Introduction: Clostridium thermocellum is considered a model organism for consolidated bioprocessing, due to its ability to hydrolyze lignocellulosic biomass more efficiently than many other organisms and to produce ethanol.In order to meet the industrial requirements of ethanol yield and titer, metabolic engineering efforts have been made resulting in a strain that successfully displays increased ethanol yield with reduced amount of some byproducts.However, the ethanol yield in this engineered strain still does not meet the industrial requirements and significant amounts of amino acids are still produced. To attempt to decrease the level of amino acid excretion intended to improve the ethanol yield in C. thermocellum, it is essential to understand its metabolism and how it is affected by different cultivation conditions and mediumcompositions. This study aimed to gain an insight in how carbon- and nitrogenlimitation affect amino acid excretion in C. thermocellum, with the hypothesisthat excess of carbon and nitrogen yields more amino acid excretion. Methods: Mass-balance based calculations of rates and yields were used to analyze the metabolism of a wild-type of C. thermocellum (DSM 1313) grownanaerobically in carbon- or nitrogen-limiting chemostats. For this, Low-Carbonmedium containing, respectively, cellobiose (5 g/L) and urea (0.15 g/L) as the limiting nutrient was used. Both cultivations were performed at 55 °C, pH 7.0and 400 RPM shaking at a dilution rate of 0.1 h-1.Conclusions: Considering yields of total amino acids excreted in both limitations, it was hypothesized that C. thermocellum exploited the amino acid excretion to maintain carbon balance around the pyruvate node caused by excess of the carbon. Based on yield of valine excreted in particular, it was hypothesized that amino acid excretion was used to maintain redox balance in the metabolism of C. thermocellum, where malate shunt could play a major role.However, results of the Carbon-limitation did not allow any conclusion of nitrogen excess having an effect on amino acid excretion in C. thermocellum.

Due to concerns for climate change and future supply of phosphorus fertilizer within agriculture, there has been an increased interest in the combustion of phosphorus containing waste residues and opportunity biomass fuels. Previous research has shown that during combustion, phosphorus has large impact on ash transformation reactions and may decrease or increase ash-related problems such as slag formation and bed agglomeration. This is a serious concern if new types of biomass are to be added for heat and power production. Additionally, plant studies and leaching tests of P-rich biomass ash indicate that the plant availability of phosphorus varies greatly with its association in the ash. As such, the ash transformation behavior of phosphorus is of great importance for the success of such ventures. While several studies have been made on the behavior of phosphorus during combustion, no comprehensive study has been made evaluating the effect of fuel composition and combustion conditions. In this work, the behavior of phosphorus was determined for a wide range of fuels and combustion conditions. More specifically, the objective was to determine (i) the effect of fuel ash composition and combustion technologies on the fate of phosphorus during combustion, (ii) investigate potential difference in the behavior of phosphorus during combustion of sewage sludge and plant based biomassand (iii)the effect of phosphorus on slag formation and bed agglomeration for the co-combustion of a wide range of plant based biomasses. The investigation was carried out by comparing experimental data gathered from the combustion of 26different biomass fuelsor fuel blends in a bench scale bubbling fluidized bed (5 kW, 18 experiments), an underfed pellet burner (20kW, 10 experiments) and a swirling powder burner (150 kW, 7 experiments). This included chemical characterization of bed ash, bottom ash and fly ash fractions by X-ray diffraction (XRD), scanning electron microscopy coupled with energy dispersive spectroscopy (SEM-EDS) in addition to qualitative measures of slagging-and bed agglomeration tendencies. It was found that phosphorus, irrespective of combustion technology and fuel composition, was mainly found in bed-, and bottom ash fractions and/or coarse fly ash fractions (>1μm). Based on the crystalline phase composition of the phosphates found in bed-, bottom-and coarse fly ash samples, phosphate speciation was correlated to the molar ratio between P, Ca and Mg for all three combustion technologies. Based on these results, it would be possible to control the behavior of phosphorus during combustion and the plant availability of phosphates in biomassash by designing fuel blends based on their fuel ash composition. In fluidized bed combustion, it was found that for similar combustion conditions and fuel ash compositions (with respect to K, Ca and P), the speciation of phosphorus in coarse ash fractions was significantly different from experiments with plant based biomass compared to sewage sludge. Unlike ash from plant based biomass, the crystalline phase composition of ash from sewage sludge did not change with the relative concentration of K, Ca andP in the fuel. The results suggest that the reaction pathway of phosphorus during combustion of sewage sludge is different to plant based biomass due to difference in the association of phosphorus in the fuel. The effect of phosphorus on slag formation and bed agglomeration in biomass combustion was mainly related to the relative fuel ash concentration of K, Ca, Mg, Si and P. In fluidized bed combustion, P contributes to the formation of agglomerates through the melt induced mechanism, through complex interaction with K, Ca, Mg and Si. Similarly, in fixed bed combustion the composition of slag indicatedthatslag formation involves the formation of P and Si rich ash melt with a varying content of K, Ca and Mg. In both cases, the severity of problems was related to the melting behavior of the (CaO,MgO)-K2O-(SiO2,P2O5) multicomponent system.

No description available.

Two dimensional (2D) materials have received growing interest because of their unique properties compared to their bulk counterparts. Graphene is the archetype 2D solid, but other materials beyond graphene, such as MoS2 and BN have become potential candidates for several applications. Recently, a new family of 2D materials of early transition metal carbides and carbonitrides (Ti2CTx, Ti3C2Tx, Ti3CNTx, Ta4C3Tx, and more), labelled MXenes, has been discovered, where T stands for the surface-terminating groups. Before the present work, MXenes had only been synthesized in the form of exfoliated and delaminated powders, which is not suitable for electronic applications. In this thesis, I demonstrate the synthesis of MXenes as epitaxial thin films, a more suitable form for electronic and photonic applications. Results show that 2D epitaxial Ti3C2Tx films - produced by HF and NH4HF2 etching of magnetron sputter-grown Ti3AlC2 - exhibit metallic conductive behaviour down to 100 K and are 90% transparent to light in the visible-infrared range. The results from this work may open the door for MXenes as potential candidates for transparent conductive electrodes as well as in electronic, photonic and sensing applications. MXenes have been shown to intercalate cations and molecules between their layers that in turn can alter the surface termination groups. There is therefore a need to study the surface chemistries of synthetized MXenes to be able to study the effect of intercalation as well as altering the surface termination groups on the electronic structure and chemical states of the elements present in MXene layers. X-ray Photoelectron Spectroscopy (XPS) in-depth characterization was used to investigate surface chemistries of Ti3C2Tx and Ti2CTx. This thesis includes the discussion of the effect of Ar+ sputtering and the number of layers on the surface chemistry of MXenes. This study serves as a baseline for chemical modification and tailoring of the surface chemistry groups to potential uses and applications. New MXene phases, Nb2CTx and V2CTx, are shown in this thesis to be produced from HF chemical etching of Nb2AlC and V2AlC powders. Characterization of the produced MXenes was carried out using Scanning Electron Microscopy (SEM), X-Ray Diffraction (XRD), Transmission Electron Microscope (TEM) and XPS. Nb2CTx and V2CTx showed promising performance as electrodes for Li-ion batteries. In this thesis, electrochemical etching was used in an attempt to produce 2D metal carbides (MXene) from their ternary metal carbides, Ti3SiC2, Ti3AlC2 and Ti2AlC MAX phases. MAX phases in the form of highly dense bulk produced by Hot Isostatic Press. Several etching solutions were used such as HF, NaCl and HCl. Unlike the HF chemical etching of MAX phases, which results in MXenes, the electrochemical etching resulted in Carbide Derived Carbon (CDC). Here, I show the characterization of the produced CDC using several techniques such as XRD, TEM, Raman spectroscopy, and XPS. Electrochemical characterization was performed in the form of cyclic voltammetry, which sheds light on the etching mechanism. / <p>The series name <em>Linköping Studies in Science and Technology Licentiate Thesis</em> in this publication is incorrect. Correct name is <em>Linköping Studies in Science and Technology. Thesis</em>.</p>

The field of polariton chemistry studies molecules strongly coupled to the light field of optical cavities. The resulting modification of the potential energy landscape has been shown to allow control of the chemical and physical properties of materials and molecular ensembles. In this work, we have studied the theoretical description of molecules interacting with the vacuum field of an optical cavity, derived from the Pauli-Fierz Hamiltonian. We extend the molecular Tavis-Cummings model to include coupling terms arising from the static dipole moments that are present in molecules as well as the dipole self-energy. Since this representation complicates the distinction between photon and matter degrees of freedom, a transformation to the coherent state basis is required. To verify the importance of these additional coupling terms in the molecular model, we simulated the excited state dynamics and spectroscopy of MgH+ molecules resonantly coupled to a cavity vacuum mode. We observe a significant difference in the dynamics when the interaction terms are included individually, compared to a naive molecular Tavis-Cummings model. A reduced effect is obtained when a combined contribution is considered, indicating that considering both terms is essential in the system description. In addition, a strong asymmetry in the spectrum is observed, which can be explained as an influence of the vibrational states and the molecular Franck-Condon factors. To make the analysis of large ensembles computationally accessible, we developed an effective model which is based on a two-level system model.

Biomaterials are essentially synthetic materials that can be adapted to medical and biological applications. To meet the criteria for clinical use, a thorough evaluation of the biological properties of the biomaterials is required. This means that reliable cell cultures (in vitro studies) are needed. The aim of this project has been to build a universal user-friendly biomaterial-on-a-chip system. Using microfluidic system with materials embedded and a control flow on top of biomaterials to perform typical biological characterizations. Ideally, all types of biomaterials could be evaluated using this system by simply changing a few fabrication parameters. Calcium-deficient hydroxyapatite (CDHA), medical-grade titanium alloy (Ti6Al4V) and gelatin have been used as models to test the performance of the system. The results showed that all materials tested could be successfully integrated in the system. Three characterizations, stability test, drug release and protein adsorption, were studied using this system. The drug release pattern and protein adsorption behavior under the dynamic conditions were different in comparison with static conditions. This is significant since it proves that the outcome of characterization studies is linked to the test method used.

Microbiota’s influence on human health and disease is a growing research field including neurodegenerative diseases such as Parkinson’s disease (PD). The disease symptoms involve movement disorder, manifesting tremor, rigidity, bradykinesia and instability. At the molecular level, the disease exhibits; aggregated alfa-synuclein trapped inside neurons in the brain, in so called Lewy bodies, and loss of dopaminergic neurons in substantia nigra.The working hypothesis of this project is that human microbiome composition and interactions mediate environment and lifestyle influences on disease expression of PD. To validate this hypothesis, a mouse model (C57BL/J6 mice) was used. Two knock-in mouse lines were used; one carrying the wild type, human Leucine-Rich-Repeat-Kinase 2 (LRRK2) and the second carrying the most common Caucasian LRKK2/G2019S mutant. LRRK2 is a tyrosine kinase known to interact with Nucleotide-binding oligomerization domain-containing protein 2 (NOD2), a cytosolic microbe peptide sensing receptor. To establish the tools and knowledge required for the analyses, the initial part of the project was to analyze the expression levels of LRRK2 and NOD2 in wild-type C57BL/J6 mice in specific pathogen free (SPF), and mice devoid of exposure to living microbes, so called germ-free (GF) mice. Along with this analyse, expression levels of the transgenic LRKK2 proteins in the genetically modified mice was monitored. The focus was on the following tissues: striatum, midbrain, hippocampus, small intestine and large intestine and applied immune-histochemistry (IHC) combined with Western blot analysis.Results; significantly higher expression levels of LRRK2 were observed in microbe exposed mice versus GF mice with the exception of the large intestine which showed the opposite. Moreover, NOD2 showed a trend of lower expression levels in all brain GF areas tested with the exception to striatum. For the transgenic human knock-in LRKK2 proteins, increased expression of hLRKK2 were observed in striatum and large intestine compared to G2019S. Reduced hLRKK2 expression was observed in midbrain. The results suggest a strong correlation between LRRK2 expression and the gut microbiota and a need for continued research to better understand the role our indigenous microbiome may play in onset/progression of PD. / Mikroflorans betydelse för människors hälsa och sjukdomar är ett framväxande och banbrytande forskningsfält. Forskning har inte bara visat på mikroflorans betydelse för friska tillstånd utan också för utveckling av sjukdomar, så som Parkinsons sjukdom (PD). PD är en neurodegenerativ sjukdom med symptom som innefattar rörelsestörningar; tremor, stelhet, bradykinesi och instabilitet. På molekylär nivå ses aggregerat alfa-synuclein inuti neuroner i hjärnan, i så kallade Lewy-kroppar samt förlust av dopaminerga neuroner i substantia nigra.&lt;/p&gt;&lt;p&gt;Hypotesen som utformats i detta projekt utgick ifrån att mikroflorans sammansättning och interaktioner, medierar miljö- och livsstilsfaktorer vilket leder till utveckling av PD. För att testa hypotesen användes musmodellen C57BL / J6 i vildtyp form samt i transgen form. De transgena formerna bestod av två olika knock-in modeller; en som bär den vilda typen av humant Leucin-Rich-Repeat-Kinase 2 (hLRRK2) och en som bär den vanligaste kaukasiska mutationen av samma protein, G2019S. LRRK2 är ett tyrosin kinas som interagerar med Nucleotide-binding-oligomerization-domain-containing-protein 2 (NOD2), en cytosolisk mikrobpeptidreceptor. Analyser av LRRK2 och NOD2 utfördes på vildtypen av C57BL / J6-möss i specifikt patogenfria (SPF) förhållanden samt på möss som saknar exponering för levande mikrober, så kallade bakteriefria (GF). I de transgena mössen analyserades de genetiskt modifierade LRKK2-proteinerna, hLRRK2 och G2019S, samt NOD2 i möss i SPF förhållanden. Följande vävnader undersöktes; striatum, mellanhjärnan, hippocampus, tunntarmen och tjocktarmen med immunhistokemi (IHC) i kombination med Western blot-analys.&lt;/p&gt;&lt;p&gt;Resultaten visade på en betydligt högre uttrycksnivå av LRRK2 i mikrobexponerade möss jämfört med GF möss med undantag för tjocktarmen där resultatet visade det motsatta.  Dessutom visade resultaten en trend på lägre uttrycksnivåer av NOD2 i alla analyserade områden i hjärnan med undantag för striatum. För de transgena humana knock-in-LRKK2-proteinerna observerades ökat uttryck av LRKK2 i striatum och tjocktarm jämfört med G2019S, samt reducerat LRKK2 uttryck i mellanhjärnan. Resultaten visar på en stark korrelation mellan LRRK2-uttryck och tarmens mikroflora och implicerar förbättrad förståelse av mikroflorans roll i början och under progression av PD.

In this thesis, a section of a lithium ion battery module, including five cells and an indirect liquid cooling system, was modelled in COMSOL Multiphysics 5.3a. The purpose of this study was to investigate the thermal properties of such a model, including heat generation per cell and temperature distribution. Additionally, the irreversible and reversible heat generation, the cell voltage and the internal resistance were investigated. The study also includes the relation between heat generation and C-­‐rates, and an evaluation of COMSOL Multiphysics 5.3a as a software. It was found that having liquid cooling is beneficial for the thermal management, as the coolant flow helps to transfer away the heat generated within the battery. The results also show that it is important to not go below a set cell voltage at which the cell is considered fully discharged. If a control mechanism to stop the battery is not implemented, the generated heat, and consequently the temperature, increase drastically. COMSOL Multiphysics 5.3a was considered a suitable software for the modelling. For future research it is of interest to expand the model to a full scale module to fully investigate the temperature distribution where more cells are being cooled by the same coolant loop.

Clay minerals are planar hydrous aluminium phyllosilicates with a high surface area-to-volume ratio. Previous studies have shown that the surface of clay minerals can adsorb DNA, and the amount adsorbed is usually measured by ultraviolet-visible light (UV-Vis) spectroscopy. In this study, a one-pot Fourier transform infrared (FTIR) setup is tested to allow for real-time liquid reaction monitoring. Once the required components are identified, continuous measurement of FTIR spectra can be performed allowing for real-time monitoring of the ongoing reaction without further manual operation. Compared with the existing adsorption quantification methods, the one-pot FTIR is thus simpler and more efficient for studying DNA adsorption to clay. For the interaction to proceed in such a setting, a clay sample must be made into a stable thin film in contact with liquid water during the adsorption of DNA. In this study, two types of clay minerals, Montmorillonite and Nontronite, were tested to explore the viability of the one-pot FTIR spectroscopy in monitoring the interaction between DNA and the clays. The results indicated that when the target component in the liquid is sufficient (such as water and clay), one-pot FTIR can be conducted to record its changing concentration as a function of time, except for DNA in the dry-to-wet measurements. This may be due to interference from the DNA being added as a diluted liquid, for FTIR is a water-sensitive technique.

The main objective of the research described in this thesis has been the design and synthesis of inhibitors of the enzyme dihydrofolate reductase (DHFR) intended for local administration and devoid of systemic side-effects. The blocking of the enzymatic activity of DHFR is a key element in the treatment of many diseases, including cancer, bacterial and protozoal infections, and also opportunistic infections associated with AIDS (Pneumocystis carinii pneumonia, PCP). Recent research indicates that the enzyme also is involved in various autoimmune diseases, e.g., rheumatoid arthritis, inflammatory bowel diseases and psoriasis. Many useful antifolates have been developed to date although problems remain with toxicity and selectivity, e.g., the well-established, classical antifolate methotrexate exerts a high activity but also high toxicity. The new antifolates described herein were designed to retain the pharmacophore of methotrexate, but encompassing an ester group, so that they also would serve as substrates for the endogenous hydrolytic enzymes, e.g., esterases. Such antifolates would optimally comprise good examples of soft drugs because they in a controlled fashion would be rapidly and predictably metabolized to non-toxic metabolites after having exerted their biological effect at the site of administration. A preliminary screening of a large series of simpler aromatic esters as model compounds in a biological assay consisting of esterases from different sources was performed. The structural features of the least reactive ester were substituted for the methyleneamino bridge in methotrexate to produce analogues that were chemically stable but potential substrates for DHFR as well as for the esterases. The new inhibitor showed desirable activity towards rat liver DHFR, being only eight times less potent then methotrexate. Furthermore, the derived metabolites were found to be poor substrates for the same enzyme. The new compound showed good activity in a mice colitis model in vivo, but a pharmacokinetic study revealed that the half-life of the new compound was similar to methotrexate. A series of compounds characterized by a high lipophilicity and thus expected to provide better esterase substrates were designed and synthesized. One of these analogues in which three methoxy groups were substituted for the glutamic residue of methotrexate exhibited favorable pharmacokinetics. This compound is structurally similar to another potent DHFR inhibitor, trimetrexate, used in the therapy of PCP (vide supra). The new inhibitor that undergoes a fast metabolism in vivo is suitable as a model to further investigate the soft drug concept.