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• 1.
University of Illinois at Urbana Champaign, Urbana, IL, USA; Beckman Institute, Urbana, IL, USA.
Institute of Integrative Biology, University of Liverpool, Liverpool, IL, USA. Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom. Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom. Universitätsmedizin Mannheim, Mannheim, Germany. Department of Pathology, Emory University, Atlanta, GA, USA. European Molecular Biology Laboratory, Hamburg, Germany. European Molecular Biology Laboratory, Hamburg, Germany. Department for Integrative Pathophysiology, Universitätsmedizin Mannheim, Mannheim, Germany. University of Illinois at Urbana Champaign, Urbana, IL, USA Beckman Institute, Urbana, IL, USA. Department of Pathology, Emory University, Atlanta, GA, USA. Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.
Stretching of Twitchin Kinase2012In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 102, no 3 Supplement 1, p. 361a-362aArticle in journal (Refereed)

The giant proteins from the titin family, that form cytoskeletal filaments, have emerged as key mechanotransducers in the sarcomere. These proteins contain a conserved kinase region, which is auto-inhibited by a C-terminal tail domain. The inhibitory tail domain occludes the active sites of the kinases, thus preventing ATP from binding. It was proposed that through application of a force, such as that arising during muscle contraction, the inhibitory tail becomes detached, lifting inhibition. The force-sensing ability of titin kinase was demonstrated in AFM experiments and simulations [Puchner, et al., 2008, PNAS:105, 13385], which showed indeed that mechanical forces can remove the autoinhibitory tail of titin kinase. We report here steered molecular dynamics simulations (SMD) of the very recently resolved crystal structure of twitchin kinase, containing the kinase region and flanking fibronectin and immuniglobulin domains, that show a variant mechanism. Despite the significant structural and sequence similarity to titin kinase, the autoinhibitory tail of twitchin kinase remains in place upon stretching, while the N-terminal lobe of the kinase unfolds. The SMD simulations also show that the detachment and stretching of the linker between fibronectin and kinase regions, and the partial extension of the autoinhibitory tail, are the primary force-response. We postulate that this stretched state, where all structural elements are still intact, may represent the physiologically active state.

• 2.
Vilnius University, Lithuania; Centre Phys Science and Technology, Lithuania.
Centre Phys Science and Technology, Lithuania. Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering. Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering. Centre Phys Science and Technology, Lithuania. Vilnius University, Lithuania.
Role of coherence and delocalization in photo-induced electron transfer at organic interfaces2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, no 32914Article in journal (Refereed)

Photo-induced charge transfer at molecular heterojunctions has gained particular interest due to the development of organic solar cells (OSC) based on blends of electron donating and accepting materials. While charge transfer between donor and acceptor molecules can be described by Marcus theory, additional carrier delocalization and coherent propagation might play the dominant role. Here, we describe ultrafast charge separation at the interface of a conjugated polymer and an aggregate of the fullerene derivative PCBM using the stochastic Schrodinger equation (SSE) and reveal the complex time evolution of electron transfer, mediated by electronic coherence and delocalization. By fitting the model to ultrafast charge separation experiments, we estimate the extent of electron delocalization and establish the transition from coherent electron propagation to incoherent hopping. Our results indicate that even a relatively weak coupling between PCBM molecules is sufficient to facilitate electron delocalization and efficient charge separation at organic interfaces.

• 3.
Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
Finite Temperature, Magnetic, and Many-Body Effects in Ab Initio Simulations of Alloy Thermodynamics2013In: TMS2013 Supplemental Proceedings, John Wiley & Sons, 2013, p. 617-626Chapter in book (Refereed)

Ab initio electronic structure theory is known as a useful tool for prediction of materials properties. However, majority of simulations still deal with calculations in the framework of density functional theory with local or semi-local functionals carried out at zero temperature. We present new methodological solution.s, which go beyond this approach and explicitly take finite temperature, magnetic, and many-body effects into account. Considering Ti-based alloys, we discuss !imitations of the quasiharmonic approximation for the treatment of lattice vibrations, and present an accurate and easily extendable method to calculate free ,energies of strongly anharmonic solids. We underline the necessity to going beyond the state-of-the-art techniques for the determination of effective cluster interactions in systems exhibiting mctal-to-insulator transition, and describe a unified cluster expansion approach developed for this class of materials. Finally, we outline a first-principles method, disordered local moments molecular dynamics, for calculations of thermodynamic properties of magnetic alloys, like Cr1-x,.AlxN, in their high-temperature paramagnetic state. Our results unambiguously demonstrate importance of finite temperature effects in theoretical calculations ofthermodynamic properties ofmaterials.

• 4.
Linköping University, Department of Physics, Chemistry and Biology, Molecular Surface Physics and Nano Science. Linköping University, Faculty of Science & Engineering.
Investigation of nanoparticle-cell interactions for development of next generation of biocompatible MRI contrast agents2018Doctoral thesis, comprehensive summary (Other academic)

Progress in synthesis technologies and advances in fundamental understanding of materials with low dimensionality has led to the birth of a new scientific field, nanoscience, and to strong expectations of multiple applications of nanomaterials. The physical properties of small particles are unique, bridging the gap between atoms and molecules, on one side, and bulk materials on the other side. The work presented in this thesis investigates the potential of using magnetic nanoparticles as the next generation of contrast agents for biomedical imaging. The focus is on gadolinium-based nanoparticles and cellular activity including the uptake, morphology and production of reactive oxygen species.

Gd ion complexes, like Gd chelates, are used today in the clinic, world-wide. However, there is a need for novel agents, with improved contrast capabilities and increased biocompatibility. One avenue in their design is based on crystalline nanoparticles. It allows to reduce the total number of Gd ions needed for an examination. This can be done by nanotechnology, which allows one to improve and fine tune the physico- chemical properties on the nanomaterial in use, and to increase the number of Gd atoms at a specific site that interact with protons and thereby locally increase the signal. In the present work, synthesis, purification and surface modification of crystalline Gd2O3-based nanoparticles have been performed. The nanoparticles are selected on the basis of their physical properties, that is they show enhanced magnetic properties and therefore may be of high potential interest for applications as contrast agents.

The main synthesis method of Gd2O3 nanoparticles in this work was the modified “polyol” route, followed by purification of as-synthesized DEG-Gd2O3 nanoparticles suspensions. In most cases the purification step involved dialysis of the nanoparticle samples. In this thesis, organosilane were chosen as an exchange agent for further functionalization. Moreover, several paths have been explored for modification of the nanoparticles, including Tb3+ doping and capping with sorbitol.

Biocompatibility of the newly designed nanoparticles is a prerequisite for their use in medical applications. Its evaluation is a complex process involving a wide range of biological phenomena. A promising path adopted in this work is to study of nanoparticle interactions with isolated blood cells. In this way one could screen nanomaterial prior to animal studies.

The primary cell type considered in the thesis are polymorphonuclear neutrophils (PMN) which represent a type of the cells of human blood belonging to the granulocyte family of leukocytes. PMNs act as the first defense of the immune system against invading pathogens, which makes them valuable for studies of biocompatibility of newly synthesized nanoparticles. In addition, an immortalized murine alveolar macrophage cell line (MH-S), THP-1 cell line, and Ba/F3 murine bone marrow-derived cell line were considered to investigate the optimization of the cell uptake and to examine the potential of new intracellular contrast agent for magnetic resonance imaging.

In paper I, the nanoparticles were investigated in a cellular system, as potential probes for visualization and targeting intended for bioimaging applications. The production of reactive oxygen species (ROS) by means of luminol-dependent chemiluminescence from human neutrophils was studied in presence of Gd2O3 nanoparticles. In paper II, a new design of functionalized ultra-small rare earth-based nanoparticles was reported. The synthesis was done using polyol method followed by PEGylation, and dialysis. Supersmall gadolinium oxide (DEG-Gd2O3) nanoparticles, in the range of 3-5 nm were obtained and carefully characterized. Neutrophil activation after exposure to this nanomaterial was studied by means of fluorescence microscopy. In paper III, cell labeling with Gd2O3 nanoparticles in hematopoietic cells was monitored by magnetic resonance imaging (MRI). In paper IV, ultra-small gadolinium oxide nanoparticles doped with terbium ions were synthesized as a potentially bifunctional material with both fluorescent and magnetic contrast agent properties. Paramagnetic behavior was studied. MRI contrast enhancement was received, and the luminescent/ fluorescent property of the particles was attributable to the Tb3+ ion located on the crystal lattice of the Gd2O3 host. Fluorescent labeling of living cells was obtained. In manuscript V, neutrophil granulocytes were investigated with rapid cell signaling communicative processes in time frame of minutes, and their response to cerium-oxide based nanoparticles were monitored using capacitive sensors based on Lab-on-a-chip technology. This showed the potential of label free method used to measure oxidative stress of neutrophil granulocytes. In manuscript VI, investigations of cell-(DEGGd2O3) nanoparticle interactions were carried out. Plain (DEG-Gd2O3) nanoparticles, (DEG-Gd2O3) nanoparticles in presence of sorbitol and (DEG-Gd2O3) nanoparticles capped with sorbitol were studied. Relaxation studies and measurements of the reactive oxygen species production by neutrophils were based on chemiluminescence. Cell morphology was evaluated as a parameter of the nanoparticle induced inflammatory response by means of the fluorescence microscopy.

The thesis demonstrates high potential of novel Gd2O3-based nanoparticles for development of the next generation contrast agents, that is to find biocompatible compounds with high relaxivity that can be detected at lower doses, and in the future enable targeting to provide great local contrast.

1. Effects of gadolinium oxide nanoparticles on the oxidative burst from human neutrophil granulocytes
Open this publication in new window or tab >>Effects of gadolinium oxide nanoparticles on the oxidative burst from human neutrophil granulocytes
2012 (English)In: Nanotechnology, ISSN 0957-4484, E-ISSN 1361-6528, Vol. 23, no 27, p. 275101-Article in journal (Refereed) Published
##### Abstract [en]

We have previously shown that gadolinium oxide (Gd2O3) nanoparticles are promising candidates to be used as contrast agents in magnetic resonance (MR) imaging applications. In this study, these nanoparticles were investigated in a cellular system, as possible probes for visualization and targeting intended for bioimaging applications. We evaluated the impact of the presence of Gd2O3 nanoparticles on the production of reactive oxygen species (ROS) from human neutrophils, by means of luminol-dependent chemiluminescence. Three sets of Gd2O3 nanoparticles were studied, i.e. as synthesized, dialyzed and both PEG-functionalized and dialyzed Gd2O3 nanoparticles. In addition, neutrophil morphology was evaluated by fluorescent staining of the actin cytoskeleton and fluorescence microscopy. We show that surface modification of these nanoparticles with polyethylene glycol (PEG) is essential in order to increase their biocompatibility. We observed that the as synthesized nanoparticles markedly decreased the ROS production from neutrophils challenged with prey (opsonized yeast particles) compared to controls without nanoparticles. After functionalization and dialysis, more moderate inhibitory effects were observed at a corresponding concentration of gadolinium. At lower gadolinium concentration the response was similar to that of the control cells. We suggest that the diethylene glycol (DEG) present in the as synthesized nanoparticle preparation is responsible for the inhibitory effects on the neutrophil oxidative burst. Indeed, in the present study we also show that even a low concentration of DEG, 0.3%, severely inhibits neutrophil function. In summary, the low cellular response upon PEG-functionalized Gd2O3 nanoparticle exposure indicates that these nanoparticles are promising candidates for MR-imaging purposes.

##### Place, publisher, year, edition, pages
Institute of Physics, 2012
##### National Category
Engineering and Technology
##### Identifiers
urn:nbn:se:liu:diva-79667 (URN)10.1088/0957-4484/23/27/275101 (DOI)000305802000001 ()
Available from: 2012-08-14 Created: 2012-08-13 Last updated: 2018-11-12
2. Synthesis and Characterization of PEGylated Gd2O3 Nanoparticles for MRI Contrast Enhancement
Open this publication in new window or tab >>Synthesis and Characterization of PEGylated Gd2O3 Nanoparticles for MRI Contrast Enhancement
2010 (English)In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 26, no 8, p. 5753-5762Article in journal (Refereed) Published
##### Abstract [en]

Recently, much attention has been given to the development of biofunctionalized nanoparticles with magnetic properties for novel biomedical imaging. Guided, smart, targeting nanoparticulate magnetic resonance imaging (MRI) contrast agents inducing high MRI signal will be valuable tools for future tissue specific imaging and investigation of molecular and cellular events. In this study, we report a new design of functionalized ultrasmall rare earth based nanoparticles to be used as a positive contrast agent in MRI. The relaxivity is compared to commercially available Gd based chelates. The synthesis, PEGylation, and dialysis of small (3−5 nm) gadolinium oxide (DEG-Gd2O3) nanoparticles are presented. The chemical and physical properties of the nanomaterial were investigated with Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, transmission electron microscopy, and dynamic light scattering. Neutrophil activation after exposure to this nanomaterial was studied by means of fluorescence microscopy. The proton relaxation times as a function of dialysis time and functionalization were measured at 1.5 T. A capping procedure introducing stabilizing properties was designed and verified, and the dialysis effects were evaluated. A higher proton relaxivity was obtained for as-synthesized diethylene glycol (DEG)-Gd2O3 nanoparticles compared to commercial Gd-DTPA. A slight decrease of the relaxivity for as-synthesized DEG-Gd2O3 nanoparticles as a function of dialysis time was observed. The results for functionalized nanoparticles showed a considerable relaxivity increase for particles dialyzed extensively with r1 and r2 values approximately 4 times the corresponding values for Gd-DTPA. The microscopy study showed that PEGylated nanoparticles do not activate neutrophils in contrast to uncapped Gd2O3. Finally, the nanoparticles are equipped with Rhodamine to show that our PEGylated nanoparticles are available for further coupling chemistry, and thus prepared for targeting purposes. The long term goal is to design a powerful, directed contrast agent for MRI examinations with specific targeting possibilities and with properties inducing local contrast, that is, an extremely high MR signal at the cellular and molecular level.

##### Place, publisher, year, edition, pages
American Chemical Society (ACS), 2010
##### National Category
Natural Sciences
##### Identifiers
urn:nbn:se:liu:diva-54946 (URN)10.1021/la903566y (DOI)000276562300061 ()
Available from: 2010-04-23 Created: 2010-04-23 Last updated: 2018-10-29Bibliographically approved
3. Gd2O3 nanoparticles in hematopoietic cells for MRI contrast enhancement
Open this publication in new window or tab >>Gd2O3 nanoparticles in hematopoietic cells for MRI contrast enhancement
2011 (English)In: International journal of nano medicine, ISSN 1178-2013, Vol. 6, p. 3233-3240Article in journal (Refereed) Published
##### Abstract [en]

As the utility of magnetic resonance imaging (MRI) broadens, the importance of having specific and efficient contrast agents increases and in recent time there has been a huge development in the fields of molecular imaging and intracellular markers. Previous studies have shown that gadolinium oxide (Gd2O3) nanoparticles generate higher relaxivity than currently available Gd chelates: In addition, the Gd2O3 nanoparticles have promising properties for MRI cell tracking. The aim of the present work was to study cell labeling with Gd2O3 nanoparticles in hematopoietic cells and to improve techniques for monitoring hematopoietic stem cell migration by MRI. Particle uptake was studied in two cell lines: the hematopoietic progenitor cell line Ba/F3 and the monocytic cell line THP-1. Cells were incubated with Gd2O3 nanoparticles and it was investigated whether the transfection agent protamine sulfate increased the particle uptake. Treated cells were examined by electron microscopy and MRI, and analyzed for particle content by inductively coupled plasma sector field mass spectrometry. Results showed that particles were intracellular, however, sparsely in Ba/F3. The relaxation times were shortened with increasing particle concentration. Relaxivities, r1 and r2 at 1.5 T and 21°C, for Gd2O3 nanoparticles in different cell samples were 3.6–5.3 s-1 mM-1 and 9.6–17.2 s-1 mM-1, respectively. Protamine sulfate treatment increased the uptake in both Ba/F3 cells and THP-1 cells. However, the increased uptake did not increase the relaxation rate for THP-1 as for Ba/F3, probably due to aggregation and/or saturation effects. Viability of treated cells was not significantly decreased and thus, it was concluded that the use of Gd2O3 nanoparticles is suitable for this type of cell labeling by means of detecting and monitoring hematopoietic cells. In conclusion, Gd2O3 nanoparticles are a promising material to achieve positive intracellular MRI contrast; however, further particle development needs to be performed.

##### Place, publisher, year, edition, pages
Manchester, UK: Dove Medical Press Ltd, 2011
##### Keywords
gadolinium oxide, magnetic resonance imaging, contrast agent, cell labeling, Ba/F3 cells, THP-1 cells
##### National Category
Medical and Health Sciences
##### Identifiers
urn:nbn:se:liu:diva-72275 (URN)10.2147/IJN.S23940 (DOI)000298164300001 ()
##### Note

funding agencies|Swedish Research Council| 621-2007-3810 621-2009-5148 521-2009-3423 |VINNOVA| 2009-00194 |Center in Nanoscience and Technology at LiTH (CeNano)||

Available from: 2011-11-24 Created: 2011-11-24 Last updated: 2018-10-29
4. Synthesis and Characterization of Tb3+-Doped Gd2O3 Nanocrystals: A Bifunctional Material with Combined Fluorescent Labeling and MRI Contrast Agent Properties
Open this publication in new window or tab >>Synthesis and Characterization of Tb3+-Doped Gd2O3 Nanocrystals: A Bifunctional Material with Combined Fluorescent Labeling and MRI Contrast Agent Properties
2009 (English)In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 113, no 17, p. 6913-6920Article in journal (Refereed) Published
##### Abstract [en]

Ultrasmall gadolinium oxide nanoparticles doped with terbium ions were synthesized by the polyol route and characterized as a potentially bifunctional material with both fluorescent and magnetic contrast agent properties. The structural, optical, and magnetic properties of the organic-acid-capped and PEGylated Gd2O3:Tb3+ nanocrystals were studied by HR-TEM, XPS, EDX, IR, PL, and SQUID. The luminescent/fluorescent property of the particles is attributable to the Tb3+ ion located on the crystal lattice of the Gd2O3 host. The paramagnetic behavior of the particles is discussed. Pilot studies investigating the capability of the nanoparticles for fluorescent labeling of living cells and as a MRI contrast agent were also performed. Cells of two cell lines (THP-1 cells and fibroblasts) were incubated with the particles, and intracellular particle distribution was visualized by confocal microscopy. The MRI relaxivity of the PEGylated nanoparticles in water at low Gd concentration was assessed showing a higher T-1 relaxation rate compared to conventional Gd-DTPA chelates and comparable to that of undoped Gd2O3 nanoparticles.

##### National Category
Natural Sciences
##### Identifiers
urn:nbn:se:liu:diva-12944 (URN)10.1021/jp808708m (DOI)000265529700009 ()
##### Note

On the day of the defence date the status of this article was Submitted

Available from: 2008-02-21 Created: 2008-02-21 Last updated: 2018-10-29Bibliographically approved
• 5.
Leibniz Institute Polymerforsch eV, Germany; Technical University of Dresden, Germany.
Leibniz Institute Polymerforsch eV, Germany; Technical University of Dresden, Germany; Karlsruhe Institute Technology, Germany. University of Nebraska, NE 68588 USA; Biolin Science Inc, NJ 07652 USA. Leibniz Institute Polymerforsch eV, Germany. Leibniz Institute Polymerforsch eV, Germany. Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, Faculty of Science & Engineering. Leibniz Institute Polymerforsch eV, Germany; University of Nebraska, NE 68588 USA; University of Nebraska, NE 68588 USA. Leibniz Institute Polymerforsch eV, Germany; Technical University of Dresden, Germany. Leibniz Institute Polymerforsch eV, Germany; University of Nebraska, NE 68588 USA.
Quartz crystal microbalance with coupled Spectroscopic Ellipsometry-study of temperature-responsive polymer brush systems2017In: Applied Surface Science, ISSN 0169-4332, E-ISSN 1873-5584, Vol. 421, p. 843-851Article in journal (Refereed)

Using a combined setup of quartz crystal microbalance with dissipation monitoring together with spectroscopic ellipsometry, the thermo-responsive behavior of two different brush systems (poly(N-isopropyl acrylamide) and poly(2-oxazoline)s) was investigated and compared to the behavior of the free polymer in solution. Poly(2-oxazoline)s with three different hydrophilicities were prepared by changing the content of a hydrophilic comonomer. While both polymer types exhibit a sharp, discontinuous thermal transition in solution, in the brush state the transition gets broader in the case of poly(N-isopropyl acrylamide) and is transformed into a continuous transition for poly(2-oxazoline)s. The position of the transition in solution is influenced by the degree of hydrophilicity of the poly(2-oxazoline). The difference in areal mass detected by quartz crystal microbalance and by spectroscopic ellipsometry, has been attributed to the chain segment density profile of the polymer brushes. Applying this density profile information, for poly(N-isopropyl acrylamide) two different swelling stages could be identified, while for poly(2-oxazoline) the transition between a parabolic and more step-wise profile is found continuous. The different swelling characteristics were attributed to the different miscibility behavior types, with the brush state acting similar to a crosslinked system. (C) 2017 Elsevier B.V. All rights reserved.

• 6.
Totalförsvarets Forskningsinstitut, FOI, Stockholm, Sweden.
Swedish National Forensic Centre (NFC), Linköping, Sweden. Totalförsvarets Forskningsinstitut, FOI, Stockholm, Sweden.
Chemometrics comes to court: evidence evaluation of chem–bio threat agent attacks2015In: Journal of Chemometrics, ISSN 0886-9383, E-ISSN 1099-128X, Vol. 29, no 5, p. 267-276Article in journal (Refereed)

Forensic statistics is a well-established scientific field whose purpose is to statistically analyze evidence in order to support legal decisions. It traditionally relies on methods that assume small numbers of independent variables and multiple samples. Unfortunately, such methods are less applicable when dealing with highly correlated multivariate data sets such as those generated by emerging high throughput analytical technologies. Chemometrics is a field that has a wealth of methods for the analysis of such complex data sets, so it would be desirable to combine the two fields in order to identify best practices for forensic statistics in the future. This paper provides a brief introduction to forensic statistics and describes how chemometrics could be integrated with its established methods to improve the evaluation of evidence in court.

The paper describes how statistics and chemometrics can be integrated, by analyzing a previous know forensic data set composed of bacterial communities from fingerprints. The presented strategy can be applied in cases where chemical and biological threat agents have been illegally disposed.

• 7.
Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology.
Improved Methods for Characterization of Protein Dynamics by NMR spectroscopy and Studies of the EphB2 Kinase Domain2015Doctoral thesis, comprehensive summary (Other academic)

Proteins are essential for all known forms of life and in many lethal diseases protein failure is the cause of the disease. To understand proteins and the processes they are involved in, it is valuable to know their structures as well as their dynamics and interactions. The structures may not be directly inspected because proteins are too small to be visible in a light microscope, which is why indirect methods such as nuclear magnetic resonance (NMR) spectroscopy have to be utilized. This method provides atomic information about the protein and, in contrast to other methods with similar resolution, the measurements are performed in solution resulting in more physiological conditions, enabling analysis of dynamics. Important dynamical processes are the ones on the millisecond timeframe, which may contribute to interactions of proteins and their catalysis of chemical reactions, both of significant value for the function of the proteins.

To better understand proteins, not only do we need to study them, but also develop the methods we are using. This thesis presents four papers about improved NMR techniques as well as a fifth where the kinase domain of ephrinB receptor 2 (EphB2) has been studied regarding the importance of millisecond dynamics and interactions for the activation process. The first paper presents the software COMPASS, which combines statistics and the calculation power of a computer with the flexibility and experience of the user to facilitate and speed up the process of assigning NMR signals to the atoms in the protein. The computer program PINT has been developed for easier and faster evaluation of NMR experiments, such as those that evaluate protein dynamics. It is especially helpful for NMR signals that are difficult to distinguish, so called overlapped peaks, and the soft- ware also converts the detected signals to the indirectly measured physical quantities, such as relaxation rate constants, principal for dynamics. Next are two new versions of the Carr-Purcell-Maiboom-Gill (CPMG) dispersion pulse sequences, designed to measure millisecond dynamics in a way so that the signals are more separated than in standard experiments, to reduce problems with overlaps. To speed up the collection time of the data set, a subset is collected and the entire data set is then reconstructed, by multi-dimensional decomposition co-processing. Described in the thesis is also a way to produce suitably labeled proteins, to detect millisecond dynamics at Cα positions in proteins, using the CPMG dispersion relaxation experiment at lower protein concentrations. Lastly, the kinase domain of EphB2 is shown to be more dynamic on the millisecond time scale as well as more prone to interact with itself in the active form than in the inactive one. This is important for the receptor function of the protein, when and how it mediates signals.

To conclude, this work has extended the possibilities to study protein dynamics by NMR spectroscopy and contributed to increased understanding of the activation process of EphB2 and its signaling mechanism.

1. Fast and Accurate Resonance Assignment of Small-to-Large Proteins by Combining Automated and Manual Approaches
Open this publication in new window or tab >>Fast and Accurate Resonance Assignment of Small-to-Large Proteins by Combining Automated and Manual Approaches
2015 (English)In: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 11, no 1, p. e1004022-Article in journal (Refereed) Published
##### Abstract [en]

The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available.

##### Place, publisher, year, edition, pages
Public Library of Science, 2015
##### National Category
Chemical Sciences
##### Identifiers
urn:nbn:se:liu:diva-115010 (URN)10.1371/journal.pcbi.1004022 (DOI)000349309400013 ()25569628 (PubMedID)
##### Note

Funding Agencies|Swedish Research Council [Dnr. 2012-5136]

Available from: 2015-03-09 Created: 2015-03-06 Last updated: 2017-12-04
2. PINT: a software for integration of peak volumes and extraction of relaxation rates
Open this publication in new window or tab >>PINT: a software for integration of peak volumes and extraction of relaxation rates
2013 (English)In: Journal of Biomolecular NMR, ISSN 0925-2738, E-ISSN 1573-5001, Vol. 56, no 3, p. 191-202Article in journal (Refereed) Published
##### Abstract [en]

We present the software Peak INTegration (PINT), designed to perform integration of peaks in NMR spectra. The program is very simple to run, yet powerful enough to handle complicated spectra. Peaks are integrated by fitting predefined line shapes to experimental data and the fitting can be customized to deal with, for instance, heavily overlapped peaks. The results can be inspected visually, which facilitates systematic optimization of the line shape fitting. Finally, integrated peak volumes can be used to extract parameters such as relaxation rates and information about low populated states. The utility of PINT is demonstrated by applications to the 59 residue SH3 domain of the yeast protein Abp1p and the 289 residue kinase domain of murine EphB2.

##### Place, publisher, year, edition, pages
Springer Verlag (Germany), 2013
##### Keywords
Peak integration, Overlapped peaks, Relaxation rates, Protein dynamics
##### National Category
Cell and Molecular Biology
##### Identifiers
urn:nbn:se:liu:diva-95951 (URN)10.1007/s10858-013-9737-7 (DOI)000321544600001 ()
##### Note

Funding Agencies|Swedish Research Council||

Available from: 2013-08-19 Created: 2013-08-12 Last updated: 2018-01-11Bibliographically approved
3. Measurement of Protein Backbone 13CO and 15N Relaxation Dispersion at High Resolution
Open this publication in new window or tab >>Measurement of Protein Backbone 13CO and 15N Relaxation Dispersion at High Resolution
##### Abstract [en]

Three-dimensional pulse sequences for the measurement of Carr-Purcell-Meiboom-Gill relaxation dispersions and new methods for co-processing non-uniformly sampled data are presented. The new methodology was validated for the disordered protein IgA and for an SH3 domain from Abp1p in exchange between its free form and bound to a peptide from the protein Ark1p. We show that the results are similar to ones obtained using traditional experiments and that accurate excited state chemical shifts can be determined. Furthermore, we show that jackknife analysis of down sampled spectra yields robust estimates of peak intensities errors, eliminating the need for recording duplicate data points. The methodology should be useful for characterization of millisecond dynamics in small to medium-sized proteins with poorly dispersed spectra.

##### National Category
Chemical Sciences
##### Identifiers
urn:nbn:se:liu:diva-117070 (URN)
Available from: 2015-04-15 Created: 2015-04-15 Last updated: 2015-04-15Bibliographically approved
4. Fractional enrichment of proteins using [2-13C]-glycerol as the carbon source facilitates measurement of excited state 13Cα chemical shifts with improved sensitivity
Open this publication in new window or tab >>Fractional enrichment of proteins using [2-13C]-glycerol as the carbon source facilitates measurement of excited state 13Cα chemical shifts with improved sensitivity
2015 (English)In: Journal of Biomolecular NMR, ISSN 0925-2738, E-ISSN 1573-5001, Vol. 62, no 3, p. 341-351Article in journal (Refereed) Published
##### Abstract [en]

A selective isotope labeling scheme based on the utilization of [2-13C]-glycerol as the carbon source during protein overexpression has been evaluated for the measurement of excited state 13Cα chemical shifts using Carr–Purcell–Meiboom–Gill (CPMG) relaxation dispersion (RD) experiments. As expected, the fractional incorporation of label at the Cα positions is increased two-fold relative to labeling schemes based on [2-13C]-glucose, effectively doubling the sensitivity of NMR experiments. Applications to a binding reaction involving an SH3 domain from the protein Abp1p and a peptide from the protein Ark1p establish that accurate excited state 13Cα chemical shifts can be obtained from RD experiments, with errors on the order of 0.06 ppm for exchange rates ranging from 100 to 1000 s−1, despite the small fraction of 13Cα–13Cβ spin-pairs that are present for many residue types. The labeling approach described here should thus be attractive for studies of exchanging systems using 13Cα spin probes.

##### Place, publisher, year, edition, pages
Springer Netherlands, 2015
##### Keywords
CPMG, 13Cα labeling, [2-13C]-Glycerol, Excited states
##### National Category
Chemical Sciences
##### Identifiers
urn:nbn:se:liu:diva-117073 (URN)10.1007/s10858-015-9948-1 (DOI)000357489200010 ()
##### Note

At the time for thesis presentation publication was in status: Manuscript

At the time for thesis presentation name of publication was: Fractional enrichment using [2-13C]-glycerol as the carbon source facilitates measurements of excited state 13Cα chemical shifts with improved sensitivity

Available from: 2015-04-15 Created: 2015-04-15 Last updated: 2017-12-04Bibliographically approved
5. Conformational Dynamics and Multimerization of Active Forms of the EphrinB Receptor 2 Kinase Domain
Open this publication in new window or tab >>Conformational Dynamics and Multimerization of Active Forms of the EphrinB Receptor 2 Kinase Domain
##### Abstract [en]

Active and autoinhibited forms of the ephrinB receptor 2 (EphB2) kinase domain have been studied using NMR spectroscopy. The project was initiated because of the finding that the crystal structures of active forms of the kinase domain and previous NMR studies suggested that a change in inter-lobe flexibility and the sampling of catalytically competent excited states conformations are responsible for activity. Using Carr-Purcell-Meiboom-Gill relaxation dispersion experiments, we have measured millisecond dynamics to identify such states. We have also performed concentration dependent relaxation experiments and analytical ultracentrifugation experiments that report on the effective protein size to look for possible differences in self-association for active and autoinhibited forms of the EphB2 kinase domain. We show that the active but not autoinhibited forms exchange between a ground state and an excited state at a rate of 1900 s-1. Similar results were found for the S677/680A mutant of the protein. The nature and importance of the excited state is still unknown. Our most important finding is that active forms of the kinase domain self-associate in a concentration dependent manner and form tetramers and possibly larger oligomers. Multimerization of the kinase domain may enable the assembly of complexes of downstream proteins and could be important for Eph signaling.

##### Keywords
Kinase activation | Eph receptors | chemical exchange | nmr spectroscopy | protein dynamics | self-association
##### National Category
Chemical Sciences
##### Identifiers
urn:nbn:se:liu:diva-117071 (URN)
Available from: 2015-04-15 Created: 2015-04-15 Last updated: 2015-04-15Bibliographically approved
• 8.
Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology.
Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology. Departments of Medical Genetics, Biochemistry and Chemistry, The University of Toronto, Canada. Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology.
Fractional enrichment of proteins using [2-13C]-glycerol as the carbon source facilitates measurement of excited state 13Cα chemical shifts with improved sensitivity2015In: Journal of Biomolecular NMR, ISSN 0925-2738, E-ISSN 1573-5001, Vol. 62, no 3, p. 341-351Article in journal (Refereed)

A selective isotope labeling scheme based on the utilization of [2-13C]-glycerol as the carbon source during protein overexpression has been evaluated for the measurement of excited state 13Cα chemical shifts using Carr–Purcell–Meiboom–Gill (CPMG) relaxation dispersion (RD) experiments. As expected, the fractional incorporation of label at the Cα positions is increased two-fold relative to labeling schemes based on [2-13C]-glucose, effectively doubling the sensitivity of NMR experiments. Applications to a binding reaction involving an SH3 domain from the protein Abp1p and a peptide from the protein Ark1p establish that accurate excited state 13Cα chemical shifts can be obtained from RD experiments, with errors on the order of 0.06 ppm for exchange rates ranging from 100 to 1000 s−1, despite the small fraction of 13Cα–13Cβ spin-pairs that are present for many residue types. The labeling approach described here should thus be attractive for studies of exchanging systems using 13Cα spin probes.

• 9.
Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology.
Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology. Molecular Structure and Function Program, Hospital for Sick Children; Department and Biochemistry, University of Toronto, Canada. cDepartment and Biochemistry, University of Toronto; Department of Molecular Genetics, University of Toronto; Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Canada. Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology.
Conformational Dynamics and Multimerization of Active Forms of the EphrinB Receptor 2 Kinase DomainManuscript (preprint) (Other academic)

Active and autoinhibited forms of the ephrinB receptor 2 (EphB2) kinase domain have been studied using NMR spectroscopy. The project was initiated because of the finding that the crystal structures of active forms of the kinase domain and previous NMR studies suggested that a change in inter-lobe flexibility and the sampling of catalytically competent excited states conformations are responsible for activity. Using Carr-Purcell-Meiboom-Gill relaxation dispersion experiments, we have measured millisecond dynamics to identify such states. We have also performed concentration dependent relaxation experiments and analytical ultracentrifugation experiments that report on the effective protein size to look for possible differences in self-association for active and autoinhibited forms of the EphB2 kinase domain. We show that the active but not autoinhibited forms exchange between a ground state and an excited state at a rate of 1900 s-1. Similar results were found for the S677/680A mutant of the protein. The nature and importance of the excited state is still unknown. Our most important finding is that active forms of the kinase domain self-associate in a concentration dependent manner and form tetramers and possibly larger oligomers. Multimerization of the kinase domain may enable the assembly of complexes of downstream proteins and could be important for Eph signaling.

• 10.
Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology.
The Swedish NMR Centre, University of Gothenburg, Sweden. Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology. The Swedish NMR Centre, University of Gothenburg, Sweden.
Measurement of Protein Backbone 13CO and 15N Relaxation Dispersion at High ResolutionManuscript (preprint) (Other academic)

Three-dimensional pulse sequences for the measurement of Carr-Purcell-Meiboom-Gill relaxation dispersions and new methods for co-processing non-uniformly sampled data are presented. The new methodology was validated for the disordered protein IgA and for an SH3 domain from Abp1p in exchange between its free form and bound to a peptide from the protein Ark1p. We show that the results are similar to ones obtained using traditional experiments and that accurate excited state chemical shifts can be determined. Furthermore, we show that jackknife analysis of down sampled spectra yields robust estimates of peak intensities errors, eliminating the need for recording duplicate data points. The methodology should be useful for characterization of millisecond dynamics in small to medium-sized proteins with poorly dispersed spectra.

• 11.
Jonkoping Univ, Sweden.
Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, Faculty of Science & Engineering. Jonkoping Univ, Sweden; RISE Res Inst Sweden, Sweden. Jonkoping Univ, Sweden.
Effect of SiC particle size and heat-treatment on microhardness and corrosion resistance of NiP electrodeposited coatings2018In: Journal of Alloys and Compounds, ISSN 0925-8388, E-ISSN 1873-4669, Vol. 769, p. 1080-1087Article in journal (Refereed)

Electrodeposition of NiP composite coatings with nano and sub-micron sized SiC has been carried out to investigate the possibility of replacing hard chromium coatings. The composition and structure of the coatings were evaluated by energy dispersive X-ray spectroscopy (EDS) and X-ray diffraction (XRD) analysis, respectively. Microhardness was measured by Vickers indentation and polarization measurements were carried out to study the corrosion behavior of the coatings. The results showed that submicron particles can be codeposited with a higher content as compared to nano sized ones. However, even if a smaller amount of the nano-sized SiC particles are incorporated in the coating, the contribution to an increasing microhardness was comparable with the submicron sized particles, which can be related to the higher density of codeposited particles. SiC particles did not change the anodic polarization behavior of NiP coatings in a 3.5% NaCl solution. Finally, the effect of heat-treatment on the coatings properties at 400 degrees C for 1 h was studied to investigate the contribution of particles and heat-treatment on hardness and corrosion properties. It was found that the heat-treatment doubled the microhardness and changed the anodic polarization behavior of the coatings from passive to active with respect to the asplated conditions. (C) 2018 Elsevier B.V. All rights reserved.

• 12.
Aalto University, Finland.
Stanford University, CA 94305 USA. Aalto University, Finland. University of Montpellier, France. University of Twente, Netherlands. Bulgarian Academic Science, Bulgaria. Masaryk University, Czech Republic. Huazhong University of Science and Technology, Peoples R China. University of Grenoble Alpes, France. University of Ghent, Belgium. Ruhr University of Bochum, Germany. St Petersburg State University, Russia. Institute Theoret and Expt Phys, Russia. Fdn Bruno Kessler, Italy. VTT Technical Research Centre Finland, Finland. Lam Research Corp, OR 97062 USA. Seoul National University, South Korea; Seoul National University, South Korea. Globalfoundries, NY 12203 USA. Aalto University, Finland. Aalto University, Finland; Abo Akad University, Finland. St Petersburg Electrotech University of LETI, Russia. MIT, MA 02139 USA. Techinsights, Canada. Ioffe Institute, Russia. Aalto University, Finland. University of Ghent, Belgium. Sentech Instruments GmbH, Germany. NovaldMedical Ltd Oy, Finland. NovaldMedical Ltd Oy, Finland; University of Helsinki, Finland. STMicroelectronics, Italy. Seagate Technology Ireland, North Ireland. University of Helsinki, Finland. Aalto University, Finland. Aalto University, Finland. Technical University, Russia. Technical University, Russia. CDER, Algeria. Technical University of Chemnitz, Germany. Summa Semicond Oy, Finland. Mil University of Technology, Poland. ASELSAN Inc, Turkey. St Petersburg Electrotech University of LETI, Russia. Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering. KOBUS, France. University of Helsinki, Finland. VTT Technical Research Centre Finland, Finland. University of Ghent, Belgium. Aalto University, Espoo, Finland. Tallinn University of Technology, Estonia. Eindhoven University of Technology, Netherlands; TNO, Netherlands. University of Jyvaskyla, Finland. University of Maryland, MD 20742 USA. Aalto University, Finland. IRDEP CNRS, France; IPVF, France. Seitek50, FL 32135 USA. Fraunhofer Institute Ceram Technology and Syst IKTS, Germany. Lund University, Sweden; Lund University, Sweden. Uppsala University, Sweden. Delft University of Technology, Netherlands. CNR, Italy. VTT Technical Research Centre Finland, Finland. Immanuel Kant Balt Federal University, Russia.
Recommended reading list of early publications on atomic layer deposition-Outcome of the "Virtual Project on the History of ALD"2017In: Journal of Vacuum Science & Technology. A. Vacuum, Surfaces, and Films, ISSN 0734-2101, E-ISSN 1520-8559, Vol. 35, no 1, article id 010801Article, review/survey (Refereed)

Atomic layer deposition (ALD), a gas-phase thin film deposition technique based on repeated, self-terminating gas-solid reactions, has become the method of choice in semiconductor manufacturing and many other technological areas for depositing thin conformal inorganic material layers for various applications. ALD has been discovered and developed independently, at least twice, under different names: atomic layer epitaxy (ALE) and molecular layering. ALE, dating back to 1974 in Finland, has been commonly known as the origin of ALD, while work done since the 1960s in the Soviet Union under the name "molecular layering" (and sometimes other names) has remained much less known. The virtual project on the history of ALD (VPHA) is a volunteer-based effort with open participation, set up to make the early days of ALD more transparent. In VPHA, started in July 2013, the target is to list, read and comment on all early ALD academic and patent literature up to 1986. VPHA has resulted in two essays and several presentations at international conferences. This paper, based on a poster presentation at the 16th International Conference on Atomic Layer Deposition in Dublin, Ireland, 2016, presents a recommended reading list of early ALD publications, created collectively by the VPHA participants through voting. The list contains 22 publications from Finland, Japan, Soviet Union, United Kingdom, and United States. Up to now, a balanced overview regarding the early history of ALD has been missing; the current list is an attempt to remedy this deficiency. (C) 2016 Author(s).

• 13.
Linköping University, Department of Physics, Chemistry and Biology, Plasma and Coating Physics. Linköping University, The Institute of Technology. Uppsala University, Sweden.
Aarhus University, Denmark; Danish Technology Institute, Denmark. University of Paris Saclay, France. Uppsala University, Sweden. Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, Faculty of Science & Engineering. Linköping University, Department of Physics, Chemistry and Biology, Nanoscale engineering. Linköping University, Faculty of Science & Engineering. Linköping University, Department of Physics, Chemistry and Biology, Plasma and Coating Physics. Linköping University, Faculty of Science & Engineering.
Synthesis of hydrogenated diamondlike carbon thin films using neon-acetylene based high power impulse magnetron sputtering discharges2016In: Journal of Vacuum Science & Technology. A. Vacuum, Surfaces, and Films, ISSN 0734-2101, E-ISSN 1520-8559, Vol. 34, no 6, article id 061504Article in journal (Refereed)

Hydrogenated diamondlike carbon (DLC:H) thin films exhibit many interesting properties that can be tailored by controlling the composition and energy of the vapor fluxes used for their synthesis. This control can be facilitated by high electron density and/or high electron temperature plasmas that allow one to effectively tune the gas and surface chemistry during film growth, as well as the degree of ionization of the film forming species. The authors have recently demonstrated by adding Ne in an Ar-C high power impulse magnetron sputtering (HiPIMS) discharge that electron temperatures can be effectively increased to substantially ionize C species [Aijaz et al., Diamond Relat. Mater. 23, 1 (2012)]. The authors also developed an Ar-C2H2 HiPIMS process in which the high electron densities provided by the HiPIMS operation mode enhance gas phase dissociation reactions enabling control of the plasma and growth chemistry [Aijaz et al., Diamond Relat. Mater. 44, 117 (2014)]. Seeking to further enhance electron temperature and thereby promote electron impact induced interactions, control plasma chemical reaction pathways, and tune the resulting film properties, in this work, the authors synthesize DLC: H thin films by admixing Ne in a HiPIMS based Ar/C2H2 discharge. The authors investigate the plasma properties and discharge characteristics by measuring electron energy distributions as well as by studying discharge current characteristics showing an electron temperature enhancement in C2H2 based discharges and the role of ionic contribution to the film growth. These discharge conditions allow for the growth of thick (amp;gt;1 mu m) DLC: H thin films exhibiting low compressive stresses (similar to 0.5 GPa), high hardness (similar to 25 GPa), low H content (similar to 11%), and density in the order of 2.2 g/cm(3). The authors also show that film densification and change of mechanical properties are related to H removal by ion bombardment rather than subplantation. (C) 2016 American Vacuum Society.

• 14.
Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Faculty of Science & Engineering.
Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering. Linköping University, Department of Science and Technology. Linköping University, Faculty of Science & Engineering. Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering. Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Faculty of Science & Engineering. Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Faculty of Science & Engineering.
Thermoelectric Properties of Polymeric Mixed Conductors2016In: Advanced Functional Materials, ISSN 1616-301X, E-ISSN 1616-3028, Vol. 26, no 34, p. 6288-6296Article in journal (Refereed)

The thermoelectric (TE) phenomena are intensively explored by the scientific community due to the rather inefficient way energy resources are used with a large fraction of energy wasted in the form of heat. Among various materials, mixed ion-electron conductors (MIEC) are recently being explored as potential thermoelectrics, primarily due to their low thermal conductivity. The combination of electronic and ionic charge carriers in those inorganic or organic materials leads to complex evolution of the thermovoltage (Voc) with time, temperature, and/or humidity. One of the most promising organic thermoelectric materials, poly(3,4-ethyelenedioxythiophene)-polystyrene sulfonate (PEDOT-PSS), is an MIEC. A previous study reveals that at high humidity, PEDOT-PSS undergoes an ionic Seebeck effect due to mobile protons. Yet, this phenomenon is not well understood. In this work, the time dependence of the Voc is studied and its behavior from the contribution of both charge carriers (holes and protons) is explained. The presence of a complex reorganization of the charge carriers promoting an internal electrochemical reaction within the polymer film is identified. Interestingly, it is demonstrated that the time dependence behavior of Voc is a way to distinguish between three classes of polymeric materials: electronic conductor, ionic conductor, and mixed ionic–electronic conductor

• 15.
Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Faculty of Science & Engineering.
Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Faculty of Science & Engineering. Innventia AB, Sweden. Innventia AB, Sweden. Mat Research Centre, India. Mat Research Centre, India. Innventia AB, Sweden. Innventia AB, Sweden. Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Faculty of Science & Engineering.
Room temperature synthesis of transition metal silicide-conducting polymer micro-composites for thermoelectric applications2017In: Synthetic metals, ISSN 0379-6779, E-ISSN 1879-3290, Vol. 225, p. 55-63Article in journal (Refereed)

Organic polymer thermoelectrics (TE) as well as transition metal (TM) silicides are two thermoelectric class of materials of interest because they are composed of atomic elements of high abundatice; which is a prerequisite for mass implementation of thermoelectric (TE) solutions for solar and waste heat recovery. But both materials have drawbacks when it comes to finding low-cost manufacturing. The metal silicide needs high temperature (amp;gt;1000 degrees C) for creating TE legs in a device from solid powder, but it is easy to achieve long TE legs in this case. On the contrary, organic TEs are synthesized at low temperature from solution. However, it is difficult to form long legs or thick films because of their low solubility. In this work, we propose a novel method for the room temperature synthesis of TE composite containing the microparticles of chromium disilicide; CrSi2 (inorganic filler) in an organic matrix of nanofibrillated cellulose-poly(3,4-ethyelenedioxythiophene)-polystyrene sulfonate (NFC-PEDOT:PSS). With this method, it is easy to create long TE legs in a room temperature process. The originality of the approach is the use of conducting polymer aerogel microparticles mixed with CrSi2 microparticles to obtain a composite solid at room temperature under pressure. We foresee that the method can be scaled up to fabricate and pattern TE modules. The composite has an electrical conductivity (sigma) of 5.4 +/- 0.5 S/cm and the Seebeck coefficient (a) of 88 +/- 9 mu V/K, power factor (alpha(2)sigma) of 4 +/- 1 mu Wm(-1) K-2 at room temperature. At a temperature difference of 32 degrees C, the output power/unit area drawn across the load, with the resistance same as the internal resistance of the device is 0.6 +/- 0.1 mu W/cm(2). (C) 2017 Elsevier B.V. All rights reserved.

The full text will be freely available from 2019-02-23 16:25
• 16.
Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology. Division of Organic Chemistry, Department of Biochemistry and Organic Chemistry, BMC, Box 576, Uppsala UniVersity, SE-751 23 Uppsala, Sweden. Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
Assembly of Polypeptide-Functionalized Gold Nanoparticles through a Heteroassociation- and Folding-Dependent Bridging2008In: Nano letters (Print), ISSN 1530-6984, E-ISSN 1530-6992, Vol. 8, no 8, p. 2473-2478Article in journal (Refereed)

Gold nanoparticles were functionalized with a synthetic polypeptide, de novo-designed to associate with a charge complementary linker polypeptide in a folding-dependent manner. A heterotrimeric complex that folds into two disulphide-linked four-helix bundles is formed when the linker polypeptide associates with two of the immobilized peptides. The heterotrimer forms in between separate particles and induces a rapid and extensive aggregation with a well-defined interparticle spacing. The aggregated particles are redispersed when the disulphide bridge in the linker polypeptide is reduced.

• 17.
Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering.
Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering. Division of Organic Chemistry, Department of Biochemistry and Organic Chemistry, BMC, Box 576, Uppsala University, SE-751 23 Uppsala, Sweden. Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering. 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)

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.

• 18.
Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
Max Planck Institute Colloids and Interfaces, Germany. IMDEA Energy Institute, Spain. University of Liege ULg, Belgium. POLYMAT University of Basque Country UPV EHU, Spain. Max Planck Institute Colloids and Interfaces, Germany. POLYMAT University of Basque Country UPV EHU, Spain. University of Liege ULg, Belgium. POLYMAT University of Basque Country UPV EHU, Spain. KIOMedPharma, Belgium. University of Bordeaux, France. Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering. Max Planck Institute Colloids and Interfaces, Germany. University of Liege ULg, Belgium. Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering. University of Liege ULg, Belgium. IMDEA Energy Institute, Spain. POLYMAT University of Basque Country UPV EHU, Spain; Basque Fdn Science, Spain. POLYMAT University of Basque Country UPV EHU, Spain. University of Bordeaux, France. Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering. 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)

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

• 19.
Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering. Poznan University of Tech, Poland. Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering. 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)

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.

• 20.
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)

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.

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
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
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
• 21.
Linköping University, Department of Physics, Chemistry and Biology.
Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Department of Physics, Chemistry and Biology. 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

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.

• 22.
Linköping University, Department of Physics, Chemistry and Biology, Chemistry.
Synthesis and Characterization of Acrylfentanyl Metabolites2017Independent thesis Basic level (degree of Bachelor), 10,5 credits / 16 HE creditsStudent thesis

Acrylfentanyl is a synthetic opioid that has been widely used in the last year. To help in the fight against synthetic drugs two potential metabolites of acrylfentanyl, one monohydroxy and one dihydroxy were synthesized. These metabolites will hopefully later be implemented in the analytical methods for metabolites of acrylfentanyl in urine by the Swedish National Board of Forensic Medicine.

To have metabolites for analysis are very important as they are the main target in drug testing.

The method used to synthesize the metabolites is a five-step synthesis with an additional 6th step for the dihydroxy metabolite. The methods used in the synthesis includes protection of amine with tert-butyloxycarbonyl, reductive amination with sodium triaceto boronhydride, alkylation and demethylation with boron tribromide. The methods used produced good results with high yields in nearly all steps.

• 23. Alfredsson, Maria
Uppsala universitet, Strukturkemi.
A comparison of Hartree-Fock, MP2, and DFT results for the HCN dimer and crystal1996In: INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Vol. 60, no 3, p. 767-777Article in journal (Refereed)

A number of hydrogen-bond related quantities-geometries, interaction energies, dipole moments, dipole moment derivatives, and harmonic vibrational frequencies-were calculated at the Hartree-Fock, MP2, and different DFT levels for the HCN dimer and the pe

• 24.
University of Sindh, Pakistan.
Luleå University of Technology, Sweden. University of Sindh, Pakistan. University of Sindh, Pakistan. Shah Abdul Latif University, Pakistan. Tsinghua University, Peoples R China. University of Sindh, Pakistan. Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Faculty of Science & Engineering. Chinese Academic Science, Peoples R China. University of Sindh, Pakistan; Chinese Academic Science, Peoples R China.
Functional CuO Microstructures for Glucose Sensing2018In: Journal of Electronic Materials, ISSN 0361-5235, E-ISSN 1543-186X, Vol. 47, no 2, p. 1519-1525Article in journal (Refereed)

CuO microstructures are produced in the presence of water-soluble amino acids by hydrothermal method. The used amino acids include isoleucine, alpha alanine, and arginine as a soft template and are used for tuning the morphology of CuO nanostructures. The crystalline and morphological investigations were carried out by x-ray diffraction (XRD) and scanning electron microscopy techniques. The XRD study has shown that CuO material obtained in the presence of different amino acids is of high purity and all have the same crystal phase. The CuO microstructures prepared in the presence of arginine were used for the development of sensitive and selective glucose biosensor. The linear range for the glucose detection are from 0.001 mM to 30 mM and limit of detection was found to be 0.0005 mM. The sensitivity was estimated around 77 mV/decade. The developed biosensor is highly selective, sensitive, stable and reproducible. The glucose biosensor was used for the determination of real human blood samples and the obtained results are satisfactory. The CuO material is functional therefore can be capitalized in wide range of applications such as lithium ion batteries, all oxide solar cells and supercapacitors.

• 25.
Linköping University, Department of Physics, Chemistry and Biology, Biosensors and Bioelectronics. Linköping University, Faculty of Science & Engineering. Zanjan University, Iran.
Zanjan University, Iran. Linköping University, Department of Physics, Chemistry and Biology, Biosensors and Bioelectronics. Linköping University, Faculty of Science & Engineering. Linköping University, Department of Physics, Chemistry and Biology, Biosensors and Bioelectronics. Linköping University, Faculty of Science & Engineering.
Correction: A high-performance glucose biosensor using covalently immobilised glucose oxidase on a poly(2,6-diaminopyridine)/carbon nanotube electrode (vol 116, pg 801, 2013)2016In: Talanta: The International Journal of Pure and Applied Analytical Chemistry, ISSN 0039-9140, E-ISSN 1873-3573, Vol. 153, p. 414-415Article in journal (Refereed)

A highly-sensitive glucose biosensor amenable to ultraminiaturisation was fabricated by immobilization of glucose oxidase (wGOX), onto a poly(2,6-diaminopyridine)/multi-walled carbon nanotube/glassy carbon electrode (poly(2,6-DP)/MWCNT/GCE). Cyclic voltammetry was used for both the electrochemical synthesis of poly-(2,6-DP) on the surface of a MWCNT-modified GC electrode, and characterization of the polymers deposited on the GC electrode. The synergistic effect of the high active surface area of both the conducting-polymer, i.e., poly-(2,6-DP) and MWCNT gave rise to a remarkable improvement in the electrocatalytic properties of the biosensor. The transfer coefficient (alpha), heterogeneous electron transfer rate constant and Michaelis-Menten constant were calculated to be 0.6, 4 s-1 and 0.22 mM at pH 7.4, respectively. The GOx/poly(2,6-DP)/MWCNT/GC bioelectrode exhibited two linear responses to glucose in the concentration ranging from 0.42 mu M to 8.0 mM with a correlation coefficient of 0.95, sensitivity of 52.0 mu AmM-1 cm-2, repeatability of 1.6% and long-term stability, which could make it a promising bioelectrode for precise detection of glucose in the biological samples. (C) 2016 Elsevier B.V. All rights reserved.

• 26.
Linnaeus University, Sweden; Corning Inc, NY 14831 USA.
Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, Faculty of Science & Engineering. Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, Faculty of Science & Engineering. Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering. Linnaeus University, Sweden. Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, Faculty of Science & Engineering. Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, Faculty of Science & Engineering.
Synthesis and characterization of the mechanical and optical properties of Ca-Si-O-N thin films deposited by RF magnetron sputtering2017In: Surface & Coatings Technology, ISSN 0257-8972, E-ISSN 1879-3347, Vol. 315, p. 88-94Article in journal (Refereed)

Ca-Si-O-N thin films were deposited on commercial soda-lime silicate float glass, silica wafers and sapphire substrates by RF magnetron co-sputtering from Ca and Si targets in an Ar/N-2/O-2 gas mixture. Chemical composition, surface morphology, hardness, reduced elastic modulus and optical properties of the films were investigated using X-ray photoelectron spectroscopy, scanning electron microscopy, nanoindentation, and spectroscopic ellipsometry. It was found that the composition of the films can be controlled by the Ca target power, predominantly, and by the reactive gas flow. Thin films in the Ca-Si-O-N system are composed of N and Ca contents up to 31 eq. % and 60 eq. %, respectively. The films thickness ranges from 600 to 3000 nm and increases with increasing Ca target power. The films surface roughness varied between 2 and 12 nm, and approximately decreases with increasing power of Ca target. The hardness (4-12 GPa) and reduced elastic modulus (65-145 GPa) of the films increase and decrease with the N and Ca contents respectively. The refractive index (1.56-1.82) is primarily dictated by the N content. The properties are compared with findings for bulk glasses in the Ca-Si-(Al)-O-N systems, and it is concluded that Ca-Si-O-N thin films have higher values of hardness, elastic modulus and refractive index than bulk glasses of similar composition. (C) 2017 Elsevier B.V. All rights reserved.

The full text will be freely available from 2019-02-13 13:58
• 27.
Linnaeus University, Sweden.
Novel transparent Mg-Si-O-N thin films with high hardness and refractive index2016In: Vacuum, ISSN 0042-207X, E-ISSN 1879-2715, Vol. 131Article in journal (Refereed)

There is an increasing demand for glass materials with better mechanical and optical properties for display and electronic applications. This paper describes the deposition of novel thin films of Mg-circle divide-Si-O-N onto float glass substrates. Amorphous thin films in the Mg-Si-O-N system with high nitrogen and magnesium contents were deposited by reactive RF magnetron co-sputtering from Mg and Si targets in Ar/N-2/O-2 gas mixtures. The thin films studied span an unprecedented range of compositions up to 45 at% Mg and 80 at% N out of cations and anions respectively. Thin films in the Mg-Si-O-N system were found to be homogeneous and transparent in the visible region. Mechanical properties like hardness (H) and reduced elastic modulus (Er) show high values, up to 21 GPa and 166 GPa respectively. The refractive index (1.87-2.00) increases with increasing magnesium and nitrogen contents. (C) 2016 Elsevier Ltd. All rights reserved.

• 28.
University of Sindh, Pakistan.
University of Bristol, UK. University of Sindh, Pakistan. University of Sindh, Pakistan. University of Sindh, Pakistan. University of Sindh, Pakistan. University of Sindh, Pakistan. Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Faculty of Science & Engineering.
Glutaric Acid Assisted Fabrication of CuO Nanostructures and their Application in Development of Highly Sensitive Electrochemical Sensor System for Carbamates2016In: Electroanalysis, ISSN 1040-0397, E-ISSN 1521-4109, Vol. 28, no 7, p. 1634-1640Article in journal (Refereed)

This work describes the fabrication of unique arrow head shaped CuO nanostructures using simple hydrothermal treatment method. The highly attractive features were obtained by the application of glutaric acid utilised simultaneous as template and functionalising agent. The functionalised nanostructures were known to possess excellent potential towards the electro-catalytic oxidation of carbofuran pesticide. The generated intense electrochemical signal with lower potential value enabled sensitive and selective determination of carbofuran up to 1 x 10(-3) mu M with wide sensing window in range of 0.01 to 0.16 mu M. The feasibility of the developed sensor system for the practical application was also studied by testing its potential in real sample extracts of various vegetables. The excellent recoveries demonstrated the analytical robustness of the developed sensor system. The sensor system utilises a new and simple approach towards sensitive determination of toxic pesticides reflecting its wide spectrum application in various fields.

• 29.
University of Bristol, England; University of Sindh, Pakistan.
Dr MA Kazi Institute Chemistry University of Sindh, Pakistan. University of Sindh, Pakistan. Mehran University of Engn and Technology, Pakistan. Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Faculty of Science & Engineering.
Practice of diclofenac sodium for the hydrothermal growth of NiO nanostructures and their application for enzyme free glucose biosensor2016In: Microsystem Technologies: Micro- and Nanosystems Information Storage and Processing Systems, ISSN 0946-7076, E-ISSN 1432-1858, Vol. 22, no 10, p. 2549-2557Article in journal (Refereed)

In this study diclofenac sodium (DFS), an analgesic drug has been employed as an effective template for the synthesis of NiO nanostructures. The NiO nanostructures were synthesised using low temperature hydrothermal growth method, both in the presence and absence of the DFS drug. The synthesised nanostructures were studied for their structural, compositional and electrochemical properties using scanning electron microscopy, X-ray diffraction and cyclic voltammetry. The synthesised nanostructures were then utilised for the modification of glassy carbon electrode which were then utilised for the electro-catalytic enzyme free glucose sensing in alkaline media. The competitive experiments suggested that although, both nanostructures possess excellent capability of glucose sensing, the NiO nanoflakes modified electrode was found to be twice as much as sensitive (2584 A mu A mM(-1) cm(-2)) as nanoflowers based electrode (1154 A mu A mM(-1) cm(-2)). The NiO nanoflakes based sensor further demonstrated excellent anti-interference potential in the presence of common interferents like uric acid, ascorbic acid and dopamine. In addition, the successful application NiO nanoflakes based sensor to determine real blood glucose concentration further suggest its feasibility for real sample analysis.

• 30.
University of Bristol, England; University of Sindh, Pakistan.
King Saud University, Saudi Arabia; Sohag University, Egypt. University of Bristol, England. University of Sindh, Pakistan. King Saud University, Saudi Arabia. University of Sindh, Pakistan. Univ Sindh, Natl Ctr Excellence Analyt Chem, Jamshoro 76080, Pakistan. Univ Sindh, Dr MA Kazi Inst Chem, Jamshoro 76080, Pakistan. Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Faculty of Science & Engineering.
Highly sensitive determination of atropine using cobalt oxide nanostructures: Influence of functional groups on the signal sensitivity2016In: Analytica Chimica Acta, ISSN 0003-2670, E-ISSN 1873-4324, Vol. 948, p. 30-39Article in journal (Refereed)

This study describes sensitive determination of atropine using glassy carbon electrodes (GCE) modified with Co3O4 nanostructures. The as-synthesised nanostructures were grown using cysteine (CYS), glutathione (GSH) and histidine (HYS) as effective templates under hydrothermal action. The obtained morphologies revealed interesting structural features, including both cavity-based and flower-shaped structures. The as-synthesised morphologies were noted to actively participate in electro-catalysis of atropine (AT) drug where GSH-assisted structures exhibited the best signal response in terms of current density and over-potential value. The study also discusses the influence of functional groups on the signal sensitivity of atropine electro-oxidation. The functionalisation was carried with the amino acids originally used as effective templates for the growth of Co3O4 nanostructures. The highest increment was obtained when GSH was used as the surface functionalising agent. The GSH-functionalised Co3O4-modified electrode was utilised for the electro-chemical sensing of AT in a concentration range of 0.01 -0.46 mu M. The developed sensor exhibited excellent working linearity (R-2 = 0.999) and signal sensitivity up to 0.001 mu M of AT. The noted high sensitivity of the sensor is associated with the synergy of superb surface architectures and favourable interaction facilitating the electron transfer kinetics for the electro-catalytic oxidation of AT. Significantly, the developed sensor demonstrated excellent working capability when used for AT detection in human urine samples with strong anti-interference potential against common co-existing species, such as glucose, fructose, cysteine, uric acid, dopamine and ascorbic acid. (C) 2016 Elsevier B.V. All rights reserved.

• 31.
Linköping University, The Tema Institute, Department of Water and Environmental Studies. Linköping University, Faculty of Arts and Sciences.
Borén, HansLinköping University, The Tema Institute, Department of Water and Environmental Studies. Linköping University, Faculty of Arts and Sciences.Grimvall, AndersLinköping University, The Tema Institute, Department of Water and Environmental Studies. Linköping University, Faculty of Arts and Sciences.
Humic substances in the aquatic and terrestrial environment : proceedings of an international symposium, Linköping, Sweden, August 21-23, 19891991Conference proceedings (editor) (Refereed)

The state of the art on isolation techniques, ion binding theory, biologic activity in the aquatic environment as well as the formation of mutagenic compounds from chlorination is reviewed by worldwide-known experts. Additional papers describe current research on the topics: isolation, fractionation and characterization; biological and chemical transformation and degradation; complex formation and interactions with solids; biologic activity, halogenation of humic substances.

• 32.
Linköping University, Department of Physics, Chemistry and Biology.
Method development for identification of N-linked glycans by high performance anion exchange chromatography with pulsed amperometric detection and time of flight mass spectrometry2011Independent thesis Basic level (university diploma), 10,5 credits / 16 HE creditsStudent thesis

In the biopharmaceutical industry, identification of glycans in a glycoprotein is a regulatory requirement and is a part of the characterization of the protein. Glycans are constructed of several monosaccharides linked together. N-linked glycans, which have been studied in this project, are attached to the nitrogen atom in asparagine.

A method for separating N-linked glycans by high performance anion exchange chromatography had already been developed at the department. To develop a method for identification of the N-glycans by mass spectrometry, a desalting method on porous graphitic carbon (PGC) columns was used and optimized resulting in the eluents A (0,05% TFA in ACN:water 5:95 v/v) and B (0,05% TFA in ACN:water 50:50 v/v). Also the sample introduction on the mass spectrometer was optimized and resulted in a sensitive on-line liquid chromatography mass spectrometry (LC-MS) approach which gave mass spectrometric peaks with high signal to noise ratios and with high mass accuracy.

The developed procedure was then successfully used on glycans cleaved from a glycoprotein separated by high performance anion exchange chromatography with pulsed amperometric detector.

• 33.
Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Faculty of Science & Engineering.
Toward the Optimization of Low-temperature Solution-based Synthesis of ZnO Nanostructures for Device Applications2017Doctoral thesis, comprehensive summary (Other academic)

One-dimensional (1D) nanostructures (NSs) of Zinc Oxide (ZnO) such as nanorods (NRs) have recently attracted considerable research attention due to their potential for the development of optoelectronic devices such as ultraviolet (UV) photodetectors and light-emitting diodes (LEDs). The potential of ZnO NRs in all these applications, however, would require synthesis of high crystal quality ZnO NRs with precise control over the optical and electronic properties. It is known that the optical and electronic properties of ZnO NRs are mostly influenced by the presence of native (intrinsic) and impurities (extrinsic) defects. Therefore, understanding the nature of these intrinsic and extrinsic defects and their spatial distribution is critical for optimizing the optical and electronic properties of ZnO NRs. However, identifying the origin of such defects is a complicated matter, especially for NSs, where the information on anisotropy is usually lost due to the lack of coherent orientation.

Thus, the aim of this thesis is towards the optimization of the lowtemperature solution-based synthesis of ZnO NRs for device applications. In this connection, we first started with investigating the effect of the precursor solution stirring durations on the deep level defects concentration and their spatial distribution along the ZnO NRs. Then, by choosing the optimal stirring time, we studied the influence of ZnO seeding layer precursor’s types, and its molar ratios on the density of interface defects. The findings of these investigations were used to demonstrate ZnO NRs-based heterojunction LEDs. The ability to tune the point defects along the NRs enabled us further to incorporate cobalt (Co) ions into the ZnO NRs crystal lattice, where these ions could occupy the vacancies or interstitial defects through substitutional or interstitial doping. Following this, high crystal quality vertically welloriented ZnO NRs have been demonstrated by incorporating a small amount of Co into the ZnO crystal lattice. Finally, the influence of Co ions incorporation on the reduction of core-defects (CDs) in ZnO NRs was systematically examined using electron paramagnetic resonance (EPR).

1. Effect of precursor solutions stirring on deep level defects concentration and spatial distribution in low temperature aqueous chemical synthesis of zinc oxide nanorods
Open this publication in new window or tab >>Effect of precursor solutions stirring on deep level defects concentration and spatial distribution in low temperature aqueous chemical synthesis of zinc oxide nanorods
2015 (English)In: AIP Advances, ISSN 2158-3226, E-ISSN 2158-3226, Vol. 5, no 8, article id 087180Article in journal (Refereed) Published
##### Abstract [en]

Hexagonal c-axis oriented zinc oxide (ZnO) nanorods (NRs) with 120-300 nm diameters are synthesized via the low temperature aqueous chemical route at 80 degrees C on silver-coated glass substrates. The influence of varying the precursor solutions stirring durations on the concentration and spatial distributions of deep level defects in ZnO NRs is investigated. Room temperature micro-photoluminesnce (mu-PL) spectra were collected for all samples. Cathodoluminescence (CL) spectra of the as-synthesized NRs reveal a significant change in the intensity ratio of the near band edge emission (NBE) to the deep-level emission (DLE) peaks with increasing stirring durations. This is attributed to the variation in the concentration of the oxygen-deficiency with increasing stirring durations as suggested from the X-ray photoelectron spectroscopy analysis. Spatially resolved CL spectra taken along individual NRs revealed that stirring the precursor solutions for relatively short duration (1-3 h), which likely induced high super saturation under thermodynamic equilibrium during the synthesis process, is observed to favor the formation of point defects moving towards the tip of the NRs. In contrary, stirring for longer duration (5-15 h) will induce low super saturation favoring the formation of point defects located at the bottom of the NRs. These findings demonstrate that it is possible to control the concentration and spatial distribution of deep level defects in ZnO NRs by varying the stirring durations of the precursor solutions.

##### Place, publisher, year, edition, pages
AMER INST PHYSICS, 2015
##### National Category
Condensed Matter Physics
##### Identifiers
urn:nbn:se:liu:diva-122070 (URN)10.1063/1.4929981 (DOI)000360655900089 ()
##### Note

Funding Agencies|Avdanced Functional Materials (AFM) SFO project at Linkoping Univeristy, Sweden

Available from: 2015-12-18 Created: 2015-10-19 Last updated: 2017-12-01
2. Influence of ZnO seed layer precursor molar ratio on the density of interface defects in low temperature aqueous chemically synthesized ZnO nanorods/GaN light-emitting diodes
Open this publication in new window or tab >>Influence of ZnO seed layer precursor molar ratio on the density of interface defects in low temperature aqueous chemically synthesized ZnO nanorods/GaN light-emitting diodes
2016 (English)In: Journal of Applied Physics, ISSN 0021-8979, E-ISSN 1089-7550, Vol. 119, no 16, p. 165702-Article in journal (Refereed) Published
##### Abstract [en]

Low temperature aqueous chemical synthesis (LT-ACS) of zinc oxide (ZnO) nanorods (NRs) has been attracting considerable research interest due to its great potential in the development of light-emitting diodes (LEDs). The influence of the molar ratio of the zinc acetate (ZnAc): KOH as a ZnO seed layer precursor on the density of interface defects and hence the presence of non-radiative recombination centers in LT-ACS of ZnO NRs/GaN LEDs has been systematically investigated. The material quality of the as-prepared seed layer as quantitatively deduced by the X-ray photoelectron spectroscopy is found to be influenced by the molar ratio. It is revealed by spatially resolved cathodoluminescence that the seed layer molar ratio plays a significant role in the formation and the density of defects at the n-ZnO NRs/p-GaN heterostructure interface. Consequently, LED devices processed using ZnO NRs synthesized with molar ratio of 1:5M exhibit stronger yellow emission (similar to 575 nm) compared to those based on 1:1 and 1:3M ratios as measured by the electroluminescence. Furthermore, seed layer molar ratio shows a quantitative dependence of the non-radiative defect densities as deduced from light-output current characteristics analysis. These results have implications on the development of high-efficiency ZnO-based LEDs and may also be helpful in understanding the effects of the ZnO seed layer on defect-related non-radiative recombination. Published by AIP Publishing.

##### Place, publisher, year, edition, pages
AMER INST PHYSICS, 2016
##### National Category
Materials Chemistry
##### Identifiers
urn:nbn:se:liu:diva-129174 (URN)10.1063/1.4947593 (DOI)000375929900043 ()
##### Note

Funding Agencies|Swedish Government Strategic Research Area in Materials Science on Functional Materials at Linkoping University (Faculty Grant SFO-Mat-LiU) [2009-00971]

Available from: 2016-06-13 Created: 2016-06-13 Last updated: 2017-11-28
3. Seed layer synthesis effect on the concentration of interface defects and emission spectra of ZnO nanorods/p-GaN light-emitting diode
Open this publication in new window or tab >>Seed layer synthesis effect on the concentration of interface defects and emission spectra of ZnO nanorods/p-GaN light-emitting diode
2017 (English)In: Physica Status Solidi (a) applications and materials science, ISSN 1862-6300, E-ISSN 1862-6319, Vol. 214, no 1, article id 1600333Article in journal (Refereed) Published
##### Abstract [en]

As the low-temperature aqueous chemical synthesis (LT-ACS), holds great promises for the synthesis of one-dimensional (1D) ZnO nanostructure-based light-emitting diodes (LEDs) and hence require parameter tuning for optimal performance. N-ZnO nanorods (NRs)/p-GaN heterojunction LEDs have been synthesized by the LT-ACS using ZnO nanoparticle (NPs) seed layers prepared with different precursor solutions. The effect of these seed layers on the interface defect properties and emission intensity of the as-synthesized n-Zn/p-GaN heterojunction LEDs has been demonstrated by spatially resolved cathodoluminescence (CL) and electroluminescence (EL) measurements, respectively. A significant reduction of the interface defects in the n-ZnO NRs/p-GaN heterostructure synthesized from a seed layer prepared from zinc acetate (ZnAc) with a mixture of potassium hydroxide (KOH) and hexamethylenetetramine (HMTA) (donated as ZKH seed) compared with those prepared from ZnAc and KOH (donated as ZK seed) is observed as revealed by spatially resolved CL. Consequently, the LEDs based on n-ZnO NRs/p-GaN prepared from ZKH seed show an improvement in the yellow emission (approximate to 578nm) compared to that based on the ZK seed as deduced from the electroluminescence measurements. The improvement in the yellow EL emission on the ZKH LED probably attributed to the low presence of the non-radiative defect as deduced by light-output current (L-I) characteristics analysis.

##### Place, publisher, year, edition, pages
WILEY-V C H VERLAG GMBH, 2017
##### Keywords
GaN; interface defects; light-emitting diodes; low-temperature aqueous chemical synthesis; seed layers; ZnO
##### National Category
Condensed Matter Physics
##### Identifiers
urn:nbn:se:liu:diva-136230 (URN)10.1002/pssa.201600333 (DOI)000394423400006 ()
##### Note

Funding Agencies|Swedish Government Strategic Research Area in Materials Science on Functional Materials (Faculty Grant SFO-Mat-LiU) at Linkoping University [2009-00971]

Available from: 2017-03-31 Created: 2017-03-31 Last updated: 2017-11-29
4. EPR investigation of pure and Co-doped ZnO oriented nanocrystals
Open this publication in new window or tab >>EPR investigation of pure and Co-doped ZnO oriented nanocrystals
2017 (English)In: NANOTECHNOLOGY, ISSN 0957-4484, Vol. 28, no 3, article id 035705Article in journal (Refereed) Published
##### Abstract [en]

Pure and cobalt-doped zinc oxide aligned nanorods have been grown by the low-temperature (90 degrees C) aqueous chemical method on amorphous ZnO seed layer, deposited on a sapphire substrate. High crystallinity of these objects is demonstrated by the electron paramagnetic resonance investigation at liquid helium temperature. The successful incorporation of Co2+ ions in substitution of Zn2+ ones in the ZnO matrix has also been confirmed. A drastic reduction of intrinsic ZnO nanorods core defects is observed in the Co-doped samples, which enhances the structural quality of the NRs. The quantification of substitutional Co2+ ions in the ZnO matrix is achieved by comparison with a reference sample. The findings in this study indicate the potential of using the low-temperature aqueous chemical approach for synthesizing material for spintronics applications.

##### Place, publisher, year, edition, pages
IOP PUBLISHING LTD, 2017
##### Keywords
nanorods; magnetic properties; electron paramagnetic resonance; diluted magnetic semiconductors
##### National Category
Materials Chemistry
##### Identifiers
urn:nbn:se:liu:diva-134300 (URN)10.1088/1361-6528/28/3/035705 (DOI)000391289300001 ()27966469 (PubMedID)
##### Note

Funding Agencies|NATO project [SfP 984735]

Available from: 2017-02-06 Created: 2017-02-03 Last updated: 2017-10-06
5. An effective low-temperature solution synthesis of Co-doped [0001]-oriented ZnO nanorods
Open this publication in new window or tab >>An effective low-temperature solution synthesis of Co-doped [0001]-oriented ZnO nanorods
2017 (English)In: Journal of Applied Physics, ISSN 0021-8979, E-ISSN 1089-7550, Vol. 121, no 21, article id 215102Article in journal (Refereed) Published
##### Abstract [en]

We demonstrate an efficient possibility to synthesize vertically aligned pure zinc oxide (ZnO) and Co-doped ZnO nanorods (NRs) using the low-temperature aqueous chemical synthesis (90 degrees C). Two different mixing methods of the synthesis solutions were investigated for the Co-doped samples. The synthesized samples were compared to pure ZnO NRs regarding the Co incorporation and crystal quality. Electron paramagnetic resonance (EPR) measurements confirmed the substitution of Co2+ inside the ZnO NRs, giving a highly anisotropic magnetic Co2+ signal. The substitution of Zn2+ by Co2+ was observed to be combined with a drastic reduction in the core-defect (CD) signal (g similar to 1.956) which is seen in pure ZnO NRs. As revealed by the cathodoluminescence (CL), the incorporation of Co causes a slight red-shift of the UV peak position combined with an enhancement in the intensity of the defect-related yellow-orange emission compared to pure ZnO NRs. Furthermore, the EPR and the CL measurements allow a possible model of the defect configuration in the samples. It is proposed that the as-synthesized pure ZnO NRs likely contain Zn interstitial (Zn-i(+)) as CDs and oxygen vacancy (V-O) or oxygen interstitial (O-i) as surface defects. As a result, Co was found to likely occupy the Zn-i(+), leading to the observed CDs reduction and hence enhancing the crystal quality. These results open the possibility of synthesis of highly crystalline quality ZnO NRs-based diluted magnetic semiconductors using the low-temperature aqueous chemical method. Published by AIP Publishing.

##### Place, publisher, year, edition, pages
AMER INST PHYSICS, 2017
##### National Category
Condensed Matter Physics
##### Identifiers
urn:nbn:se:liu:diva-138890 (URN)10.1063/1.4984314 (DOI)000402768900026 ()
##### Note

Funding Agencies|NATO [984735]

Available from: 2017-06-27 Created: 2017-06-27 Last updated: 2017-10-06
6. Core-defect reduction in ZnO nanorods by cobalt incorporation
Open this publication in new window or tab >>Core-defect reduction in ZnO nanorods by cobalt incorporation
2017 (English)In: Nanotechnology, ISSN 0957-4484, E-ISSN 1361-6528, Vol. 28, no 28, article id 285705Article in journal (Refereed) Published
##### Abstract [en]

Zinc oxide (ZnO) nanorods grown by the low-temperature (90 degrees C) aqueous chemical method with different cobalt concentration within the synthesis solution (from 0% to 15%), are studied by electron paramagnetic resonance (EPR), just above the liquid helium temperature. The anisotropic spectra of substitutional Co2+ reveal a high crystalline quality and orientation of the NRs, as well as the probable presence of a secondary disordered phase of ZnO: Co. The analysis of the EPR spectra indicates that the disappearance of the paramagnetic native core-defect (CD) at g similar to 1.96 is correlated with the apparition of the Co2+ ions lines, suggesting a gradual neutralization of the former by the latter. We show that only a little amount of cobalt in the synthesis solution (about 0.2%) is necessary to suppress almost all these paramagnetic CDs. This gives insight in the experimentally observed improvement of the crystal quality of diluted ZnO: Co nanorods, as well as into the control of paramagnetic defects in ZnO nanostructures.

##### Place, publisher, year, edition, pages
IOP PUBLISHING LTD, 2017
##### Keywords
nanorods; ZnO; physics defects; electron paramagnetic resonance
##### National Category
Condensed Matter Physics
##### Identifiers
urn:nbn:se:liu:diva-139388 (URN)10.1088/1361-6528/aa716a (DOI)000404344400005 ()28475103 (PubMedID)
##### Note

Funding Agencies|NATO project Science for Peace (SfP), Novel nanostructures [984735]

Available from: 2017-08-07 Created: 2017-08-07 Last updated: 2017-10-06
• 34.
Linköping University, Department of Science and Technology. Linköping University, Faculty of Science & Engineering.
Influence of ZnO seed layer precursor molar ratio on the density of interface defects in low temperature aqueous chemically synthesized ZnO nanorods/GaN light-emitting diodes2016In: Journal of Applied Physics, ISSN 0021-8979, E-ISSN 1089-7550, Vol. 119, no 16, p. 165702-Article in journal (Refereed)

Low temperature aqueous chemical synthesis (LT-ACS) of zinc oxide (ZnO) nanorods (NRs) has been attracting considerable research interest due to its great potential in the development of light-emitting diodes (LEDs). The influence of the molar ratio of the zinc acetate (ZnAc): KOH as a ZnO seed layer precursor on the density of interface defects and hence the presence of non-radiative recombination centers in LT-ACS of ZnO NRs/GaN LEDs has been systematically investigated. The material quality of the as-prepared seed layer as quantitatively deduced by the X-ray photoelectron spectroscopy is found to be influenced by the molar ratio. It is revealed by spatially resolved cathodoluminescence that the seed layer molar ratio plays a significant role in the formation and the density of defects at the n-ZnO NRs/p-GaN heterostructure interface. Consequently, LED devices processed using ZnO NRs synthesized with molar ratio of 1:5M exhibit stronger yellow emission (similar to 575 nm) compared to those based on 1:1 and 1:3M ratios as measured by the electroluminescence. Furthermore, seed layer molar ratio shows a quantitative dependence of the non-radiative defect densities as deduced from light-output current characteristics analysis. These results have implications on the development of high-efficiency ZnO-based LEDs and may also be helpful in understanding the effects of the ZnO seed layer on defect-related non-radiative recombination. Published by AIP Publishing.

• 35.
Kungl. Tekniska Högskolan, KTH, Stockholm.
Svenska Miljöinstitutet. Innventia AB, Stockholm, Sweden. Miljö- och energisystem, Lunds Tekniska Högskola, Lund. Miljö- och energisystem, Lunds Tekniska Högskola, Lund. Department of Energy and Environment, Chalmers University of Technology, Sweden. Chalmers University of Technology, Dept. of Energy and Environment, Heat and Power Technology Division,Göteborg, Sweden. Innventia AB, Stockholm, Sweden. Svenska Miljöinstitutet. Svenska Miljöinstitutet. Volvo AB, Sweden. Kemisk Teknologi, Kungliga Tekniska Högskolan, KTH, Stockholm. Department of Chemical Engineering, Lund University, Sweden. Skolan för kemivetenskap, Kungliga Tekniska Högskolan, Stockholm. Energi och miljö/Energiteknik, Chalmers Tekniska Högskola, Göteborg. Svenska Miljöinstitutet. School of Chemical Science and Engineering, Kungliga Tekniska Högskolan, Stockholm. Biokemi och Strukturbiologi, Lunds universitet, Lund. Institutionen för kemiteknik, Lunds universitet, Lund. Linköping University, Department of Management and Engineering, Energy Systems. Linköping University, The Institute of Technology. Institutionen för kemiteknik, Lunds universitet, Lund. Institutionen för samhällsbyggnad och naturresurser, Luleå Tekniska universitet.
Research and development challenges for Swedish biofuel actors – three illustrative examples: Improvement potential discussed in the context of Well-to-Tank analyses2010Report (Other academic)

Currently biofuels have strong political support, both in the EU and Sweden. The EU has, for example, set a target for the use of renewable fuels in the transportation sector stating that all EU member states should use 10% renewable fuels for transport by 2020. Fulfilling this ambition will lead to an enormous market for biofuels during the coming decade. To avoid increasing production of biofuels based on agriculture crops that require considerable use of arable area, focus is now to move towards more advanced second generation (2G) biofuels that can be produced from biomass feedstocks associated with a more efficient land use.

Climate benefits and greenhouse gas (GHG) balances are aspects often discussed in conjunction with sustainability and biofuels. The total GHG emissions associated with production and usage of biofuels depend on the entire fuel production chain, mainly the agriculture or forestry feedstock systems and the manufacturing process. To compare different biofuel production pathways it is essential to conduct an environmental assessment using the well-to-tank (WTT) analysis methodology.

In Sweden the conditions for biomass production are favourable and we have promising second generation biofuels technologies that are currently in the demonstration phase. In this study we have chosen to focus on cellulose based ethanol, methane from gasification of solid wood as well as DME from gasification of black liquor, with the purpose of identifying research and development potentials that may result in improvements in the WTT emission values. The main objective of this study is thus to identify research and development challenges for Swedish biofuel actors based on literature studies as well as discussions with the the researchers themselves. We have also discussed improvement potentials for the agriculture and forestry part of the WTT chain. The aim of this study is to, in the context of WTT analyses, (i) increase knowledge about the complexity of biofuel production, (ii) identify and discuss improvement potentials, regarding energy efficiency and GHG emissions, for three biofuel production cases, as well as (iii) identify and discuss improvement potentials regarding biomass supply, including agriculture/forestry. The scope of the study is limited to discussing the technologies, system aspects and climate impacts associated with the production stage. Aspects such as the influence on biodiversity and other environmental and social parameters fall beyond the scope of this study.

We find that improvement potentials for emissions reductions within the agriculture/forestry part of the WTT chain include changing the use of diesel to low-CO2-emitting fuels, changing to more fuel-efficient tractors, more efficient cultivation and manufacture of fertilizers (commercial nitrogen fertilizer can be produced in plants which have nitrous oxide gas cleaning) as well as improved fertilization strategies (more precise nitrogen application during the cropping season). Furthermore, the cultivation of annual feedstock crops could be avoided on land rich in carbon, such as peat soils and new agriculture systems could be introduced that lower the demand for ploughing and harrowing. Other options for improving the WTT emission values includes introducing new types of crops, such as wheat with higher content of starch or willow with a higher content of cellulose.

From the case study on lignocellulosic ethanol we find that 2G ethanol, with co-production of biogas, electricity, heat and/or wood pellet, has a promising role to play in the development of sustainable biofuel production systems. Depending on available raw materials, heat sinks, demand for biogas as vehicle fuel and existing 1G ethanol plants suitable for integration, 2G ethanol production systems may be designed differently to optimize the economic conditions and maximize profitability. However, the complexity connected to the development of the most optimal production systems require improved knowledge and involvement of several actors from different competence areas, such as chemical and biochemical engineering, process design and integration and energy and environmental systems analysis, which may be a potential barrier.

Three important results from the lignocellulosic ethanol study are: (i) the production systems could be far more complex and intelligently designed than previous studies show, (ii) the potential improvements consist of a large number of combinations of process integration options wich partly depends on specific local conditions, (iii) the environmental performance of individual systems may vary significantly due to systems design and local conditons.

From the case study on gasification of solid biomass for the production of biomethane we find that one of the main advantages of this technology is its high efficiency in respect to converting biomass into fuels for transport. For future research we see a need for improvements within the gas up-grading section, including gas cleaning and gas conditioning, to obtain a more efficient process. A major challenge is to remove the tar before the methanation reaction.

Three important results from the biomethane study are: (i) it is important not to crack the methane already produced in the syngas, which indicates a need for improved catalysts for selective tar cracking, (ii) there is a need for new gas separation techniques to facilitate the use of air oxidation agent instead of oxygen in the gasifier, and (iii) there is a need for testing the integrated process under realistic conditions, both at atmospheric and pressurized conditions.

From the case study on black liquor gasification for the production of DME we find that the process has many advantages compared to other biofuel production options, such as the fact that black liquor is already partially processed and exists in a pumpable, liquid form, and that the process is pressurised and tightly integrated with the pulp mill, which enhances fuel production efficiency. However, to achieve commercial status, some challenges still remain, such as demonstrating that materials and plant equipment meet the high availability required when scaling up to industrial size in the pulp mill, and also proving that the plant can operate according to calculated heat and material balances. Three important results from the DME study are: (i) that modern chemical pulp mills, having a potential surplus of energy, could become important suppliers of renewable fuels for transport, (ii) there is a need to demonstrate that renewable DME/methanol will be proven to function in large scale, and (iii) there is still potential for technology improvements and enhanced energy integration.

Although quantitative improvement potentials are given in the three biofuel production cases, it is not obvious how these potentials would affect WTT values, since the biofuel production processes are complex and changing one parameter impacts other parameters. The improvement potentials are therefore discussed qualitatively. From the entire study we have come to agree on the following common conclusions: (i) research and development in Sweden within the three studied 2G biofuel production technologies is extensive, (ii) in general, the processes, within the three cases, work well at pilot and demonstration scale and are now in a phase to be proven in large scale, (iii) there is still room for improvement although some processes have been known for decades, (iv) the biofuel production processes are complex and site specific and process improvements need to be seen and judged from a broad systems perspective (both within the production plant as well as in the entire well-to-tank perspective), and (v) the three studied biofuel production systems are complementary technologies. Futher, the process of conducting this study is worth mentioning as a result itself, i.e. that many different actors within the field have proven their ability and willingness to contribute to a common report, and that the cooperation climate was very positive and bodes well for possible future collaboration within the framework of the f3 center.

Finally, judging from the political ambitions it is clear that the demand for renewable fuels will significantly increase during the coming decade. This will most likely result in opportunities for a range of biofuel options. The studied biofuel options all represent 2G biofuels and they can all be part of the solution to meet the increased renewable fuel demand.

• 36.
Lund University, Sweden .
Chalmers University of Technology, Göteborg, Sweden. Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, The Institute of Technology. Lund University, Sweden . Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, The Institute of Technology. Chalmers University of Technology, Göteborg, Sweden. Lund University, Sweden . Lund University, Sweden . Lund University, Sweden .
Charge Carrier Dynamics of Polymer: Fullerene Blends: From Geminate to Non-Geminate Recombination2014In: Advanced Energy Materials, ISSN 1614-6832, Vol. 4, no 8, article id 1301706Article in journal (Refereed)

The charge carrier dynamics of a new polymer-fullerene blend are examined on the femtosecond to the millisecond time scale. The full time range is globally fitted using a chemical reaction rate model that includes all key processes, charge generation, energy transfer, charge separation, and recombination, over the full 12 orders of magnitude in time and a factor of 33 in light intensity. Particular attention is paid to the charge recombination processes and it is found that they are highly material specific. Comparison of the dynamics to those of a previously studied polymer: fullerene blend reveals that while for one blend the recombination dynamics are mainly controlled by geminate recombination, the charge recombination in the presently studied polymer: fullerene blend are entirely controlled by non-geminate electron-hole recombination. Carrier density dependence of the non-geminate recombination rate is analyzed and a correlated disorder model of site energies is proposed to explain the observed dependency.

• 37.
Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology. Thaksin University, Thailand.
Excitons and biexcitons in InGaN quantum dot like localization centers2014In: Nanotechnology, ISSN 0957-4484, Vol. 25, no 49, p. 495702-Article in journal (Refereed)

Indium segregation in a narrow InGaN single quantum well creates quantum dot (QD) like exciton localization centers. Cross-section transmission electron microscopy reveals varying shapes and lateral sizes in the range ∼1–5 nm of the QD-like features, while scanning near field optical microscopy demonstrates a highly inhomogeneous spatial distribution of optically active individual localization centers. Microphotoluminescence spectroscopy confirms the spectrally inhomogeneous distribution of localization centers, in which the exciton and the biexciton related emissions from single centers of varying geometry could be identified by means of excitation power dependencies. Interestingly, the biexciton binding energy (Ebxx) was found to vary from center to center, between 3 to −22 meV, in correlation with the exciton emission energy. Negative binding energies are only justified by a three-dimensional quantum confinement, which confirms QD-like properties of the localization centers. The observed energy correlation is proposed to be understood as variations of the lateral extension of the confinement potential, which would yield smaller values of Ebxx for reduced lateral extension and higher exciton emission energy. The proposed relation between lateral extension and Ebxx is further supported by the exciton and the biexciton recombination lifetimes of a single QD, which suggest a lateral extension of merely ∼3 nm for a QD with strongly negative Ebxx = −15.5 meV.

• 38.
Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
Structural insights into protein-protein interactions governing regulation in transcription initiation and ubiquitination2015Doctoral thesis, comprehensive summary (Other academic)

Virtually every aspect of the cellular processes in eukaryotes requires that the interactions between protein molecules are well coordinated in different regulatory pathways. Any protein dysfunction involved in these regulatory pathways might lead to various pathological conditions. Understanding the structural and functional peculiarities of these proteins molecular machineries will help in formulating structure-based drug design.

The first regulatory process studied here is the RNA polymerase-II mediated transcription of the eukaryotic protein-coding genes to produce mRNAs. This process requires the formation of the ‘transcription initiation’ by the assembly of Pre-Initiation Complex (PIC) formation at a core promoter region. Regulation at this initiation level is a key mechanism for the control of gene expression that governs cellular growth and differentiation. The transcription Factor IID (TFIID) is a conserved multiprotein general transcription factor with an essential role in  nucleating the PIC formation, composed of TATA Binding Protein (TBP) and about 14 TBP Associated Factors (TAFs). The here presented crystal structure (1.97Å) of TBP bound to TAND1 and TAND2 domains from TAF1 reveals a detailed molecular pattern of interactions involving both transcriptionally activating and repressing regions in TBP, thereby uncovering central principles for anchoring of TBP-binding motifs. Together with NMR and cellular analysis, this work provides the structural basis of competitive binding with TFIIA to modulate TBP in promoter recognition.

In eukaryotes, another fundamental mechanism in the regulation of cellular physiology is the posttranslational modification of substrate proteins by ubiquitin, termed ‘ubiquitination’. Important actors in this mechanism are the ubiquitin-ligases (E3s) that culminate the transfer of ubiquitin to the substrate and govern the specificity of this system. One E3 ligase in particular, TRIM21, defines a subgroup of the Tripartite Motif (TRIM) family, which belongs to the major RING-type of E3 ubiquitin ligases, and plays an important role in pathogenesis of autoimmunity by mediating ubiquitination of transcription factors. The crystal structure (2.86Å) of the RING domain from TRIM21 in complex with UBE2E1, an E2 conjugating enzyme, together with the NMR and SAXS analysis as well as biochemical functional analysis, reveals the molecular basis for the dynamic binding interfaces. The TRIM21 mode of ubiquitin recognition and activation for catalytic transfer of ubiquitin can be modeled onto the entire TRIM family.

Finally, we explored the concepts of conformational selection in proteins as a possible key component for protein-mediated transcriptional regulation. In this framework, MexR, a bacterial repressor of the MexAB-OprM efflux pump, and its mutant Arg21Trp were studied as an example for proteins presenting different conformations. The residue Arg21Trp mutation is clinically identified to cause of Multi-Drug Resistant (MDR) by attenuated DNA binding, and leads to the overexpression of the MexAB-OprM efflux pump. With the crystal structure (2.19Å) of MexR mutant Arg21Trp, in combination with MD-simulations and SAXS for both wild-type and mutant, we could unravel the atomic details of the wild-type conformations consisting in subsets of populations of DNA bound and unbound forms. Remarkably, the mutant Arg21Trp stabilize the DNA unbound state and shifts MexR in a pre-existing equilibrium, from a repressed to a derepressed state.

Taken together, these studies substantially broaden our knowledge at a molecular level in protein interactions that are involved in transcriptional regulation and ubiquitination, studied by a carefully selected combination of complementary structural methods spanning different resolutions and time scales.

1. High-resolution structure of TBP with TAF1 reveals anchoring patterns in transcriptional regulation
Open this publication in new window or tab >>High-resolution structure of TBP with TAF1 reveals anchoring patterns in transcriptional regulation
2013 (English)In: Nature Structural & Molecular Biology, ISSN 1545-9993, E-ISSN 1545-9985, Vol. 20, no 8, p. 1008-+Article in journal (Refereed) Published
##### Abstract [en]

The general transcription factor TFIID provides a regulatory platform for transcription initiation. Here we present the crystal structure (1.97 angstrom) and NMR analysis of yeast TAF1 N-terminal domains TAND1 and TAND2 bound to yeast TBP, together with mutational data. We find that yeast TAF1-TAND1, which in itself acts as a transcriptional activator, binds TBPs concave DNA-binding surface by presenting similar anchor residues to TBP as does Mot1 but from a distinct structural scaffold. Furthermore, we show how TAF1-TAND2 uses an aromatic and acidic anchoring pattern to bind a conserved TBP surface groove traversing the basic helix region, and we find highly similar TBP-binding motifs also presented by the structurally distinct TFIIA, Mot1 and Brf1 proteins. Our identification of these anchoring patterns, which can be easily disrupted or enhanced, provides insight into the competitive multiprotein TBP interplay critical to transcriptional regulation.

##### Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 75 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USA, 2013
##### National Category
Engineering and Technology
##### Identifiers
urn:nbn:se:liu:diva-96977 (URN)10.1038/nsmb.2611 (DOI)000322715300016 ()
##### Note

Funding Agencies|Swedish Research Council|621-2011-6028621-2012-5250621-2012-5136|VINNOVA|P32045-1|Swedish Cancer Foundation|11 0681|Swedish Child Cancer Foundation|PROJ09/092|Forum Scientium Award||Canadian Institutes for Health Research|MT-13611|Japan Society for the Promotion of Science|23370077|Knut and Alice Wallenberg foundation||Canada Research Chair||

Available from: 2013-09-05 Created: 2013-09-02 Last updated: 2017-12-06
2. Mutation-Induced Population Shift in the MexR Conformational Ensemble Disengages DNA Binding: A Novel Mechanism for MarR Family Derepression
Open this publication in new window or tab >>Mutation-Induced Population Shift in the MexR Conformational Ensemble Disengages DNA Binding: A Novel Mechanism for MarR Family Derepression
2016 (English)In: Structure, ISSN 0969-2126, E-ISSN 1878-4186, Vol. 24, no 8, p. 1311-1321Article in journal (Refereed) Published
##### Abstract [en]

MexR is a repressor of the MexAB-OprM multidrug efflux pump operon of Pseudomonas aeruginosa, where DNA-binding impairing mutations lead to multidrug resistance (MDR). Surprisingly, the crystal structure of an MDR-conferring MexR mutant R21W (2.19 angstrom) presented here is closely similar to wildtype MexR. However, our extended analysis, by molecular dynamics and small-angle X-ray scattering, reveals that the mutation stabilizes a ground state that is deficient of DNA binding and is shared by both mutant and wild-type MexR, whereas the DNA-binding state is only transiently reached by the more flexible wild-type MexR. This population shift in the conformational ensemble is effected by mutation-induced allosteric coupling of contact networks that are independent in the wild-type protein. We propose that the MexR-R21W mutant mimics derepression by small-molecule binding to MarR proteins, and that the described allosteric model based on population shifts may also apply to other MarR family members.

##### Place, publisher, year, edition, pages
CELL PRESS, 2016
##### National Category
Structural Biology
##### Identifiers
urn:nbn:se:liu:diva-131908 (URN)10.1016/j.str.2016.06.008 (DOI)000383244600012 ()27427478 (PubMedID)
##### Note

Funding Agencies|European Communitys Seventh Framework Program (FP7) under BioStruct-X [283570]; Swedish e-Science Research Center; Swedish Research Council; Tage Erlander Visiting Professor grant.

The original status of this article was Manuscript and the titel was Population shift disengages DNA binding in a multidrug resistance MexR mutant.

Available from: 2016-10-13 Created: 2016-10-11 Last updated: 2018-05-06
3. Anti-Ro52 Autoantibodies from Patients with Sjögren's Syndrome Inhibit the Ro52 E3 Ligase Activity by Blocking the E3/E2 Interface
Open this publication in new window or tab >>Anti-Ro52 Autoantibodies from Patients with Sjögren's Syndrome Inhibit the Ro52 E3 Ligase Activity by Blocking the E3/E2 Interface
2011 (English)In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 286, no 42, p. 36478-36491Article in journal (Refereed) Published
##### Abstract [en]

Ro52 (TRIM21) is an E3 ligase of the tripartite motif family that negatively regulates proinflammatory cytokine production by ubiquitinating transcription factors of the interferon regulatory factor family. Autoantibodies to Ro52 are present in patients with lupus and Sjögren's syndrome, but it is not known if these autoantibodies affect the function of Ro52. To address this question, the requirements for Ro52 E3 ligase activity were first analyzed in detail. Scanning a panel of E2 ubiquitin-conjugating enzymes, we found that UBE2D1–4 and UBE2E1–2 supported the E3 ligase activity of Ro52 and that the E3 ligase activity of Ro52 was dependent on its RING domain. We also found that the N-terminal extensions in the class III E2 enzymes affected their interaction with Ro52. Although the N-terminal extension in UBE2E3 made this E2 enzyme unable to function together with Ro52, the N-terminal extensions in UBE2E1 and UBE2E2 allowed for a functional interaction with Ro52. Anti-Ro52-positive patient sera and affinity-purified anti-RING domain autoantibodies inhibited the E3 activity of Ro52 in ubiquitination assays. Using NMR, limited proteolysis, ELISA, and Ro52 mutants, we mapped the interactions between Ro52, UBE2E1, and anti-Ro52 autoantibodies. We found that anti-Ro52 autoantibodies inhibited the E3 ligase activity of Ro52 by sterically blocking the E2/E3 interaction between Ro52 and UBE2E1. Our data suggest that anti-Ro52 autoantibodies binding the RING domain of Ro52 may be actively involved in the pathogenesis of rheumatic autoimmune disease by inhibiting Ro52-mediated ubiquitination.

##### Place, publisher, year, edition, pages
American Society for Biochemistry and Molecular Biology, 2011
##### National Category
Natural Sciences
##### Identifiers
urn:nbn:se:liu:diva-53170 (URN)10.1074/jbc.M111.241786 (DOI)000296538300033 ()
##### Note

Funding agencies|Swedish Research Council||Swedish Foundation for Strategic Research||VINNOVA||CeNano||Swedish Cancer Society||Karolinska Institutet||Linkoping University||King Gustaf Vs 80-Year Foundation||Heart-Lung Foundation||Stockholm County Council||Gustafsson Foundation||Soderberg Foundation||National Cancer Institute of Canada||Swedish Rheumatism Association||Wallenberg Foundation||

Available from: 2010-01-18 Created: 2010-01-18 Last updated: 2017-12-12Bibliographically approved
4. Structure of a TRIM21 - UBE2El complex reveals the specificity of E2 and ubiquitin recognition by TRIM E3 RINGs
Open this publication in new window or tab >>Structure of a TRIM21 - UBE2El complex reveals the specificity of E2 and ubiquitin recognition by TRIM E3 RINGs
##### Abstract [en]

TRIM21, a RlNG-containing E3 ubiquitin-ligase of the TRIM  $\tiny(\underline{tri}partite \ \underline{m}otif)$ protein family, is a major autoantigen in SLE and Sjögren's syndrome as well as a modifier of interferon regulatory factors, thereby regulating innate immune signalling. We herein report the 2.86 Å crystal structure ofhuman TRIM211-91 comprising the RING domain (residues 16-55), in complex with the human E2 conjugating UBE2El enzyme (also denoted UbcH6). The crystal structure, joint with analysis by NMR and SAXS as well as structure-directed mutations and functional assays provides a detailed view of the specificity-determining contacts that support specific E2 recognition in the TRIM family. A detailed comparison of our structure with known E2 bound ubiquitin complexes, supported by biochemical analyses, reveals the molecular basis for TRIM21 interactions with donor ubiquitin that activates catalytic ubiquitin transfer. Finally, our structure convincingly demonstrates the placement of the Ub-targeted Lys61 of the adjacent TRIM21$\small^,$1- 91 close to the catalytically active UBE2El cysteine, and how the Lys61 amide is activated fora nucleophilic attack by hydrogen-bondeffected deshielding by conserved acidic residues at the E2 active site. In all, our structural findings provide molecular details ofthe selectivity involved in TRIM21 interactions with its cognate UBE2E1 enzyme and how TRIM21 positions ubiquitin in a catalytic conformation for ubiquitin transfer, and presents a snapshot of the Ub ligation step on a specific target residue of TRIM211-91 as an auto-ubiquitinated pseudo-substrate at high concentration. Increased structural and functional understanding of the TRIM mediated ubiquitination will aid development ofnovel therapeutic approaches in the entire TRIM family ofproteins.

##### National Category
Chemical Sciences Biochemistry and Molecular Biology
##### Identifiers
urn:nbn:se:liu:diva-122466 (URN)
Available from: 2015-11-03 Created: 2015-11-03 Last updated: 2015-11-13Bibliographically approved
• 39.
Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
Rheumatology Unit, Department of Medicine, Center for Molecular Medicine L8:04, Karolinska Institutet, Stockholm, Sweden. Rheumatology Unit, Department of Medicine, Center for Molecular Medicine L8:04, Karolinska Institutet, Stockholm, Sweden. European Molecular Biology Laboratory, Grenoble Outstation, Grenoble, France. Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering. School of Molecular Bioscience, The University of Sydney, New South Wales, Australia. Rheumatology Unit, Department of Medicine, Center for Molecular Medicine L8:04, Karolinska Institutet, Stockholm, Sweden. Department of Medical Biochemistry and Biophysics, Protein Science Facility, Karolinska Institutet, Stockholm, Sweden. Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
Structure of a TRIM21 - UBE2El complex reveals the specificity of E2 and ubiquitin recognition by TRIM E3 RINGsManuscript (preprint) (Other academic)

TRIM21, a RlNG-containing E3 ubiquitin-ligase of the TRIM  $\tiny(\underline{tri}partite \ \underline{m}otif)$ protein family, is a major autoantigen in SLE and Sjögren's syndrome as well as a modifier of interferon regulatory factors, thereby regulating innate immune signalling. We herein report the 2.86 Å crystal structure ofhuman TRIM211-91 comprising the RING domain (residues 16-55), in complex with the human E2 conjugating UBE2El enzyme (also denoted UbcH6). The crystal structure, joint with analysis by NMR and SAXS as well as structure-directed mutations and functional assays provides a detailed view of the specificity-determining contacts that support specific E2 recognition in the TRIM family. A detailed comparison of our structure with known E2 bound ubiquitin complexes, supported by biochemical analyses, reveals the molecular basis for TRIM21 interactions with donor ubiquitin that activates catalytic ubiquitin transfer. Finally, our structure convincingly demonstrates the placement of the Ub-targeted Lys61 of the adjacent TRIM21$\small^,$1- 91 close to the catalytically active UBE2El cysteine, and how the Lys61 amide is activated fora nucleophilic attack by hydrogen-bondeffected deshielding by conserved acidic residues at the E2 active site. In all, our structural findings provide molecular details ofthe selectivity involved in TRIM21 interactions with its cognate UBE2E1 enzyme and how TRIM21 positions ubiquitin in a catalytic conformation for ubiquitin transfer, and presents a snapshot of the Ub ligation step on a specific target residue of TRIM211-91 as an auto-ubiquitinated pseudo-substrate at high concentration. Increased structural and functional understanding of the TRIM mediated ubiquitination will aid development ofnovel therapeutic approaches in the entire TRIM family ofproteins.

• 40.
Linköping University, Department of Physics, Chemistry and Biology, Chemistry.
Gymnasiekemin, förr och nu: En historisk överblick hur gymnasiekemin har förändrats över tid och hur detta kan ha bidragit till elevers förståelse för kemi2018Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
• 41.
Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences.
Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences. University of Dhaka, Bangladesh. Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences. Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences. Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences. Research Unit: Environmental Sciences and Management, North-West University, Potchefstroom, South Africa.
Evaluating gas chromatography with a halogen-specific detectorfor the determination of disinfection by-products in drinking water2018In: Environmental science and pollution research international, ISSN 0944-1344, E-ISSN 1614-7499Article in journal (Refereed)

The occurrence of disinfection by-products (DBPs) in drinking water has become an issue of concern during the past decades. The DBPs pose health risks and are suspected to cause various cancer forms, be genotoxic and have negative developmental effects. The vast chemical diversity of DBPs makes comprehensive monitoring challenging. Only few of the DBPs are regulated and included in analytical protocols. In this study, a method for simultaneous measurement of 20 DBPs from five different structural classes (both regulated and non-regulated) was investigated and further developed for 11 DBPs using solid phase extraction and gas chromatography coupled with a halogen specific detector (XSD). The XSD was highly selective towards halogenated DBPs, providing chromatograms with little noise. The method allowed detection down to 0.05 µg/L and showed promising results for the simultaneous determination of a range of neutral DBP classes. Compounds from two classes of emerging DBPs, more cytotoxic than the “traditional” regulated DBPs, were successfully determined using this method. However, haloacetic acids (HAAs) should be analyzed separately as some HAA methyl esters may degrade giving false positives of trihalomethanes (THMs). The method was tested on real water samples from two municipal waterworks where the target DBP concentrations were found below the regulatory limits of Sweden.

• 42.
Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
Chemical and electronic structure of electroluminescent materials and interfaces in polymer-LEDs2000Licentiate thesis, comprehensive summary (Other academic)

Following the discovery that conjugated polymers can be used as the emitting layer in light­ emitting devices, extensive studies on these materials have been carried out. In a few years, due to the development of new materials and an increasing knowledge of the underlying chemistry and physics, the performance has improved a lot. One of the important factors that determine the performance of the devices is the chemistry upon interface formation. In the simplest single-layer device there are two interfaces, the interface between the conjugated polymer and the anode and cathode respectively. This thesis deals to a large extent with investigations of the chemical and electronic structure at these interfaces by means of X-ray photoelectron spectroscopy (XPS) and ultraviolet photoelectron spectroscopy (UPS). The first chapters give a short introduction to conjugated polymers, polymer LEDs and photoelectron spectroscopy on conjugated material. The following three chapters provide some background information in the subject areas of the papers with some references to closely related studies. The first paper compares the device performance characteristics upon using two different anodes, indium tin oxide (ITO) and fluorine tin oxide (FTO). The second and third papers report on chemical interactions between the ITO-anode and the precursor polymer of PPV, one of  the most frequently used conjugated polymers. The fourth and final paper reports on the early stage of interface formation between two different metal atoms (lithium and sodium), and a conjugated molecule.

• 43.
Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
Imaging surface plasmon resonance2008Doctoral thesis, comprehensive summary (Other academic)

The central theme of this thesis is the use of imaging Surface Plasmon Resonance (iSPR) as a tool in the characterization of surfaces with laterally varying properties. Within the scope of this work, an instrument for iSPR analysis was designed and built. SPR is a very sensitive technique for monitoring changes in optical properties in the immediate vicinity of a sensor surface, which is very useful in biosensing and surface science research. We have employed SPR in the Kretschmann configuration, wherein surface plasmons are excited by means of an evanescent field arising from total internal reflection from the backside of the sensor surface. In iSPR, the signal is the reflectivity of TM-polarized light which is measured using an imaging detector, typically a CCD camera. Advantages of this technique include extreme surface sensitivity and, because detection is done from the backside, compatibility with complex samples. In addition, SPR is a non-labeling technique, and in imaging mode, a lateral resolution in the µm range can be attained.

The imaging SPR instrument could be operated in either wavelength interrogation mode or in intensity mode. In the former case, the objective is to find the SPR wave-length, λSPR, which is the wavelength at which the reflected intensity is at a minimum. In intensity mode, a snapshot of the intensity reflectance is taken at a fixed wavelength hand incidence angle.

In biosensor science, the use of an imaging technique offers a major advantage by enabling parallelization and thereby increasing throughput. We have, for example, used iSPR in biochemical interaction analysis to monitor immobilization and specific binding to protein and synthetic polypeptide micro arrays. The primary interest has been the study of soft matter surfaces that possess properties interesting in the field of biomimetics or for applications in biosensing. Specifically, the surfaces studied in this thesis include patterned self-assembled monolayers of thiolates on gold, a graft polymerized poly(ethylene glycol) (PEG) based hydrogel, a dextran hydrogel, and a polyelectrolyte charge gradient. Our results show that the PEG-based hydrogel is very well suited for use as a platform in protein immobilization in an array format, owing to the very low unspecific binding. In addition, well defined microarray templates were designed by patterning of hydrophobic barriers on dextran and monolayer surfaces. A polypeptide affinity microarray was further designed and immobilized on such a patterned monolayer substrate, in order to demonstrate the potential of analyte quantification with high sensitivity over a large dynamic range.

Furthermore, iSPR was combined with electrochemistry to enable laterally resolved studies of electrochemical surface reactions. Using this combination, the electrochemical properties of surfaces patterned with self assembled monolayers can be studied in parallel, with a spatial resolution in the µm regime. We have also employed electrochemistry and iSPR for the investigation of potential and current density gradients on bipolar electrodes.

The imaging SPR instrument could be operated in either wavelength interrogation mode or in intensity mode. In the former case, the objective is to find the SPR wave-length, λSPR, which is the wavelength at which the reflected intensity is at a minimum. In intensity mode, a snapshot of the intensity reflectance is taken at a fixed wavelength hand incidence angle.In biosensor science, the use of an imaging technique offers a major advantage by enabling parallelization and thereby increasing throughput. We have, for example, used iSPR in biochemical interaction analysis to monitor immobilization and specific binding to protein and synthetic polypeptide micro arrays. The primary interest has been the study of soft matter surfaces that possess properties interesting in the field of biomimetics or for applications in biosensing. Specifically, the surfaces studied in this thesis include patterned self-assembled monolayers of thiolates on gold, a graft polymerized poly(ethylene glycol) (PEG) based hydrogel, a dextran hydrogel, and a polyelectrolyte charge gradient. Our results show that the PEG-based hydrogel is very well suited for use as a platform in protein immobilization in an array format, owing to the very low unspecific binding. In addition, well defined microarray templates were designed by patterning of hydrophobic barriers on dextran and monolayer surfaces. A polypeptide affinity microarray was further designed and immobilized on such a patterned monolayer substrate, in order to demonstrate the potential of analyte quantification with high sensitivity over a large dynamic range.Furthermore, iSPR was combined with electrochemistry to enable laterally resolved studies of electrochemical surface reactions. Using this combination, the electrochemical properties of surfaces patterned with self assembled monolayers can be studied in parallel, with a spatial resolution in the µm regime. We have also employed electrochemistry and iSPR for the investigation of potential and current density gradients on bipolar electrodes.

1. Protein Microarrays on Carboxymethylated Dextran Hydrogels: Immobilization, Characterization and Application
Open this publication in new window or tab >>Protein Microarrays on Carboxymethylated Dextran Hydrogels: Immobilization, Characterization and Application
2004 (English)In: Microchimica Acta, ISSN 0026-3672, E-ISSN 1436-5073, Vol. 147, no 1-2, p. 21-30Article in journal (Refereed) Published
##### Abstract [en]

Tetraoctadecylammonium bromide (TOAB, (CH3(CH2)17)4N+Br) has been used to print temporary hydrophobic barriers on carboxymethylated dextran (CMD) hydrogels to create a generic platform for protein microarray applications. The primary reason for printing temporary hydrophobic barriers is to prevent cross-contamination and overflow during microdrop dispensing. Equally important is to eliminate the risk for non-specific binding to the barriers during analyte exposure. This has been accomplished by introducing a regeneration step that removes the barriers after ligand immobilization. The overall fabrication process was characterized by microscopic wetting, atomic force microscopy, imaging ellipsometry, fluorescence microscopy, surface plasmon microscopy and biospecific interaction analysis. A series of model proteins including transferrin, Protein A, anti-myoglobin and bovine serum albumin was spotted into the TOAB-defined areas under different experimental conditions, e.g. at increased humidity and reduced substrate temperature or with glycerol as an additive in the protein solution. Much emphasis was devoted to studies aiming at exploring the homogeneity and activity of the immobilized proteins. The printed barriers were removed after protein immobilization using tert-n-butyl alcohol (TBA). TBA was found to be a very efficient agent as compared to previously used salt regeneration solutions, and the regeneration time could be reduced from 30 to 10 minutes. Finally, the potential of using the well established CMD hydrogel chemistry as a platform for protein microarrays was exploited using surface plasmon microscopy.

##### Keywords
Reversible hydrophobic barrier, microcontact printing, piezodispensing, protein microarrays, surface plasmon microscopy
##### National Category
Other Basic Medicine
##### Identifiers
urn:nbn:se:liu:diva-14919 (URN)10.1007/s00604-004-0223-5 (DOI)
Available from: 2008-09-30 Created: 2008-09-30 Last updated: 2018-01-13
2. Imaging SPR for detection of local electrochemical processes on patterned surfaces
Open this publication in new window or tab >>Imaging SPR for detection of local electrochemical processes on patterned surfaces
2008 (English)In: Sensors and actuators. B, Chemical, ISSN 0925-4005, E-ISSN 1873-3077, Vol. 134, no 2, p. 545-550Article in journal (Refereed) Published
##### Abstract [en]

Imaging surface plasmon resonance (iSPR) was used in conjunction with voltammetry to investigate the possibility of detecting local electrochemical processes in situ on chemically modified electrodes. More specifically, a pattern of self-assembled monolayers (SAMs) of thiocholesterol and 1-hexadecanethiol was microcontact printed on gold substrates, and the blocking characteristics on different parts of the pattern were investigated. The SPR images reflected the changes in the refractive index over the working electrode due to electrochemical processes, which in the present case showed the ability of the SAMs to impede faradaic reactions. The results show that differences in packing densities or porosity of SAMs in different regions of a patterned surface can be visualized as electrochemical images using iSPR. The strength of utilizing an optical detection method for electrochemical characterization lies in the ability to achieve lateral resolution in real-time. Electrochemical reactions can also be used to enhance the contrast in SPR images of thin layers of components with similar thicknesses and refractive indices.

##### Keywords
Imaging surface plasmon resonance, Microcontact printing, Local electrochemical analysis, Surface analysis
##### National Category
Inorganic Chemistry
##### Identifiers
urn:nbn:se:liu:diva-14884 (URN)10.1016/j.snb.2008.05.042 (DOI)
Available from: 2008-09-29 Created: 2008-09-29 Last updated: 2017-12-13
3. Formation of Molecular Gradients on Bipolar Electrodes
Open this publication in new window or tab >>Formation of Molecular Gradients on Bipolar Electrodes
2008 (English)In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 47, no 16, p. 3034-3036Article in journal (Refereed) Published
##### Keywords
Bipolar electrodes, electrochemistry, imaging, molecular gradients, surface chemistry
##### National Category
Inorganic Chemistry
##### Identifiers
urn:nbn:se:liu:diva-14881 (URN)10.1002/anie.200705824 (DOI)
Available from: 2008-09-29 Created: 2008-09-29 Last updated: 2017-12-13Bibliographically approved
4. Gradient Hydrogel Matrix for Microarray and Biosensor Applications: An Imaging SPR Study
Open this publication in new window or tab >>Gradient Hydrogel Matrix for Microarray and Biosensor Applications: An Imaging SPR Study
2009 (English)In: Biomacromolecules, ISSN 1525-7797, E-ISSN 1526-4602, Vol. 10, no 1, p. 142-148Article in journal (Refereed) Published
##### Abstract [en]

A biosensor matrix based on UV-initiated graft copolymerized poly(ethylene glycol) methacrylate and 2-hydroxyethyl methacrylate has been studied using imaging surface plasmon resonance (iSPR). By using a photo mask and a programmable shutter to vary the exposure time laterally, a gradient of matrix spots with physical thicknesses ranging from a few to tens of nanometers was generated. To maximize the dynamic range, imaging SPR was employed in wavelength interrogation mode. By finding the minimum in the reflectance spectra from each pixel of an image, SPR wavelength maps were constructed. The shift in SPR wavelength upon biospecific interaction was then measured both as a function of matrix thickness and composition. The performance of the matrix was evaluated in terms of immobilization of human serum albumin, biomolecular interaction with its antibody, and nonspecific binding of human fibrinogen. In addition, a low molecular weight interaction pair based on a synthetic polypeptide and calmodulin was also studied to explore the size selectivity of the hydrogel matrix. Our results show that the gradient matrix exhibits excellent properties for quick evaluation and screening of optimal hydrogel performance. The mixed hydrogel matrices display very low levels of nonspecific binding. It is also evident that the low molecular weight calmodulin is capable of freely diffusing and interacting throughout the entire hydrogel matrix, whereas the much larger albumin and its corresponding antibody, in particular, are partly/completely hindered from penetrating the interior of the matrix. This size-selectivity is attributed to a significant UV-initiated cross-linking or branching of the matrix during fabrication and/or protein mediated multipoint attachment during immobilization.

##### National Category
Natural Sciences
##### Identifiers
urn:nbn:se:liu:diva-16523 (URN)10.1021/bm801029b (DOI)
Available from: 2009-01-30 Created: 2009-01-30 Last updated: 2017-12-14
Open this publication in new window or tab >>Lateral Control of Protein Adsorption on Charged Polymer Gradients
2009 (English)In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 25, no 6, p. 3755-3762Article in journal (Refereed) Published
##### Abstract [en]

This work describes the fabrication, characterization, and protein adsorption behavior of charged polymer gradients. The thin gradient films were fabricated by a two-step technique using UV-initiated free-radical polymerization in a reactor with a moving shutter. A homogeneous layer of cationic poly(2-aminoethyl methacrylate hydrochloride) was first formed, followed by a layer of oppositely charged poly(2-carboxyethyl acrylate) with a continuously increasing thickness. Adsorption from protein solutions as well as human blood plasma was investigated by imaging surface plasmon resonance and infrared microscopy. The results showed excessive protein adsorption in the areas where one of the polymers dominated the composition, while there was a clear minimum at an intermediate position of the gradient. The charge of the surface was estimated by direct force measurements and found to correlate well with the protein adsorption, showing the lowest net charge in the same area as the protein adsorption minimum. We therefore hypothesize that a combination of the charged polymers, in the right proportions, can result in a protein-resistant surface due to balanced charges.

##### National Category
Natural Sciences
##### Identifiers
urn:nbn:se:liu:diva-17501 (URN)10.1021/la803443d (DOI)
Available from: 2009-03-27 Created: 2009-03-27 Last updated: 2017-12-13
6. A multiple-ligand approach to extending the dynamic range of analyte quantification in protein microarrays
Open this publication in new window or tab >>A multiple-ligand approach to extending the dynamic range of analyte quantification in protein microarrays
2009 (English)In: Biosensors and bioelectronics, ISSN 0956-5663, Vol. 24, no 8, p. 2458-2464Article in journal (Refereed) Published
##### Abstract [en]

This work describes a concept for extending the dynamic range of quantification in an affinity biosensor assay by using a set of ligands with different affinities toward a common analyte. For a demonstration of the principle, three synthetic, biotinylated polypeptides capable of binding a model protein analyte with different affinities (10-9 M ≤ Kd ≤ 10-7 M) were immobilized in a microarray format on a gold slide covered with an oligo(ethylene glycol)-containing alkane thiolate self-assembled monolayer. For controllable immobilization, coupling was mediated by the biotinneutravidin interaction. A five-element affinity array, comprising single-peptide spots as well as spots where peptides were immobilized in mixtures, was realized by means of piezodispensation. Imaging surface plasmon resonance was used to study binding of the analyte to the different spots. The lower limit of quantification was ~3 nM and the corresponding upper limit was increased by more than an order of magnitude compared to if only the highest-affinity ligand would have been used. Affinity array sensors with multiple ligands for each analyte are particularly interesting for omitting dilution steps and providing highly accurate data in assays where several analytes such as disease biomarkers with extremely variable concentrations are quantified in parallel.

##### Keywords
Imaging surface plasmon resonance, Biosensor, Affinity microarray, Analyte quantification, Synthetic polypeptide
##### National Category
Chemical Sciences
##### Identifiers
urn:nbn:se:liu:diva-14922 (URN)10.1016/j.bios.2008.12.030 (DOI)
Available from: 2008-09-30 Created: 2008-09-30 Last updated: 2015-05-29
• 44.
Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering.
Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering. Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering. Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering.
A multiple-ligand approach to extending the dynamic range of analyte quantification in protein microarrays2009In: Biosensors and bioelectronics, ISSN 0956-5663, Vol. 24, no 8, p. 2458-2464Article in journal (Refereed)

This work describes a concept for extending the dynamic range of quantification in an affinity biosensor assay by using a set of ligands with different affinities toward a common analyte. For a demonstration of the principle, three synthetic, biotinylated polypeptides capable of binding a model protein analyte with different affinities (10-9 M ≤ Kd ≤ 10-7 M) were immobilized in a microarray format on a gold slide covered with an oligo(ethylene glycol)-containing alkane thiolate self-assembled monolayer. For controllable immobilization, coupling was mediated by the biotinneutravidin interaction. A five-element affinity array, comprising single-peptide spots as well as spots where peptides were immobilized in mixtures, was realized by means of piezodispensation. Imaging surface plasmon resonance was used to study binding of the analyte to the different spots. The lower limit of quantification was ~3 nM and the corresponding upper limit was increased by more than an order of magnitude compared to if only the highest-affinity ligand would have been used. Affinity array sensors with multiple ligands for each analyte are particularly interesting for omitting dilution steps and providing highly accurate data in assays where several analytes such as disease biomarkers with extremely variable concentrations are quantified in parallel.

• 45.
Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
Linköping University, Department of Physics, Chemistry and Biology, Applied Physics . Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
Imaging SPR for detection of local electrochemical processes on patterned surfaces2008In: Sensors and actuators. B, Chemical, ISSN 0925-4005, E-ISSN 1873-3077, Vol. 134, no 2, p. 545-550Article in journal (Refereed)

Imaging surface plasmon resonance (iSPR) was used in conjunction with voltammetry to investigate the possibility of detecting local electrochemical processes in situ on chemically modified electrodes. More specifically, a pattern of self-assembled monolayers (SAMs) of thiocholesterol and 1-hexadecanethiol was microcontact printed on gold substrates, and the blocking characteristics on different parts of the pattern were investigated. The SPR images reflected the changes in the refractive index over the working electrode due to electrochemical processes, which in the present case showed the ability of the SAMs to impede faradaic reactions. The results show that differences in packing densities or porosity of SAMs in different regions of a patterned surface can be visualized as electrochemical images using iSPR. The strength of utilizing an optical detection method for electrochemical characterization lies in the ability to achieve lateral resolution in real-time. Electrochemical reactions can also be used to enhance the contrast in SPR images of thin layers of components with similar thicknesses and refractive indices.

• 46.
Wayne State University, MI 48202 USA.
University of Iceland, Iceland; Stockholm University, Sweden. Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering. University of Utah, USA. Ruhr University of Bochum, Germany. Wayne State University, USA. University of Cambridge, England. University of Cambridge, England. University of Utah, USA. University of Calif San Diego, USA.
Modeling Molecular Interactions in Water: From Pairwise to Many Body Potential Energy Functions2016In: Chemical Reviews, ISSN 0009-2665, E-ISSN 1520-6890, Vol. 116, no 13, p. 7501-7528Article, review/survey (Refereed)

Almost 50 years have passed from the first computer simulations of water, and a large number of molecular models have been proposed since then to elucidate the unique behavior of water across different phases. In this article, we review the recent progress in the development of analytical potential energy functions that aim at correctly representing many-body effects. Starting from the many-body expansion of the interaction energy, specific focus is on different classes of potential energy functions built upon a hierarchy of approximations and on their ability to accurately reproduce reference data obtained from state-of-the-art electronic structure calculations and experimental measurements. We show that most recent potential energy functions, which include explicit short-range representations of two-body and three-body effects along with a physically correct description of many-body effects at all distances, predict the properties of water from the gas to the condensed phase with unprecedented accuracy, thus opening the door to the long-sought "universal model" capable of describing the behavior of water under different conditions and in different environments.

• 47.
Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, The Institute of Technology.
Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, The Institute of Technology.
Polaron stability in molecular semiconductors: theoretical insight into the impact of the temperature, electric field and the system dimensionality2015In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 14, p. 8973-8982Article in journal (Refereed)

A semi-empirical Holstein-Peierls model is used to study the temperature effects on the polaron stability in organic semiconductors at a molecular scale. The approach takes into account both intra- and intermolecular electron-lattice interactions and is aimed at describing charge transport in the system. Particularly, we present a systematic numerical investigation to characterize the influence of both temperature and electric field on the stability as well as mobility of the polaron. It is found that the parameter space for which the polaron is dynamically stable is quite limited and the variations in some of these parameters strongly depend on the temperature. The electric field can play a role in further localizing the charge causing a compression of the lattice distortions associated with the polaron, increasing thereby its stability, up to a field strength of approximately 2.0 mV angstrom(-1). Considering field strengths higher than this critical value, the polaron is annihilated spreading charge through the lattice. Furthermore, we have studied the polaron mobility as a function of the anisotropy of the system, going from a one-dimensional system via a highly anisotropic two-dimensional system to a uniform two-dimensional system. There is a clearly observed mobility edge for the polaron; it exhibits a high mobility in the one-dimensional system but as the coupling in the second dimension is turned on the polaron slows down and becomes immobile in the uniform system. The results provided by this transport mechanism are in good agreement with experimental observations and may provide guidance to improve the charge transport in organic optoelectronic devices.

• 48.
Dundalk Inst Technol, Ireland.
Univ Limerick, Ireland. Univ Limerick, Ireland. Univ Limerick, Ireland. Linköping University, Department of Science and Technology, Physics and Electronics. Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering. Dundalk Inst Technol, Ireland.
Redox switching of polyoxometalate-doped polypyrrole films in ionic liquid media2018In: Electrochimica Acta, ISSN 0013-4686, E-ISSN 1873-3859, Vol. 265, p. 254-258Article in journal (Refereed)

The surface immobilization of the parent Dawson polyoxometalate (POM) as a counter-ion for the electropolymerization of polypyrrole (PPy) or as an electrode-adhered solid was utilized for voltammetric studies of the surface adhered POM in room temperature ionic liquids (RTIL). Illustrating the efficiency of intermediate stabilization, voltammetry at POM-modified electrodes in a PF6-based RTIL revealed richer redox behaviour and higher stabilization in comparison with aqueous electrolytes and with BF4-based RTIL, respectively. High stability of the POM-doped PPy towards continuous charge-discharge voltammetric redox cycles was confirmed by minor changes in film morphology observed after the cycling in RTILs. (c) 2017 Elsevier Ltd. All rights reserved.

The full text will be freely available from 2019-12-15 13:11
• 49.
IIUM, Malaysia.
IIUM, Malaysia. IIUM, Malaysia. Linköping University, Department of Physics, Chemistry and Biology, Biosensors and Bioelectronics. Linköping University, Faculty of Science & Engineering.
Modeling of a Novel Biosensor with Integrated Mass and Electrochemical Sensing Capabilities2016In: 2016 IEEE EMBS CONFERENCE ON BIOMEDICAL ENGINEERING AND SCIENCES (IECBES), IEEE , 2016, p. 420-425Conference paper (Refereed)

Rapid development in technology and society has generated diverse developments in many fields including biosensors in healthcare application. Here, the design of integrated biosensor comprises mass sensing (Quartz Crystal Microbalance) and electrochemistry sensing (Electrochemical Impedance Spectroscopy, EIS and Cyclic Voltammetry, CV) will be presented. The integrated sensor system is developed based on the innovative use of the top electrode of a quartz crystal microbalance (QCM) resonator as a working electrode for the electrochemistry technique. Integration of QCM with the electrochemistry technique is realized by fabricating a semicircular counter electrode near the upper electrode on the same side of the quartz crystal. CV and EIS measurement was conducted using finite element modeling, COMSOL (TM) 5.2 with the probe marker of 1 mmol L-1 of [Fe(CN)(6)](3-/4-). CV test was done to study the effect between increasing scan rate and peak current (anodic and cathodic) in observing the reversible electrochemical process. This observation is crucial in ensuring the electrochemical processes follow the Randles-Sevcik equation in characterizing the platform changes behavior. Later, EIS test was performed in order to measure the radius of the semicircle which reflects the charge transfer resistance (R-CT) of the redox marker. To show the effectiveness of this sensor, gold immobilization surface was electrochemically simulated and reported. Thus, an ultra-sensitive biosensor that capable to produce multi-analysis in the detection of biological targets in terms of electrochemical change of electrode interfaces, which is the crucial step towards the engineering of advanced bioelectronics.

• 50.
Huazhong University of Science and Technology, Peoples R China.
Huazhong University of Science and Technology, Peoples R China. Huazhong University of Science and Technology, Peoples R China. Huazhong University of Science and Technology, Peoples R China. Wuhan Institute Technology, Peoples R China. Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, Faculty of Science & Engineering. Huazhong University of Science and Technology, Peoples R China; Chinese Academic Science, Peoples R China.
Honeycomb-inspired design of ultrafine SnO2@C nanospheres embedded in carbon film as anode materials for high performance lithium- and sodium-ion battery2017In: Journal of Power Sources, ISSN 0378-7753, E-ISSN 1873-2755, Vol. 359, p. 340-348Article in journal (Refereed)

Tin oxide (SnO2) has been considered as one of the most promising anodes for advanced rechargeable batteries due to its advantages such as high energy density, earth abundance and environmental friendly. However, its large volume change during the Li-Sn/Na-Sn alloying and de-alloying processes will result in a fast capacity degradation over a long term cycling. To solve this issue, in this work we design and synthesize a novel honeycomb-like composite composing of carbon encapsulated SnO2 nanospheres embedded in carbon film by using dual templates of SiO2 and NaCl. Using these composites as anodes both in lithium ion batteries and sodium-ion batteries, no discernable capacity degradation is observed over hundreds of long term cycles at both low current density (100 mA g(-1)) and high current density (500 mA g(-1)). Such a good cyclic stability and high delivered capacity have been attributed to the high conductivity of the supported carbon film and hollow encapsulated carbon shells, which not only provide enough space to accommodate the volume expansion but also prevent further aggregation of SnO2 nanoparticles upon cycling. By engineering electrodes of accommodating high volume expansion, we demonstrate a prototype to achieve high performance batteries, especially high-power batteries. (C) 2017 Elsevier B.V. All rights reserved.

The full text will be freely available from 2019-06-09 14:10
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