Government Strategic Research Area in Materials Science on Functional Materials at Linkoping University [2009-00971]

    Available from: 2015-07-06 Created: 2015-07-06 Last updated: 2017-12-04
    3. High performance PEDOT/lignin biopolymer composites for electrochemical supercapacitors
    Open this publication in new window or tab >>High performance PEDOT/lignin biopolymer composites for electrochemical supercapacitors
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    2016 (English)In: Journal of Materials Chemistry A, ISSN 2050-7488, Vol. 4, no 5, p. 1838-1847Article in journal (Refereed) Published
    Abstract [en]

    Developing sustainable organic electrode materials for energy storage applications is an urgent task. We present a promising candidate based on the use of lignin, the second most abundant biopolymer in nature. This polymer is combined with a conducting polymer, where lignin as a polyanion can behave both as a dopant and surfactant. The synthesis of PEDOT/Lig biocomposites by both oxidative chemical and electrochemical polymerization of EDOT in the presence of lignin sulfonate is presented. The characterization of PEDOT/Lig was performed by UV-Vis-NIR spectroscopy, FTIR infrared spectroscopy, thermogravimetric analysis, scanning electron microscopy, cyclic voltammetry and galvanostatic charge-discharge. PEDOT doped with lignin doubles the specific capacitance (170.4 F g(-1)) compared to reference PEDOT electrodes (80.4 F g(-1)). The enhanced energy storage performance is a consequence of the additional pseudocapacitance generated by the quinone moieties in lignin, which give rise to faradaic reactions. Furthermore PEDOT/Lig is a highly stable biocomposite, retaining about 83% of its electroactivity after 1000 charge/discharge cycles. These results illustrate that the redox doping strategy is a facile and straightforward approach to improve the electroactive performance of PEDOT.

    Place, publisher, year, edition, pages
    ROYAL SOC CHEMISTRY, 2016
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:liu:diva-125323 (URN)10.1039/c5ta10096h (DOI)000368839200035 ()
    Note

    Funding Agencies|Power Papers project from the Knut and Alice Wallenberg foundation; Wallenberg Scholar grant from the Knut and Alice Wallenberg foundation; Marie Curie network Renaissance (NA); European Research Council by Starting Grant Innovative Polymers for Energy Storage (iPes) [306250]; Basque Government

    Available from: 2016-02-23 Created: 2016-02-19 Last updated: 2017-11-30
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  • 167.
    Akbar, Muhammad
    et al.
    COMSATS Univ Islamabad, Pakistan; Hubei Univ, Peoples R China.
    Alvi, Farah
    COMSATS Univ Islamabad, Pakistan.
    Shakir, Muhammad Imran
    Univ Calif Los Angeles, CA 90095 USA.
    Rehman, Saif Ur
    COMSATS Univ Islamabad, Pakistan.
    Rafique, Asia
    COMSATS Univ Islamabad, Pakistan.
    Mushtaq, Naveed
    COMSATS Univ Islamabad, Pakistan; Hubei Univ, Peoples R China.
    Raza, Rizwan
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, Faculty of Science & Engineering. COMSATS Univ Islamabad, Pakistan.
    Effect of sintering temperature on properties of LiNiCuZn-Oxide: a potential anode for solid oxide fuel cell2019In: MATERIALS RESEARCH EXPRESS, ISSN 2053-1591, Vol. 6, no 10, article id 105505Article in journal (Refereed)
    Abstract [en]

    Crystal structure and surface morphology play vital role in the performance of Solid Oxide Fuel cells (SOFCs) anode. Sufficient electrocatalytic activity and high conductivity are the key requirements for anode to enhance the electrochemical capability. In current work, sintering temperature effects are investigated on the properties of advanced LiNiCuZn-Oxide based electrode for solid oxide fuel cells (SOFCs). The powders were prepared by simple solid-state reaction method was followed by sintering at different temperatures (700 degrees C-1200 degrees C). Moreover, various characterization techniques have been employed to investigate the sintering temperatures effects on the crystallite size, morphology, particle size, energy band gap and absorption peaks. The energy gap (Eg) was observed to increase from 2.94 eV to 3.32 eV and dc conductivity decreased from 9.084 Scm(-1) to 0.46 Scm(-1) by increasing sintering temperature from 700 degrees C to 1200 degrees C. Additionally, the best fuel cell performance of 0.90 Wcm(-2) was achieved for LiNiCuZn-Oxide sintered at 700 degrees C using H-2/air as a fuel and oxidant and it decreased to 0.17 Wcm(-2) for powders sintered at 1200 degrees C. Based on these results, we can conclude that 700 degrees C is the best optimum temperature for these chemical compositions, where all parameters of electrode are as per SOFCs requirement.

  • 168.
    Akerlind, C
    et al.
    Swedish Defence Research Agency.
    Arwin, Hans
    Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, The Institute of Technology.
    Jakobsson, Fredrik
    Linköping University, Department of Science and Technology. Linköping University, The Institute of Technology.
    Kariis, H
    Swedish Defence Research Agency.
    Järrendahl, Kenneth
    Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, Faculty of Science & Engineering.
    Optical properties and switching of a Rose Bengal derivative: A spectroscopic ellipsometry study2011In: THIN SOLID FILMS, ISSN 0040-6090, Vol. 519, no 11, p. 3582-3586Article in journal (Refereed)
    Abstract [en]

    Optical properties in terms of the complex-valued dielectric function were determined for spin-coated films of a Rose Bengal derivative using variable angle of incidence spectroscopic ellipsometry in the visible and infrared wavelength regions. In addition, the thickness and roughness of the films were determined and related to the solution concentration of Rose Bengal. Switching between two different oxidation states of the Rose Bengal derivative was investigated. The two states were chemically induced by exposure to vapors of hydrochloric acid and ammonia, respectively. A substantial and reversible change of the optical properties of the films was observed.

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  • 169.
    Akke, Mikael
    et al.
    Department of Biophysical Chemistry, Lund University.
    Lundström, Patrik
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Biotechnology. Linköping University, The Institute of Technology.
    Conformational Dynamics by Relaxation Dispersion2012In: Encyclopedia of Biophysics / [ed] Gordon C. K. Roberts., Elsevier, 2012Chapter in book (Other academic)
    Abstract [en]

    The Encyclopedia of Biophysics is envisioned both as an easily accessible source of information and as an introductory guide to the scientific literature. It includes entries describing both Techniques and Systems. In the Techniques entries, each of the wide range of methods which fall under the heading of Biophysics are explained in detail, together with the value and the limitations of the information each provides. Techniques covered range from diffraction (X-ray, electron and neutron) through a wide range of spectroscopic methods (X-ray, optical, EPR, NMR) to imaging (from electron microscopy to live cell imaging and MRI), as well as computational and simulation approaches.In the Systems entries, biophysical approaches to specific biological systems or problems – from protein and nucleic acid structure to membranes, ion channels and receptors – are described. These sections, which place emphasis on the integration of the different techniques, therefore provide an inroad into Biophysics from a biological more than from a technique-oriented physical/chemical perspective. Thus the Encyclopedia is intended to provide a resource both for biophysicists interested in methods beyond those used in their immediate sub-discipline and for those readers who are approaching biophysics from either a physical or biological background.

  • 170.
    Akoto, Brenda
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Is spring burning a viable management tool for species-rich grasslands?2012Independent thesis Advanced level (degree of Master (Two Years)), 80 credits / 120 HE creditsStudent thesis
    Abstract [en]

    Semi- natural grasslands are species-rich and also one of the most threatened biotopes in Europe. The area of these grasslands has declined and grassland vegetation is threatened as a result of lack of management and land use change. Appropriate management is therefore required to maintain the conservation values and high species richness of semi- natural grasslands. Traditional management, that is, grazing or annual mowing is expensive, which motivates evaluation of alternative cheaper methods of management. Burning is less costly and therefore I evaluated burning along with the conventional methods. The study addressed the main question: is burning an option to mowing and grazing? I searched the literature for available studies suitable for metaanalysis, but located only detailed reports from a series of eleven Swedish long-term field trials. In addition, I collected data in the only one of these trials still running. To facilitate metaanalysis, l used different indicator systems of classification of grassland plants then calculating the odds for a random record being an indicator after one, eight, fourteen, twenty-eight and thirty-nine spring burns. The results show an increasing proportion of grassland indicators of good management in the mowed and grazed plots compared with the burnt plots, indicating a general negative effect of burning on grassland plants compared with mowing and grazing. Hence, burning is not an appropriate long-term management method if the aim is to maintain vegetation diversity in semi-natural grassland.

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  • 171.
    Akram, Usman
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Metson, Genevieve
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering. Linköping University, Centre for Climate Science and Policy Research, CSPR.
    Quttineh, Nils-Hassan
    Linköping University, Department of Mathematics, Optimization . Linköping University, Faculty of Science & Engineering.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Closing Pakistan’s yield gaps through nutrient recycling2018In: Frontiers in Sustainable Food Systems, E-ISSN 2571-581X, p. 1-14, article id 00024Article in journal (Refereed)
    Abstract [en]

    Achieving food security will require closing yield gaps in many regions, including Pakistan. Although fertilizer subsidies have facilitated increased nitrogen (N) application rates, many staple crop yields have yet to reach their maximum potential. Considering that current animal manure and human excreta (bio-supply) recycling rates are low, there is substantial potential to increase the reuse of nutrients in bio-supply. We quantified 2010 crop N, phosphorus (P), and potassium (K) needs along with bio-supply nutrient availability for Pakistani districts, and compared these values to synthetic fertilizer use and costs. We found that synthetic fertilizer use combined with low bio-supply recycling resulted in a substantial gap between nutrient supply and P and K crop needs, which would cost 3 billion USD to fill with synthetic fertilizers. If all bio-supply was recycled, it could eliminate K synthetic fertilizer needs and decrease N synthetic fertilizer needs to 43% of what was purchased in 2010. Under a full recycling scenario, farmers would still require an additional 0.28 million tons of synthetic P fertilizers, costing 2.77 billion USD. However, it may not be prohibitively expensive to correct P deficiencies. Pakistan already spends this amount of money on fertilizers. If funds used for synthetic N were reallocated to synthetic P purchases in a full bio-supply recycling scenario, crop needs could be met. Most recycling could happen within districts, with only 6% of bio-supply requiring between-district transport when optimized to meet national N crop needs. Increased recycling in Pakistan could be a viable way to decrease yield gaps.

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    Closing Pakistan’s Yield Gaps Through Nutrient Recycling
  • 172.
    Akram, Usman
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Quttineh, Nils-Hassan
    Linköping University, Department of Mathematics, Optimization . Linköping University, Faculty of Science & Engineering.
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Tonderski, Karin
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Metson, Genevieve
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.
    Enhancing nutrient recycling from excreta to meet crop nutrient needs in Sweden - a spatial analysis2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 10264Article in journal (Refereed)
    Abstract [en]

    Increased recycling of nutrient-rich organic waste to meet crop nutrient needs is an essential component of a more sustainable food system. However, agricultural specialization continues to pose a significant challenge to balancing crop nutrient needs and the nutrient supply from animal manure and human excreta locally. For Sweden, this study found that recycling all excreta (in 2007) could meet up to 75% of crop nitrogen and 81% of phosphorus needs, but that this would exceed crop potassium needs by 51%. Recycling excreta within municipalities could meet 63% of crop P nutrient needs, but large regional differences and imbalances need to be corrected to avoid over or under fertilizing. Over 50% of the total nitrogen and phosphorus in excreta is contained in just 40% of municipalities, and those have a surplus of excreta nutrients compared to crop needs. Reallocation of surpluses (nationally optimized for phosphorus) towards deficit municipalities, would cost 192 million USD (for 24 079 km of truck travel). This is 3.7 times more than the total NPK fertilizer value being transported. These results indicate that Sweden could reduce its dependence on synthetic fertilizers through investments in excreta recycling, but this would likely require valuing also other recycling benefits.

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  • 173.
    Akram, Usman
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology.
    Quttineh, Nils-Hassan
    Linköping University, Department of Mathematics, Optimization .
    Wennergren, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology.
    Tonderski, Karin
    Linköping University, Department of Physics, Chemistry and Biology, Biology.
    Metson, Geneviéve S.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology.
    Optimizing Nutrient Recycling From Excreta in Sweden and Pakistan: Higher Spatial Resolution Makes Transportation More Attractive2019In: Frontiers in Sustainable Food Systems, ISSN 2571-581X, Vol. 3Article in journal (Refereed)
    Abstract [en]

    Recycling essential plant nutrients like nitrogen (N), phosphorus (P), and potassium (K) from organic waste such as human and animal excreta will be an essential part of sustainable food systems and a circular economy. However, transportation is often cited as a major barrier to increased recycling as organic waste is heavy and bulky, and distances between areas of abundant waste may be far from areas with a need for fertilizers. We investigated the effect of increased input data spatial resolution to an optimization model on the weight, distance, and spatial patterns of transport. The model was run in Sweden and in Pakistan to examine cost-effectiveness of transporting excess excreta to areas of crop need after local recycling. Increasing the resolution of input data from political boundaries (municipalities and districts) to 0.083 decimal grids increased the amount of N requiring transport by 12% in Pakistan and increased P requiring transport by 14% in Sweden. The average distance decreased by 67% (to 44 km) in Pakistan but increased by 1 km in Sweden. Further increasing the resolution to 5 km grids in Sweden decreased the average transportation distance by 9 km (down to 123 km). In both countries, increasing resolution also decreased the number of long-distance heavy transports, and as such costs did not increase as much as total distance and weight transported. Ultimately, transportation in Pakistan seemed financially beneficial: the cost of transport only represented 13% of the NPK fertilizer value transported, and total recycling could even cover 78% of additional fertilizer purchases required. In Sweden, the cost of transporting excreta did not seem cost effective without valuing other potential benefits of increased recycling: costs were three times higher than the fertilizer value transported in excreta at the 5 km resolution. In summary, increasing input data resolution created a more realistic picture of recycling needs. This also highlighted more favorable cost to fertilizer value ratios which could make it easier to move forward with industry and government partners to facilitate productive recycling. Our analysis shows that in both countries increased recycling can result in better spatial nutrient balances.

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  • 174.
    Al-Absi, Thabit
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, The Institute of Technology.
    Efficient Characterization of Short Anelloviruses Fragments Found in Metagenomic Samples2012Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Some viral metagenomic serum samples contain a huge amount of Anellovirus, which is a genetically diverse family with a few conserved regions making it hard to efficiently characterize. Multiple sequence alignment of the Anelloviruses found in the sample must be constructed to get a clear picture of Anellovirus diversity and to identify stable regions. Using available multiple sequence alignment software directly on these fragments results in an MSA of a very poor quality due to their diversity, misaligned regions and low-quality regions present in the sequence.

    An efficient MSA must be constructed in order to characterize these Anellovirus present in the samples. Pairwise alignment is used to align one fragment to the database sequences at a time. The fragments are then aligned to the database sequences using the start and end position from the pairwise alignment results. The algorithm will also exclude non-aligned portions of the fragments, as these are very hard to handle properly and are often products of misassembly or chimeric sequenced fragments. Other tools to aid further analysis were developed, such as finding a non-overlapping window that contains the most fragments, find consensus of the alignment and extract any regions from the MSA for further analysis.

    An MSA was constructed with a high percent of correctly aligned bases compared to an MSA constructed using MSA softwares. The minimal number of genomes found in the sampled sequence was found as well as a distribution of the fragments along the database sequence. Moreover, highly conserved region and the window containing most fragments were extracted from the MSA and phylogenetic trees were constructed for these regions. 

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  • 175.
    Alagia, M.
    et al.
    ISMN-CNR, Sez. Roma1, P.le A. Moro 5, I-00185 Roma, Italy and TASC-CNR, Area Science Park, Basovizza, I-34012 Trieste, Italy.
    Lavollée, M.
    LIXAM-CNRS, F-91898 Orsay-Cedex, France.
    Richter, R.
    Sincrotrone Trieste, Area Science Park, I-34012 Basovizza, Trieste, Italy.
    Ekström, Ulf
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Carravetta, V.
    Institute of Chemical Physical Processes (CNR), Via Moruzzi 1, I-56124 Pisa, Italy.
    Stranges, D.
    Dipartimento di Chimica and INSTM, Universitá La Sapienza, P.le A. Moro 5, I-00185 Roma, Italy and ISMN-CNR, Sez. Roma1, P.le A. Moro 5, I-00185 Roma, Italy.
    Brunetti, B.
    ISMN-CNR, Sez. Roma1, P.le A. Moro 5, I-00185 Roma, Italy.
    Stranges, S.
    Dipartimento di Chimica and INSTM, Universitá La Sapienza, P.le A. Moro 5, I-00185 Roma, Italy; ISMN-CNR, Sez. Roma1, P.le A. Moro 5, I-00185 Roma, Italy; and TASC-CNR, Area Science Park, Basovizza, I-34012 Trieste, Italy.
    Probing the potential energy surface by highresolution x-ray absorption spectroscopy: The umbrella motion of the coreexcited CH3 free radical2007In: Physical Review. A, ISSN 1050-2947, Vol. 76, no 2, p. 124305-Article in journal (Refereed)
    Abstract [en]

    A detailed study of the umbrellalike vibration in inner-shell spectroscopy is presented. The high-resolution x-ray absorption spectrum for the lowest lying core excitation of the CH3 free radical was recorded. High quality potential energy surfaces (PES) for the initial and final states of the transition were calculated as a function of the symmetrical stretching and the umbrella deformation coordinates. The strong anharmonicity along the umbrella coordinate in the double-well region of the PES of the core excited state has a strong effect on the bending vibrational progressions. The excellent agreement between the experiment and theory allows an accurate spectroscopic characterization of the vibrational structure of the electronic transition, and the estimation of the umbrella inversion time of 149  fs.

  • 176.
    Alagia, Michele
    et al.
    ISMN-CNR, Rom.
    Baldacchini, Chiara
    Università di Roma "La Sapienza" .
    Betti, Maria Grazia
    Università di Roma "La Sapienza" .
    Bussolotti, Fabio
    Università di Modena e Reggio Emilia.
    Carravetta, Vincenzo
    IPCF-CNR, Pisa.
    Ekström, Ulf
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics . Linköping University, The Institute of Technology.
    Mariani, Carlo
    Università di Roma "La Sapienza" .
    Stranges, Stefano
    Università di Roma "La Sapienza" .
    Core-shell photoabsorption and photoelectron spectra of gas-phase pentacene: Experiment and theory2005In: Journal of chemical physics Online, ISSN 1089-7690, Vol. 122, no 12, p. 124305-Article in journal (Refereed)
    Abstract [en]

    The C K-edge photoabsorption and 1s core-level photoemission of pentacene (C22H14) free molecules are experimentally measured, and calculated by self-consistent-field and static-exchange approximation ab initio methods. Six nonequivalent C atoms present in the molecule contribute to the C 1s photoemission spectrum. The complex near-edge structures of the carbon K-edge absorption spectrum present two main groups of discrete transitions between 283 and 288  eV photon energy, due to absorption to * virtual orbitals, and broader structures at higher energy, involving * virtual orbitals. The sharp absorption structures to the * empty orbitals lay well below the thresholds for the C 1s ionizations, caused by strong excitonic and localization effects. We can definitely explain the C K-edge absorption spectrum as due to both final (virtual) and initial (core) orbital effects, mainly involving excitations to the two lowest-unoccupied molecular orbitals of * symmetry, from the six chemically shifted C 1s core orbitals. ©2005 American Institute of Physics

  • 177. Alam, MT
    et al.
    Yamada, T
    Carlsson, Uno
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Biochemistry.
    Ikai, A
    The importance of being knotted: Effects of the C-terminal knot structure on enzymatic and mechanical properties of bovine carbonic anhydrase II2003In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 84, no 2, p. 159A-159AConference paper (Other academic)
  • 178.
    Alam, M.T.
    et al.
    Laboratory of Biodynamics, Grad. Sch. of Biosci. and Biotech., Tokyo Inst. of Technol., 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.
    Yamada, T.
    Laboratory of Biodynamics, Grad. Sch. of Biosci. and Biotech., Tokyo Inst. of Technol., 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.
    Carlsson, Uno
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Biochemistry.
    Ikai, A.
    Laboratory of Biodynamics, Grad. Sch. of Biosci. and Biotech., Tokyo Inst. of Technol., 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.
    The importance of being knotted: Effects of the C-terminal knot structure on enzymatic and mechanical properties of bovine carbonic anhydrase II12002In: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 519, no 1-3, p. 35-40Article in journal (Refereed)
    Abstract [en]

    In order to better understand the contribution of the knotted folding pattern to the enzymatic and mechanical properties of carbonic anhydrases, we replaced Gln-253 of bovine carbonic anhydrase II with Cys, which allowed us to measure the mechanical strength of the protein against tensile deformation by avoiding knot tightening. The expressed protein, to our surprise, turned out to contain two conformational isomers, one capable of binding an enzymatic inhibitor and the other not, which led to their separation through affinity chromatography. In near- and far-UV circular dichroism and fluorescence spectra, the separated conformers were very similar to each other and to the wild-type enzyme, indicating that they both had native-like conformations. We describe new evidence which supports the notion that the difference between the two conformers is likely to be related to the completeness of the C-terminal knot formation. © 2002 Federation of European Biochemical Societies. Published by Elsevier Science B.V. All rights reserved.

  • 179. Order onlineBuy this publication >>
    Alami, Jones
    Linköping University, Department of Physics, Chemistry and Biology, Plasma and Coating Physics. Linköping University, The Institute of Technology.
    Plasma Characterization & Thin Film Growth and Analysis in Highly Ionized Magnetron Sputtering2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The present thesis addresses two research areas related to film growth in a highly ionized magnetron sputtering system: plasma characterization, and thin film growth and analysis. The deposition technique used is called high power pulsed magnetron sputtering (HPPMS). Characteristic for this technique are high energy pulses (a few Joules) of length 50-100 µs that are applied to the target (cathode) with a duty time of less than 1 % of the total pulse time. This results in a high electron density in the discharge (>1x1019 m-3) and leads to an increase of the ionization fraction of the sputtered material reaching up to 70 % for Cu.

    In this work the spatial and temporal evolution of the plasma parameters, including the electron energy distribution function (EEDF), the electron density and the electron temperature are determined using electrostatic Langmuir probes. Electron temperature measurements reveal a low effective temperature of 2-3 eV. The degree of ionization in the HPPMS discharge is explained in light of the self-sputtering yield of the target material. A simple model is therefore provided in order to compare the sputtering yield in HPPMS and that in dc magnetron sputtering (dcMS) for the same average power.

    Thin Ta films are grown using HPPMS and dcMS and their properties are studied. It is shown that enhanced microstructure and morphology of the deposited films is achieved by HPPMS. The Ta films are also deposited at a number of substrate inclination angles ranging from 0o (i.e., facing the target surface) up to 180 o (i.e., facing away from the target). Deposition rate measurements performed at all inclination angles for both techniques, reveal that growth made using HPPMS resulted in an improved film thickness at higher inclination. Furthermore, the high ionization of the Ta atoms in HPPMS discharge is found to allow for phase tailoring of the deposited films at all inclination angles by applying a bias voltage to the substrate. Finally, highly ionized magnetron sputtering of a compound MAX-phase material (Ti3SiC2) is performed, demonstrating that the HPPMS discharge could also be used to tailor the composition of the growing Ti-Si-C films.

    List of papers
    1. Evolution of the electron energy distribution and plasma parameters in a pulsed magnetron discharge
    Open this publication in new window or tab >>Evolution of the electron energy distribution and plasma parameters in a pulsed magnetron discharge
    2001 (English)In: Applied Physics Letters, ISSN 0003-6951, Vol. 78, no 22, p. 3427-Article in journal (Refereed) Published
    Abstract [en]

    We demonstrate the creation of high-density plasma in a pulsed magnetron discharge. A 2.4 MW pulse, 100 µs wide, with a repetition frequency of 50 Hz is applied to a planar magnetron discharge to study the temporal behavior of the plasma parameters: the electron energy distribution function, the electron density, and the average electron energy. The electron density in the vicinity of the substrate, 20 cm below the cathode target, peaks at 8×1017 m–3, 127 µs after initiating the pulse. Towards the end of the pulse two energy groups of electrons are present with a corresponding peak in average electron energy. With the disapperance of the high-energy electron group, the electron density peaks, and the electron energy distribution appears to be Maxwellian like. Following the electron density peak, the plasma becomes more Druyvesteyn like with a higher average electron energy.

    Keywords
    sputter deposition
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-13372 (URN)10.1063/1.1376150 (DOI)
    Available from: 2005-10-25 Created: 2005-10-25 Last updated: 2013-10-30
    2. Spatial and temporal behavior of the plasma parameters in a pulsed magnetron discharge
    Open this publication in new window or tab >>Spatial and temporal behavior of the plasma parameters in a pulsed magnetron discharge
    2002 (English)In: Surface and Coatings Technology, Vol. 161, no 2-3, p. 249-256Article in journal (Refereed) Published
    Abstract [en]

    We demonstrate the evolution of the electron, energy distribution and the plasma parameters in a high-density plasma in a pulsed magnetron discharge. The high-density plasma is created by applying a high power pulse (1–2.4 MW) with pulse length 100 μs and repetition frequency of 50 Hz to a planar magnetron discharge. The spatial and temporal behavior of the plasma parameters are investigated using a Langmuir probe; the electron energy distribution function, the electron density and the average electron energy. The electron energy distribution function during and shortly after the pulse can be represented by a bi-Maxwellian distribution indicating two energy groups of electrons. Furthermore, we report on the variation of the plasma parameters and electron energy distribution function with gas pressure in the pressure range 0.5–20 mtorr. We report electron density as high as 4×1018 m−3 at 10 mtorr and 9 cm below the target in a pulsed discharge with average power 300 W. We estimate the traveling speed of the electron density peak along the axis of the discharge. The traveling speed decreases with increased gas pressure from 4×105 cm/s at 0.5 mtorr to 0.87×105 cm s−1 at 10 mtorr. The effective electron temperature peaks at the same time independent of position in the discharge, which indicates a burst of high energy electrons at the end of the pulse.

    Keywords
    Pulsed magnetron sputtering, Time evolution, Ionized sputtering, High density plasma, Ionized metal plasma
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-13373 (URN)10.1016/S0257-8972(02)00518-2 (DOI)
    Available from: 2005-10-25 Created: 2005-10-25 Last updated: 2013-10-30
    3. Plasma dynamics in a highly ionized pulsed magnetron discharge
    Open this publication in new window or tab >>Plasma dynamics in a highly ionized pulsed magnetron discharge
    Show others...
    2005 (English)In: Plasma sources science & technology (Print), ISSN 0963-0252, E-ISSN 1361-6595, Vol. 14, no 3, p. 525-531Article in journal (Refereed) Published
    Abstract [en]

    We report on electrostatic probe measurements of a high-power pulsed magnetron discharge. Space- and time-dependent characteristics of the plasma parameters are obtained as functions of the process parameters. By applying high-power pulses (peak power of ~0.5 MW), with a pulse-on time of ~100 µs and a repetition frequency of 20 ms, peak electron densities of the order of ~1019 m− 3, i.e. three orders of magnitude higher than for a conventional dc magnetron discharge, are achieved soon after the pulse is switched on. At high sputtering gas pressures (>5 mTorr), a second peak occurs in the electron density curve, hundreds of microseconds after the pulse is switched off. This second peak is mainly due to an ion acoustic wave in the plasma, reflecting off the chamber walls. This is concluded from the time delay between the two peaks in the electron and ion saturation currents, which is shown to be dependent on the chamber dimensions and the sputtering gas composition. Finally, the electron temperature is determined, initially very high but decreasing rapidly as the pulse is turned off. The reduction seen in the electron temperature, close to the etched area of the cathode, is due to cooling by the sputtered metal atoms.

    National Category
    Engineering and Technology
    Identifiers
    urn:nbn:se:liu:diva-13374 (URN)10.1088/0963-0252/14/3/015 (DOI)
    Available from: 2005-10-25 Created: 2005-10-25 Last updated: 2017-12-13
    4. Ion-accoustic solitary waves in a high power pulsed magnetron sputtering discharge
    Open this publication in new window or tab >>Ion-accoustic solitary waves in a high power pulsed magnetron sputtering discharge
    2005 (English)In: Journal of Physics D: Applied Physics, ISSN 0022-3727, E-ISSN 1361-6463, Vol. 38, no 18, p. 3417-3421Article in journal (Refereed) Published
    Abstract [en]

    We report on the creation and propagation of ion-acoustic solitary waves in a high power pulsed magnetron sputtering discharge. A dense localized plasma is created by applying high energy pulses (4–12 J) of length 70 µs, at a repetition frequency of 50 pulses per second, to a planar magnetron sputtering source. The temporal behaviour of the electron density, measured by a Langmuir probe, shows solitary waves travelling away from the magnetron target. The velocity of the waves depends on the gas pressure but is roughly independent of the pulse energy.

    National Category
    Engineering and Technology
    Identifiers
    urn:nbn:se:liu:diva-13375 (URN)10.1088/0022-3727/38/18/015 (DOI)
    Available from: 2005-10-25 Created: 2005-10-25 Last updated: 2017-12-13
    5. Ion-assisted Physical Vapor Deposition for enhanced film properties on non-flat surfaces
    Open this publication in new window or tab >>Ion-assisted Physical Vapor Deposition for enhanced film properties on non-flat surfaces
    Show others...
    2005 (English)In: Journal of Vacuum Science & Technology. A. Vacuum, Surfaces, and Films, ISSN 0734-2101, E-ISSN 1520-8559, Vol. 23, no 2, p. 278-280Article in journal (Refereed) Published
    Abstract [en]

    We have synthesized Ta thin films on Si substrates placed along a wall of a 2-cm-deep and 1-cm-wide trench, using both a mostly neutral Ta flux by conventional dc magnetron sputtering (dcMS) and a mostly ionized Ta flux by high-power pulsed magnetron sputtering (HPPMS). Structure of the grown films was evaluated by scanning electron microscopy, transmission electron microscopy, and atomic force microscopy. The Ta thin film grown by HPPMS has a smooth surface and a dense crystalline structure with grains oriented perpendicular to the substrate surface, whereas the film grown by dcMS exhibits a rough surface, pores between the grains, and an inclined columnar structure. The improved homogeneity achieved by HPPMS is a direct consequence of the high ion fraction of sputtered species.

    Keywords
    tantalum, ion beam assisted deposition, sputter deposition, scanning electron microscopy, transmission electron microscopy, atomic force microscopy, surface structure, surface roughness, porosity, metallic thin films
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-13376 (URN)10.1116/1.1861049 (DOI)
    Available from: 2005-10-25 Created: 2005-10-25 Last updated: 2017-12-13
    6. Phase tailoring of Ta thin films by highly ionized pulsed magnetron sputtering
    Open this publication in new window or tab >>Phase tailoring of Ta thin films by highly ionized pulsed magnetron sputtering
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    2007 (English)In: Thin Solid Films, ISSN 0040-6090, E-ISSN 1879-2731, Vol. 515, no 7-8, p. 3434-3438Article in journal (Refereed) Published
    Abstract [en]

    Ta thin films were grown on Si substrates at different inclination angles with respect to the sputter source using high power impulse magnetron sputtering (HIPIMS), an ionized physical vapor deposition technique. The ionization allowed for better control of the energy and directionality of the sputtered species, and consequently for improved properties of the deposited films. Depositions were made on Si substrates with the native oxide intact. The structure of the as deposited films was investigated using X-ray diffraction, while a four-point probe setup was used to measure the resistivity. A substrate bias process-window for growth of bcc-Ta was observed. However, the process-window position changed with changing inclination angles of the substrate. The formation of this low-resistivity bcc-phase could be understood in light of the high ion flux from the HIPIMS discharge.

    Place, publisher, year, edition, pages
    Elsevier, 2007
    Keywords
    HPPMS, Ionized PVD, IPVD, Pulsed sputtering
    National Category
    Physical Sciences
    Identifiers
    urn:nbn:se:liu:diva-10442 (URN)10.1016/j.tsf.2006.10.013 (DOI)
    Note
    Original publication: J. Alamia, P. Eklunda, J.M. Anderssona, M. Lattemanna, E. Wallina, J. Bohlmarka, P. Perssona, and U. Helmersson, Phase tailoring of Ta thin films by highly ionized pulsed magnetron sputtering, 2007, Thin Solid Films, (515), 7-8, 3434-3438. http://dx.doi.org/10.1016/j.tsf.2006.10.013. Copyright: Elsevier B.V., http://www.elsevier.com/Available from: 2007-12-14 Created: 2007-12-14 Last updated: 2017-12-14Bibliographically approved
    7. High-power impulse magnetron sputtering of Ti-Si-C thin films from a Ti3SiC2 compound target
    Open this publication in new window or tab >>High-power impulse magnetron sputtering of Ti-Si-C thin films from a Ti3SiC2 compound target
    Show others...
    2006 (English)In: Thin Solid Films, ISSN 0040-6090, E-ISSN 1879-2731, Vol. 515, no 4, p. 1731-1736Article in journal (Refereed) Published
    Abstract [en]

    We have deposited Ti-Si-C thin films using high-power impulse magnetron sputtering (HIPIMS) from a Ti3SiC2 compound target. The as-deposited films were composite materials with TiC as the main crystalline constituent. X-ray diffraction and photoelectron spectroscopy indicated that they also contained amorphous SiC, and for films deposited on inclined substrates, crystalline Ti5Si3Cx. The film morphology was dense and flat, while films deposited with dc magnetron sputtering under comparable conditions were rough and porous. Due to the high degree of ionization of the sputtered species obtained in HIPIMS, it is possible to control the film composition, in particular the C content, by tuning the substrate inclination angle, the Ar process pressure, and the bias voltage.

    Place, publisher, year, edition, pages
    Institutionen för fysik, kemi och biologi, 2006
    Keywords
    HIPIMS, Titanium silicon carbide
    National Category
    Physical Sciences
    Identifiers
    urn:nbn:se:liu:diva-10437 (URN)10.1016/j.tsf.2006.06.015 (DOI)000242931900079 ()
    Note

    Original publication: J. Alami, P. Eklund, J. Emmerlich, O. Wilhelmsson, U. Jansson, H. Högberg, L. Hultman, & U. Helmersson, High-power impulse magnetron sputtering of Ti-Si-C thin films from a Ti3SiC2 compound target, 2006, Thin Solid Films, (515), 4, 1731-1736. http://dx.doi.org/10.1016/j.tsf.2006.06.015. Copyright: Elsevier B.V., http://www.elsevier.com/.

    Available from: 2007-12-14 Created: 2007-12-14 Last updated: 2017-12-14Bibliographically approved
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    FULLTEXT01
  • 180.
    Alami, Jones
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Plasma and Coating Physics . Linköping University, The Institute of Technology.
    Eklund, Per
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, The Institute of Technology.
    Andersson, Jon M.
    Linköping University, Department of Physics, Chemistry and Biology, Plasma and Coating Physics . Linköping University, The Institute of Technology.
    Lattemann, Martina
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Wallin, Erik
    Linköping University, Department of Physics, Chemistry and Biology, Plasma and Coating Physics . Linköping University, The Institute of Technology.
    Böhlmark, Johan
    Linköping University, Department of Physics, Chemistry and Biology, Plasma and Coating Physics . Linköping University, The Institute of Technology.
    Persson, Per
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, The Institute of Technology.
    Helmersson, Ulf
    Linköping University, Department of Physics, Chemistry and Biology, Plasma and Coating Physics . Linköping University, The Institute of Technology.
    Phase tailoring of Ta thin films by highly ionized pulsed magnetron sputtering2007In: Thin Solid Films, ISSN 0040-6090, E-ISSN 1879-2731, Vol. 515, no 7-8, p. 3434-3438Article in journal (Refereed)
    Abstract [en]

    Ta thin films were grown on Si substrates at different inclination angles with respect to the sputter source using high power impulse magnetron sputtering (HIPIMS), an ionized physical vapor deposition technique. The ionization allowed for better control of the energy and directionality of the sputtered species, and consequently for improved properties of the deposited films. Depositions were made on Si substrates with the native oxide intact. The structure of the as deposited films was investigated using X-ray diffraction, while a four-point probe setup was used to measure the resistivity. A substrate bias process-window for growth of bcc-Ta was observed. However, the process-window position changed with changing inclination angles of the substrate. The formation of this low-resistivity bcc-phase could be understood in light of the high ion flux from the HIPIMS discharge.

    Download full text (pdf)
    FULLTEXT01
  • 181.
    Alami, Jones
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Plasma and Coating Physics. Linköping University, The Institute of Technology.
    Eklund, Per
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, The Institute of Technology.
    Emmerlich, Jens
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, The Institute of Technology.
    Wilhelmsson, O.
    Department of Materials Chemistry, The Ångström Laboratory, Uppsala University, Uppsala, Sweden.
    Jansson, U.
    Department of Materials Chemistry, The Ångström Laboratory, Uppsala University, Uppsala, Sweden.
    Högberg, Hans
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, The Institute of Technology.
    Hultman, Lars
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, The Institute of Technology.
    Helmersson, Ulf
    Linköping University, Department of Physics, Chemistry and Biology, Plasma and Coating Physics. Linköping University, The Institute of Technology.
    High-power impulse magnetron sputtering of Ti-Si-C thin films from a Ti3SiC2 compound target2006In: Thin Solid Films, ISSN 0040-6090, E-ISSN 1879-2731, Vol. 515, no 4, p. 1731-1736Article in journal (Refereed)
    Abstract [en]

    We have deposited Ti-Si-C thin films using high-power impulse magnetron sputtering (HIPIMS) from a Ti3SiC2 compound target. The as-deposited films were composite materials with TiC as the main crystalline constituent. X-ray diffraction and photoelectron spectroscopy indicated that they also contained amorphous SiC, and for films deposited on inclined substrates, crystalline Ti5Si3Cx. The film morphology was dense and flat, while films deposited with dc magnetron sputtering under comparable conditions were rough and porous. Due to the high degree of ionization of the sputtered species obtained in HIPIMS, it is possible to control the film composition, in particular the C content, by tuning the substrate inclination angle, the Ar process pressure, and the bias voltage.

    Download full text (pdf)
    fulltext
  • 182.
    Alami, Jones
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Plasma and Coating Physics . Linköping University, The Institute of Technology.
    Gudmundsson, J. T.
    University of Iceland, Reykjavik.
    Böhlmark, Johan
    Linköping University, Department of Physics, Chemistry and Biology, Plasma and Coating Physics . Linköping University, The Institute of Technology.
    Birch, Jens
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, The Institute of Technology.
    Helmersson, Ulf
    Linköping University, Department of Physics, Chemistry and Biology, Plasma and Coating Physics . Linköping University, The Institute of Technology.
    Plasma dynamics in a highly ionized pulsed magnetron discharge2005In: Plasma sources science & technology (Print), ISSN 0963-0252, E-ISSN 1361-6595, Vol. 14, no 3, p. 525-531Article in journal (Refereed)
    Abstract [en]

    We report on electrostatic probe measurements of a high-power pulsed magnetron discharge. Space- and time-dependent characteristics of the plasma parameters are obtained as functions of the process parameters. By applying high-power pulses (peak power of ~0.5 MW), with a pulse-on time of ~100 µs and a repetition frequency of 20 ms, peak electron densities of the order of ~1019 m− 3, i.e. three orders of magnitude higher than for a conventional dc magnetron discharge, are achieved soon after the pulse is switched on. At high sputtering gas pressures (>5 mTorr), a second peak occurs in the electron density curve, hundreds of microseconds after the pulse is switched off. This second peak is mainly due to an ion acoustic wave in the plasma, reflecting off the chamber walls. This is concluded from the time delay between the two peaks in the electron and ion saturation currents, which is shown to be dependent on the chamber dimensions and the sputtering gas composition. Finally, the electron temperature is determined, initially very high but decreasing rapidly as the pulse is turned off. The reduction seen in the electron temperature, close to the etched area of the cathode, is due to cooling by the sputtered metal atoms.

  • 183.
    Alami, Jones
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Plasma and Coating Physics . Linköping University, The Institute of Technology.
    Persson, Per O. Å.
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, The Institute of Technology.
    Music, Denis
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, The Institute of Technology.
    Gudmundsson, J. T.
    University of Iceland, Reykjavik.
    Böhlmark, Johan
    Linköping University, Department of Physics, Chemistry and Biology, Plasma and Coating Physics . Linköping University, The Institute of Technology.
    Helmersson, Ulf
    Linköping University, Department of Physics, Chemistry and Biology, Plasma and Coating Physics . Linköping University, The Institute of Technology.
    Ion-assisted Physical Vapor Deposition for enhanced film properties on non-flat surfaces2005In: Journal of Vacuum Science & Technology. A. Vacuum, Surfaces, and Films, ISSN 0734-2101, E-ISSN 1520-8559, Vol. 23, no 2, p. 278-280Article in journal (Refereed)
    Abstract [en]

    We have synthesized Ta thin films on Si substrates placed along a wall of a 2-cm-deep and 1-cm-wide trench, using both a mostly neutral Ta flux by conventional dc magnetron sputtering (dcMS) and a mostly ionized Ta flux by high-power pulsed magnetron sputtering (HPPMS). Structure of the grown films was evaluated by scanning electron microscopy, transmission electron microscopy, and atomic force microscopy. The Ta thin film grown by HPPMS has a smooth surface and a dense crystalline structure with grains oriented perpendicular to the substrate surface, whereas the film grown by dcMS exhibits a rough surface, pores between the grains, and an inclined columnar structure. The improved homogeneity achieved by HPPMS is a direct consequence of the high ion fraction of sputtered species.

  • 184.
    Alarcon, E I
    et al.
    Bio-nanomaterials Chemistry and Engineering Laboratory, Division of Cardiac Surgery, University of Ottawa Heart Institute, 40 Ruskin Street, Rm H5229, Ottawa, Canada.
    Vulesevic, B
    Bio-nanomaterials Chemistry and Engineering Laboratory, Division of Cardiac Surgery, University of Ottawa Heart Institute, 40 Ruskin Street, Rm H5229, Ottawa, Canada.
    Argawal, A
    Bio-nanomaterials Chemistry and Engineering Laboratory, Division of Cardiac Surgery, University of Ottawa Heart Institute, 40 Ruskin Street, Rm H5229, Ottawa, Canada.
    Ross, A
    Bio-nanomaterials Chemistry and Engineering Laboratory, Division of Cardiac Surgery, University of Ottawa Heart Institute, 40 Ruskin Street, Rm H5229, Ottawa, Canada.
    Bejjani, P
    Bio-nanomaterials Chemistry and Engineering Laboratory, Division of Cardiac Surgery, University of Ottawa Heart Institute, 40 Ruskin Street, Rm H5229, Ottawa, Canada.
    Podrebarac, J
    Bio-nanomaterials Chemistry and Engineering Laboratory, Division of Cardiac Surgery, University of Ottawa Heart Institute, 40 Ruskin Street, Rm H5229, Ottawa, Canada.
    Ravichandran, Ranjithkumar
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering.
    Phopase, Jaywant
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering.
    Suuronen, E J
    Bio-nanomaterials Chemistry and Engineering Laboratory, Division of Cardiac Surgery, University of Ottawa Heart Institute, 40 Ruskin Street, Rm H5229, Ottawa, Canada.
    Griffith, May
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences.
    Coloured cornea replacements with anti-infective properties: expanding the safe use of silver nanoparticles in regenerative medicine.2016In: Nanoscale, ISSN 2040-3364, E-ISSN 2040-3372, Vol. 8, no 12, p. 6484-6489Article in journal (Refereed)
    Abstract [en]

    Despite the broad anti-microbial and anti-inflammatory properties of silver nanoparticles (AgNPs), their use in bioengineered corneal replacements or bandage contact lenses has been hindered due to their intense yellow coloration. In this communication, we report the development of a new strategy to pre-stabilize and incorporate AgNPs with different colours into collagen matrices for fabrication of corneal implants and lenses, and assessed their in vitro and in vivo activity.

  • 185.
    Alarcon, Emilio I.
    et al.
    University of Ottawa, Canada; University of Ottawa, Canada; University of Ottawa, Canada.
    Udekwu, Klas I.
    Karolinska Institute, Sweden.
    Noel, Christopher W.
    University of Ottawa, Canada; .
    Gagnon, Luke B. -P.
    University of Ottawa, Canada.
    Taylor, Patrick K.
    University of Ottawa, Canada.
    Vulesevic, Branka
    University of Ottawa, Canada.
    Simpson, Madeline J.
    University of Ottawa, Canada.
    Gkotzis, Spyridon
    Karolinska Institute, Sweden.
    Islam, Mohammed Mirazul
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences. Karolinska Institute, Sweden.
    Lee, Chyan-Jang
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics. Linköping University, The Institute of Technology.
    Richter-Dahlfors, Agneta
    Karolinska Institute, Sweden.
    Mah, Thien-Fah
    University of Ottawa, Canada.
    Suuronen, Erik J.
    University of Ottawa, Canada.
    Scaiano, Juan
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences. University of Ottawa, Canada.
    Griffith, May
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences. Karolinska Institute, Sweden.
    Safety and efficacy of composite collagen-silver nanoparticle hydrogels as tissue engineering scaffolds2015In: Nanoscale, ISSN 2040-3364, E-ISSN 2040-3372, Vol. 7, no 44, p. 18789-18798Article in journal (Refereed)
    Abstract [en]

    The increasing number of multidrug resistant bacteria has revitalized interest in seeking alternative sources for controlling bacterial infection. Silver nanoparticles (AgNPs), are amongst the most promising candidates due to their wide microbial spectrum of action. In this work, we report on the safety and efficacy of the incorporation of collagen coated AgNPs into collagen hydrogels for tissue engineering. The resulting hybrid materials at [AgNPs] less than0.4 mu M retained the mechanical properties and biocompatibility for primary human skin fibroblasts and keratinocytes of collagen hydrogels; they also displayed remarkable anti-infective properties against S. aureus, S. epidermidis, E. coli and P. aeruginosa at considerably lower concentrations than silver nitrate. Further, subcutaneous implants of materials containing 0.2 mu M AgNPs in mice showed a reduction in the levels of IL-6 and other inflammation markers (CCL24, sTNFR-2, and TIMP1). Finally, an analysis of silver contents in implanted mice showed that silver accumulation primarily occurred within the tissue surrounding the implant.

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    fulltext
  • 186.
    Alarcon, Emilio I
    et al.
    University of Ottawa.
    Udekwu, Klas
    Karolinska Institute.
    Skog, Mårten
    Linköping University, Department of Clinical and Experimental Medicine, Cell Biology. Linköping University, Faculty of Health Sciences.
    Pacioni, NataliL
    University of Ottawa.
    Stamplecoskie, Kevin G
    University of Ottawa.
    Gonzalez-Bejar, Maria
    University of Ottawa.
    Polisetti, Naresh
    Linköping University, Department of Clinical and Experimental Medicine. Linköping University, Faculty of Health Sciences.
    Wickham, Abeni
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics. Linköping University, The Institute of Technology.
    Richter-Dahlfors, Agneta
    Karolinska Institute.
    Griffith, May
    Linköping University, Department of Clinical and Experimental Medicine, Ophthalmology. Linköping University, Faculty of Health Sciences.
    Scaiano, Juan C
    University of Ottawa.
    The biocompatibility and antibacterial properties of collagen-stabilized, photochemically prepared silver nanoparticles2012In: Biomaterials, ISSN 0142-9612, E-ISSN 1878-5905, Vol. 33, no 19, p. 4947-4956Article in journal (Refereed)
    Abstract [en]

    Spherical 3.5 nm diameter silver nanoparticles (AgNP) stabilized in type I collagen (AgNP@collagen) were prepared in minutes (5-15 min) at room temperature by a photochemical method initiated by UVA irradiation of a water-soluble non-toxic benzoin. This biocomposite was examined to evaluate its biocompatibility and its anti-bacterial properties and showed remarkable properties. Thus, while keratinocytes and fibroblasts were not affected by AgNP@collagen, it was bactericidal against Bacillus megaterium and E. coli but only bacteriostatic against S. epidermidis. In particular, the bactericidal properties displayed by AgNP@collagen were proven to be due to AgNP in AgNP@collagen, rather than to released silver ions, since equimolar concentrations of Ag are about four times less active than AgNP@collagen based on total Ag content. This new biocomposite was stable over a remarkable range of NaCl, phosphate, and 2-(N-morpholino)ethanesulfonic acid concentrations and for over one month at 4 degrees C. Circular dichroism studies show that the conformation of collagen in AgNP@collagen remains intact. Finally, we have compared the properties of AgNP@collagen with a similar biocomposite prepared using alpha-poly-L-Lysine and also with citrate stabilized AgNP; neither of these materials showed comparable biocompatibility, stability, or anti-bacterial activity.

  • 187.
    Albani, Giorgia
    et al.
    University of Milano Bicocca, Italy; Ist Nazl Fis Nucl, Italy.
    Perelli Cippo, Enrico
    CNR, Italy.
    Croci, Gabriele
    University of Milano Bicocca, Italy; Ist Nazl Fis Nucl, Italy.
    Muraro, Andrea
    CNR, Italy.
    Schooneveld, Erik
    Rutherford Appleton Lab, England.
    Scherillo, Antonella
    Rutherford Appleton Lab, England.
    Hall-Wilton, Richard
    European Spallat Source ERIC, Sweden; Mittuniversitetet, Sweden.
    Kanaki, Kalliopi
    European Spallat Source ERIC, Sweden.
    Höglund, Carina
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering. European Spallat Source ERIC, Sweden.
    Hultman, Lars
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, Faculty of Science & Engineering.
    Birch, Jens
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, Faculty of Science & Engineering.
    Claps, Gerardo
    Ist Nazl Fis Nucl, Italy.
    Murtas, Fabrizio
    Ist Nazl Fis Nucl, Italy.
    Rebai, Marica
    University of Milano Bicocca, Italy; Ist Nazl Fis Nucl, Italy.
    Tardocchi, Marco
    CNR, Italy.
    Gorini, Giuseppe
    University of Milano Bicocca, Italy; CNR, Italy; Ist Nazl Fis Nucl, Italy.
    Evolution in boron-based GEM detectors for diffraction measurements: from planar to 3D converters2016In: Measurement science and technology, ISSN 0957-0233, E-ISSN 1361-6501, Vol. 27, no 11, article id 115902Article in journal (Refereed)
    Abstract [en]

    The so-called He-3-crisis has motivated the neutron detector community to undertake an intense Ramp;D programme in order to develop technologies alternative to standard He-3 tubes and suitable for neutron detection systems in future spallation sources such as the European spallation source (ESS). Boron-based GEM (gas electron multiplier) detectors are a promising He-3-free technology for thermal neutron detection in neutron scattering experiments. In this paper the evolution of boron-based GEM detectors from planar to 3D converters with an application in diffraction measurements is presented. The use of 3D converters coupled with GEMs allows for an optimization of the detector performances. Three different detectors were used for diffraction measurements on the INES instrument at the ISIS spallation source. The performances of the GEM-detectors are compared with those of conventional He-3 tubes installed on the INES instrument. The conceptual detector with the 3D converter used in this paper reached a count rate per unit area of about 25% relative to the currently installed He-3 tube. Its timing resolution is similar and the signal-to-background ratio (S/B) is 2 times lower.

  • 188.
    Albert, Frank W.
    et al.
    Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America,.
    Somel, Mehmet
    Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, CAS–MPG Partner Institute for Computational Biology SIBS, Shanghai, China.
    Carneiro, Miguel
    CIBIO, Centro de Investigac¸a˜o em Biodiversidade e Recursos Gene´ ticos, Vaira˜o, Portugal, and Departamento de Zoologia e Antropologia–Faculdade de Cieˆncias da Universidade do Porto, Porto, Po.
    Aximu-Petri, Ayinuer
    Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
    Halbwax, Michael
    Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany and Fernan Vaz Gorilla Project, Port-Gentil, Gabon.
    Thalmann, Olaf
    Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany and Department of Biology, University of Turku, Turku, Finland.
    Blanco-Aguiar, Jose A.
    CIBIO, Centro de Investigac¸a˜o em Biodiversidade e Recursos Gene´ ticos, Vaira˜o, Portugal, 5 Departamento de Zoologia e Antropologia–Faculdade de Cieˆncias da Universidade do Porto, Porto, Portugal and Instituto de Investigacio´n en Recursos Cinege´ticos, IREC (CSIC, UCLM, JCCM), Ciudad Real, Spain.
    Plyusnina, Irina Z.
    Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
    Trut, Lyudmila
    Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
    Villafuerte, Rafael
    Instituto de Investigacio´n en Recursos Cinege´ticos, IREC (CSIC, UCLM, JCCM), Ciudad Real, Spain.
    Ferrand, Nuno
    CIBIO, Centro de Investigac¸a˜o em Biodiversidade e Recursos Gene´ ticos, Vaira˜o, Portugal, and Departamento de Zoologia e Antropologia–Faculdade de Cieˆncias da Universidade do Porto, Porto, Portugal.
    Kaiser, Sylvia
    Department of Behavioural Biology, University of Mu¨ nster, Mu¨ nster, Germany.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Zoology. Linköping University, The Institute of Technology.
    Pääbo, Svante
    Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
    A Comparison of Brain Gene Expression Levels in Domesticated and Wild Animals2012In: PLOS Genetics, ISSN 1553-7390, Vol. 8, no 9, p. e1002962-Article in journal (Refereed)
    Abstract [en]

    Domestication has led to similar changes in morphology and behavior in several animal species, raising the questionwhether similarities between different domestication events also exist at the molecular level. We used mRNA sequencing toanalyze genome-wide gene expression patterns in brain frontal cortex in three pairs of domesticated and wild species (dogsand wolves, pigs and wild boars, and domesticated and wild rabbits). We compared the expression differences with thosebetween domesticated guinea pigs and a distant wild relative (Cavia aperea) as well as between two lines of rats selectedfor tameness or aggression towards humans. There were few gene expression differences between domesticated and wilddogs, pigs, and rabbits (30–75 genes (less than 1%) of expressed genes were differentially expressed), while guinea pigs andC. aperea differed more strongly. Almost no overlap was found between the genes with differential expression in thedifferent domestication events. In addition, joint analyses of all domesticated and wild samples provided only suggestiveevidence for the existence of a small group of genes that changed their expression in a similar fashion in differentdomesticated species. The most extreme of these shared expression changes include up-regulation in domesticates of SOX6and PROM1, two modulators of brain development. There was almost no overlap between gene expression in domesticatedanimals and the tame and aggressive rats. However, two of the genes with the strongest expression differences betweenthe rats (DLL3 and DHDH) were located in a genomic region associated with tameness and aggression, suggesting a role ininfluencing tameness. In summary, the majority of brain gene expression changes in domesticated animals are specific tothe given domestication event, suggesting that the causative variants of behavioral domestication traits may likewise bedifferent.

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  • 189.
    Albin, Gräns
    Linköping University, Department of Physics, Chemistry and Biology.
    Feto-Maternal: Communication in Broiler Chickens (Gallus gallus domesticus)2006Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Bird incubation is a natural phenomenon that balances the needs of the parents for nourishment with the needs of the fetus for heat provision and protection. In this context, any means of communication between the fetus and the parents would have an adaptive value. The aim of the study was to investigate whether putative means of fetomaternal communication would correlate to physiological changes caused by environmental alterations. Oxygen consumption was used to measure fetal well being and six independent variables associated with fetal vocalizations and fetal movements were used to evaluate their potential for communicating the fetus statu quo. Broiler fetuses (Gallus gallus domesticus) of three developmental stages (day 18, internally pipped and externally pipped) were challenged by a stepwise reduction in ambient temperature down to 30ºC. A linear drop in oxygen consumption in response to lowered temperatures was found in all three developmental stages indicating that the fetus was affected by the temperature changes. No differences correlating with temperature variations were found in any of the variables associated with fetal vocalization. Fetal vocalizations are consequently not used to communicate the thermal status of the fetus. Movement occurrence, movement intensity and ventilation frequency, however, followed a “maximum peak” trend, with a highest response at the third temperature interval (35.0-35.5ºC). Considering that the lower limit of optimal development is between 35-36ºC, the results suggest that fetal movements can be of potential use to the incubating parent to assess the well-being of the fetus.

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  • 190. Albinsson, L.
    et al.
    Ansell, Ricky
    Linköping University, Department of Physics, Chemistry and Biology, Molecular genetics . Linköping University, The Institute of Technology.
    Drotz, Weine
    Swedish National Laboratory of Forensic Sciences, Linköping.
    Single DNA analysis approach of crime scene samples2009In: Book of Abstracts, 2009, p. 142-Conference paper (Refereed)
  • 191.
    Albinsson, L.
    et al.
    Swedish National Forensic Centre - NFC, Linköping, Sweden.
    Hedman, J.
    Swedish National Forensic Centre - NFC, Linköping, Sweden.
    Ansell, Ricky
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Swedish National Forensic Centre - NFC, Linköping, Sweden.
    Mixed DNA profiles from single-donors2015In: Abstract book, 7th European Academy of Forensic Science, EAFS, Prag, Tjeckien, 2015, 2015, p. 538-Conference paper (Other academic)
    Abstract [en]

    Mosaicism and chimerism in individuals can complicate the interpretation and even lead to misinterpretation of DNA profiles in forensic casework. If a person has different DNA profiles in different tissue types, i.e. a true chimaera, wrongful exclusions can be made. Additionally, mixed chimaeras can have DNA profiles that may be mistaken for mixtures. We have set-up automatic DNA databasing processes to handle atypical single-donor DNA profiles, i.e. profiles having one or several “extra” alleles.

    Studying all reference samples analysed at NFC from 2006 until spring 2014, 2‰ of the samples showed atypical DNA profiles. To be able to set routines for handling these DNA profiles, each one was manually searched in CODIS with adjusted settings, to evaluate the frequency of false-positive hits. To tag these profiles in LIMS a new result status was implemented. Additionally, all such DNA profiles must be confirmed by analysing at least two discrete samples. In LIMS, the results are manually recorded to compose of all alleles from the samples from a suspect, i.e. containing most possible genetic information. LIMS automatically categorises the atypical DNA profiles with a special CODIS index, called “Multi-allelic offender”. The first time an atypical profile is searched, the matches are manually investigated. If a match is false, its disposition will be set to “no match” to prevent this from occurring in future searches. Automatic searches will then be performed in every day routine with moderate stringency, allowing the atypical DNA profile to match either a genotype or a mixture. If the match is true, a match-report will be created and sent to the police from the LIMS.

     

  • 192.
    Albinsson, L.
    et al.
    Swedish National Laboratory of Forensic Science, Linköping.
    Hedman, J.
    Swedish National Laboratory of Forensic Science, Linköping.
    Ansell, Ricky
    Linköping University, Department of Physics, Chemistry and Biology, Molecular genetics . Linköping University, The Institute of Technology.
    Verification of alleles by using peak height thresholds and quality control of STR profiling kits2011In: Forensic Science International: Genetics, Supplement Series, ISSN 1875-1768, Vol. 3, no 1, p. e251-e252Article in journal (Refereed)
    Abstract [en]

    In the autumn of 2010 SKL performed in-house validation of PowerPlex ESX 16 System (Promega). As the validation showed that very low amounts of DNA (∼10 pg) may provide correct allele callings (peaks above 50 rfu), we investigated the linear range, i.e., the interval of DNA amounts where a profile is well balanced and does not contain drop-outs and/or drop-ins. The linear range as indicated by our results is approximately from 0.5 ng (manufacturer's recommendation) to 2.0 ng of DNA. As minute DNA amounts may be detected using the kit, extra care needs to be taken not to report a contaminant allele as a part of the correct profile. A way to verify the correctness of a single donor profile in routine analysis, without using duplicate analysis, is to use conservative peak height thresholds. We determine STR marker specific peak height thresholds for each new lot of DNA profiling kits, based on the results from three different tests: heterozygote balance, signal intensity and repeatability, and PCR inhibitor tolerance. The tests also serve to verify the quality of the kit lot. Generally, the peak height thresholds vary between 200 and 250 rfu for heterozygote alleles, with doubled values used for homozygotes.

  • 193.
    Albinsson, L.
    et al.
    Swedish National Laboratory of Forensic Science (SKL), Linköping, Sweden.
    Hedman, J.
    Swedish National Laboratory of Forensic Science (SKL), Linköping, Sweden.
    Ansell, Ricky
    Linköping University, Department of Physics, Chemistry and Biology, Molecular genetics . Linköping University, The Institute of Technology.
    Verification of alleles by using peak height thresholds and quality control of STR profiling kits2011In: Book of Abstracts, 2011, p. 134-Conference paper (Refereed)
    Abstract [en]

    In the autumn of 2010 SKL performed in-house validation of PowerPlex ESX 16 System (Promega). As the validationshowed that very low amounts of DNA (< 10 pg) may provide correct allele callings (peaks above 50 rfu),we investigated the linear range, i.e., the interval of DNA amounts where a profile is well balanced and doesnot contain drop-outs and/or drop-ins. The linear range as indicated by our results is approximately from 0.5ng (manufacturer’s recommendation) to 2.0 ng of DNA. Profiles generated by less than 0.5 ng contained intralocus imbalances and/or drop-outs. Above 2.0 ng “bleed through” occurs due to overload of template-DNA.A way to verify the correctness of a profile, without knowing anything about the condition of the template-DNA, is to use peak height thresholds adjusted to each marker and batch of kits used. SKL performs a qualitycontrol and adjust thresholds for each batch of kits. Three main tests are performed; detection limit, inhibitortolerance and signal repeatability. The detection limit is examined to identify at which concentration intralocus imbalances and drop-outs start to increase. The ability to overcome inhibition is checked by analysingvarying amounts of blood extracted with Chelex. Finally a set of replicates of control DNA is amplified (0.5 ngtemplate-DNA) to calculate the mean peak height and standard deviation at each locus. Generally, the peakheight thresholds vary between 200 and 250 rfu for heterozygote peaks. To verify allelic peaks below the setpeak height thresholds, SKL uses consensus analysis.

  • 194.
    Albinsson, Linda
    et al.
    Swedish National Laboratory of Forensic Science (SKL), Linköping, Sweden.
    Norén, Lina
    Swedish National Laboratory of Forensic Science (SKL), Linköping, Sweden.
    Hedell, Ronny
    Swedish National Laboratory of Forensic Science (SKL), Linköping, Sweden.
    Ansell, Ricky
    Linköping University, Department of Physics, Chemistry and Biology, Molecular genetics. Linköping University, The Institute of Technology.
    Swedish population data and concordance for the kits PowerPlexÒ ESX 16 System, PowerPlexÒ ESI 16 System, AmpFlSTRÒ NGMTM, AmpFlSTRÒ SGM PlusTM and Investigator ESSplex2011In: Forensic Science International: Genetics, ISSN 1872-4973, E-ISSN 1878-0326, Vol. 5, no 3, p. e89-e92Article in journal (Other academic)
    Abstract [en]

    The European Standard Set of loci (ESS) has been extended with five additional short tandem repeat (STR) loci following the recommendations of the European Network of Forensic Science Institutes (ENFSI) and the European DNA Profiling Group (EDNAP) to increase the number of loci routinely used by the European forensic community. Subsequently, a new extended Swedish population database, based on 425 individuals, has been assembled using the new STR multiplex kits commercially available.

    Allele frequencies and statistical parameters of forensic interest for 15 autosomal STR loci (D3S1358, TH01, D21S11, D18S51, D10S1248, D1S1656, D2S1338, D16S539, D22S1045, vWA, D8S1179, FGA, D2S441, D12S391 and D19S433) were obtained from the analysis of the PowerPlex® ESX 16 System kit (Promega Corporation, USA). According to the data no evidence of deviations from Hardy–Weinberg equilibrium was found. The observed heterozygosity varies between 0.755 (TH01) and 0.892 (D1S1656). The power of discrimination was smallest for D22S1045 (0.869) and largest for D1S1656 (0.982) while the power of exclusion was smallest for TH01 (0.518) and largest for D1S1656 (0.778).

    A concordance study was performed on the five amplification systems: PowerPlex® ESX 16 System, PowerPlex® ESI 16 System (Promega Corporation, USA), AmpFlSTR® NGM™, AmpFlSTR® SGM Plus™ (Applied Biosystems, USA) and Investigator ESSplex (Qiagen, Germany) to reveal null alleles and other divergences between the kits. For the 425 DNA profiles included, AmpFlSTR® NGM™ revealed two null alleles, AmpFlSTR® SGM Plus™ revealed one, and Investigator ESSplex revealed a micro-variant, while the rest of the alleles showed full concordance between the kits tested.

  • 195.
    Albouy, Camille
    et al.
    IFREMER, France.
    Archambault, Philippe
    Univ Laval, Canada.
    Appeltans, Ward
    UNESCO, Belgium.
    Araujo, Miguel B.
    CSIC, Spain; Univ Evora, Portugal; Univ Copenhagen, Denmark.
    Beauchesne, David
    Univ Quebec Rimouski, Canada.
    Cazelles, Kevin
    Univ Guelph, Canada.
    Cirtwill, Alyssa
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering. Univ Canterbury, New Zealand.
    Fortin, Marie-Josee
    Univ Toronto, Canada.
    Galiana, Nuria
    CNRS, France.
    Leroux, Shawn J.
    Mem Univ, Canada.
    Pellissier, Loik
    Swiss Fed Inst Technol, Switzerland; Swiss Fed Res Inst WSL, Switzerland.
    Poisot, Timothee
    Univ Montreal, Canada; McGill Univ, Canada.
    Stouffer, Daniel B.
    Univ Canterbury, New Zealand.
    Wood, Spencer A.
    Univ Washington, WA 98195 USA.
    Gravel, Dominique
    Univ Montreal, Canada; Univ Sherbrooke, Canada.
    The marine fish food web is globally connected2019In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 3, no 8, p. 1153-+Article in journal (Refereed)
    Abstract [en]

    The productivity of marine ecosystems and the services they provide to humans are largely dependent on complex interactions between prey and predators. These are embedded in a diverse network of trophic interactions, resulting in a cascade of events following perturbations such as species extinction. The sheer scale of oceans, however, precludes the characterization of marine feeding networks through de novo sampling. This effort ought instead to rely on a combination of extensive data and inference. Here we investigate how the distribution of trophic interactions at the global scale shapes the marine fish food web structure. We hypothesize that the heterogeneous distribution of species ranges in biogeographic regions should concentrate interactions in the warmest areas and within species groups. We find that the inferred global metaweb of marine fish-that is, all possible potential feeding links between co-occurring species-is highly connected geographically with a low degree of spatial modularity. Metrics of network structure correlate with sea surface temperature and tend to peak towards the tropics. In contrast to open-water communities, coastal food webs have greater interaction redundancy, which may confer robustness to species extinction. Our results suggest that marine ecosystems are connected yet display some resistance to perturbations because of high robustness at most locations.

  • 196.
    Aldred, Nick
    et al.
    1School of Marine Science and Technology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK..
    Ekblad, Tobias
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Andersson, Olof
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Liedberg, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Clare, Anthony C.
    1School of Marine Science and Technology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK..
    In situ study of surface exploration by barnacle cyprids (Semibalanus balanoides) using imaging surface plasmon resonanceManuscript (preprint) (Other academic)
    Abstract [en]

    Imaging surface plasmon resonance (iSPR) was employed to investigate the interfacial adhesion phenomena that occur during the exploration of immersed surfaces by barnacle cyprids (Semibalanus balanoides). It was hypothesised that since the footprint material used by cyprids for temporary adhesion has previously been related to a large cuticular glycoprotein (SIPC), the passive deposition of cyprid footprints and the binding of SIPC to surfaces might correlate. Increased surface exploration (and footprint deposition) has also been related to increased likelihood of settlement in barnacle cyprids. If a correlation between footprint deposition and SIPC binding were to exist, therefore, there would be potential for the development of a high‐throughput assay to determine the efficacy of putative antifouling chemistries against cyprids prior to, or instead of, lengthy bio‐assays. Footprints were deposited in large numbers on carboxyl‐terminated self‐assembled monolayers (SAMs) and in very small numbers on ethylene glycol‐containing SAMs and hydrogel coatings. SIPC binding also followed the same trend. An exception to the correlation was an amineterminated SAM that accumulated few cyprid footprints, but bound SIPC strongly. It is concluded that there is great potential for the iSPR technique to be used in the evaluation of putatively non‐fouling surfaces as well as improving our understanding of the nature of the cyprid footprint material and its interactions with surfaces of different chemistry. However, the use of SIPC binding as a predictor of footprint accumulation/likelihood of settlement of cyprids to surfaces would be premature at this stage without first understanding the exceptions highlighted in this study.

  • 197.
    Aldred, Nick
    et al.
    Newcastle University.
    Ekblad, Tobias
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Andersson, Olof
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Liedberg, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Clare, Anthony S.
    Newcastle University.
    Real-Time Quantification of Microscale Bioadhesion Events In situ Using Imaging Surface Plasmon Resonance (iSPR)2011In: ACS Applied Materials and Interfaces, ISSN 1944-8244, E-ISSN 1944-8252, Vol. 3, no 6, p. 2085-2091Article in journal (Refereed)
    Abstract [en]

    From macro- to nanoscales, adhesion phenomena are all-pervasive in nature yet remain poorly understood. In recent years, studies of biological adhesion mechanisms, terrestrial and marine, have provided inspiration for "biomimetic" adhesion strategies and important insights for the development of fouling-resistant materials. Although the focus of most contemporary bioadhesion research is on large organisms such as marine mussels, insects and geckos, adhesion events on the micro/nanoscale are critical to our understanding of important underlying mechanisms. Observing and quantifying adhesion at this scale is particularly relevant for the development of biomedical implants and in the prevention of marine biofouling. However, such characterization has so far been restricted by insufficient quantities of material for biochemical analysis and the limitations of contemporary imaging techniques. Here, we introduce a recently developed optical method that allows precise determination of adhesive deposition by microscale organisms in situ and in real time; a capability not before demonstrated. In this extended study we used the cypris larvae of barnacles and a combination of conventional and imaging surface plasmon resonance techniques to observe and quantify adhesive deposition onto a range of model surfaces (CH(3)-, COOH-, NH(3)-, and mPEG-terminated SAMs and a PEGMA/HEMA hydrogel). We then correlated this deposition to passive adsorption of a putatively adhesive protein from barnacles. In this way, we were able to rank surfaces in order of effectiveness for preventing barnacle cyprid exploration and demonstrate the importance of observing the natural process of adhesion, rather than predicting surface effects from a model system. As well as contributing fundamentally to the knowledge on the adhesion and adhesives of barnacle larvae, a potential target for future biomimetic glues, this method also provides a versatile technique for laboratory testing of fouling-resistant chemistries.

  • 198.
    Aldred, Nick
    et al.
    Newcastle University, England .
    Gohad, Neeraj V.
    Clemson University, SC USA .
    Petrone, Luigi
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering.
    Orihuela, Beatriz
    Duke University, NC USA .
    Liedberg, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering.
    Ederth, Thomas
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering.
    Mount, Andrew
    Clemson University, SC USA .
    Rittschof, Dan
    Duke University, NC USA .
    Clare, Anthony S.
    Newcastle University, England .
    Confocal microscopy-based goniometry of barnacle cyprid permanent adhesive2013In: Journal of Experimental Biology, ISSN 0022-0949, E-ISSN 1477-9145, Vol. 216, no 11, p. 1969-1972Article in journal (Refereed)
    Abstract [en]

    Biological adhesives are materials of particular interest in the fields of bio-inspired technology and antifouling research. The adhesive of adult barnacles has received much attention over the years; however, the permanent adhesive of the cyprid - the colonisation stage of barnacles - is a material about which very little is presently known. We applied confocal laser-scanning microscopy to the measurement of contact angles between the permanent adhesive of barnacle cyprid larvae and self-assembled monolayers of OH- and CH3-terminated thiols. Measurement of contact angles between actual bioadhesives and surfaces has never previously been achieved and the data may provide insight into the physicochemical properties and mechanism of action of these functional materials. The adhesive is a dual-phase system post-secretion, with the behaviour of the components governed separately by the surface chemistry. The findings imply that the cyprid permanent adhesion process is more complex than previously thought, necessitating broad re-evaluation of the system. Improved understanding will have significant implications for the production of barnacle-resistant coatings as well as development of bio-inspired glues for niche applications.

  • 199.
    Aldén, Anna
    Linköping University, The Department of Physics, Chemistry and Biology.
    Optimization of the Liquefaction Process in Bioethanol Production & Development of Method for Quantification of Nonsolubilized Starch in Mash2008Independent thesis Basic level (professional degree), 20 points / 30 hpStudent thesis
    Abstract [en]

    Ethanol production at Lantmännen Agroetanol AB in Norrköping began in December 2000. The objective of this master's thesis is to find and optimize factors affecting the yield of the liquefaction, a part of the upstream process. To measure successfulness of liquefaction it is desired that amount of non-solubilized starch is quantified, and hence a method for determination of non-solubilized starch in mash has to be developed.

    Starch is a carbon reserve in plants. Starch granules are polymers of amylose and amylopectin which are polysaccharides of glucose. When a starch/water solution is heated the starch granules start to absorb water and swell, a process termed gelatinization. The swelling makes the granules susceptible to hydrolysis by enzymes such as alpha-amylase, this is called liquefaction. Eventually the granular structure is broken and the slurry contains solubilized starch which can be saccharified to glucose by glucoamylase. In the bioethanol production process, the milled grain is mixed with water and enzymes. The slurry is heated, gelatinization and liquefaction occurs. Saccharification occurs simultaneously to fermentation. Ethanol is purified from the fermented mash during downstream processing.

    Starch in the form of starch granules cannot be quantified. The adopted principle for determination of non-solubilized starch in liquefied mash is to wash away the solubilized starch, then quantitatively hydrolyze non-solubilized starch to glucose and quantify glucose.

    To find and optimize factors significant for yield of liquefaction multiple factor experiments were conducted where eight factors were studied. pH, temperature in mixtank and temperature in liquefaction tank 1 were the most significant factors. The temperature in liquefaction tank 1 should be kept as is is at 74°C. A small rise in pH should shorten the mean length of dextrins which is preferable. An increase of pH from 5.2 to 5.4 is therefore proposed. The temperature in mixtank should also be increased by a few degrees. The yield of the process should be carefully evaluated during the modifications.

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  • 200.
    Aleckovic, Ehlimana
    et al.
    Linköping University, Department of Physics, Chemistry and Biology.
    Andersson, Linnea
    Linköping University, Department of Physics, Chemistry and Biology.
    Chamoun, Sherley
    Linköping University, Department of Physics, Chemistry and Biology.
    Einarsson, Ellen
    Linköping University, Department of Physics, Chemistry and Biology.
    Ekstedt, Ebba
    Linköping University, Department of Physics, Chemistry and Biology.
    Eriksen, Emma
    Linköping University, Department of Physics, Chemistry and Biology.
    Madan-Andersson, Maria
    Linköping University, Department of Physics, Chemistry and Biology.
    Method Development for Determining the Stability of Heat Stable Proteins Combined with Biophysical Characterization of Human Calmodulin and the Disease Associated Variant D130G2016Independent thesis Basic level (degree of Bachelor), 10,5 credits / 16 HE creditsStudent thesis
    Abstract [en]

    Calmodulin is a highly conserved calcium ion binding protein expressed in all eukaryotic species. The 149 amino acid residues in the primary structure are organized in seven α helices with the highly flexible central α helix connecting the two non-cooperative domains of calmodulin. Each domain contains two EF-hand motifs to which calcium ions bind in a cooperative manner, hence the binding of four calcium ions saturate one calmodulin molecule. In the cardiovascular area calmodulin is involved in the activation of cardiac muscle contraction, and mutations that arise in the genetic sequence of the protein often have severe consequences. One such consequential mutation that can arise brings about the replacement of the highly conserved aspartic acid with glycine at position 130 in the amino acid sequence. In this research, the thermal and chemical stability within the C domain of the D130G variant of human calmodulin was investigated using a new method only requiring circular dichroism spectroscopic measurements. Affinity studies within the C domain of the D130G variant of human calmodulin were performed using fluorescence spectroscopy, and the ligands chosen for this purpose were trifluoperazine and p- HTMI. All analytical experiments were performed with the C domain of wild type human calmodulin as a reference. From the new method, it was concluded that the C domain of the D130G variant of human calmodulin has a slightly decreased stability in terms of Tm and Cm values compared to the C domain of wild type human calmodulin. The affinity analyses indicated that neither trifluoperazine nor p-HTMI discriminates between the C domain of the D130G variant of human calmodulin and the C domain of wild type human calmodulin in terms of dissociation constants. The pivotal outcome from this research is that the new method is applicable for determination of the stability parameters Tm and Cm of heat stable proteins. 

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