Rapid and accurate species identification and antibiotic susceptibility testing are of great importance for patients with sepsis and to stop over- and misuse of antibiotics contributing to antibiotic resistance. QuickMIC™ is a rapid antibiotic susceptibility testig system based on a microfluidic technology solution developed by Gradientech that measure MICs on bacteria from positive blood culture bottles. By combining QuickMIC™ with a rapid system for detection and identification, the time to detection, identification and antibiotic susceptibiolity testing could be shortened with days compared to pipelines used today which could mean the difference of life and death for patients. The T2Bacteria® panel and T2Dx® instrument developed by T2 biosystems is an FDA-cleared test for rapid detection and identification of bacteria from whole blood based on magnetic molecular resonance technology. The time to result of the T2Dx® instrument is 3-4 hours and the time to result for QuickMIC™ is 2-4 hours. In this project, the possibilities and benefits of such a pipeline have been studied by comparison to a pipeline typically used today. Time, accuracy and practical aspects have been investigated during the project and the results are promising for future further studies.

Detta arbete är en beställning från Vidilab AB som går ut på att kartlägga resistensmekanismer hos nematoder samt ta fram en resistensassay. Beställningen grundar sig i problematiken kring dagens metoder för resistensbestämning, som går ut på att analysera förekomsten av ägg i avföringen från betande djur innan respektive efter avmaskning. Vidilab efterlyser en molekylär diagnostikmetod för resistensbestämning innan boskapsdjuren behandlas med anthelmintika. Som avgränsning har projektet riktat in sig på resistensmekanismer hos nematoden Haemonchus contortus som i första hand parasiterar får. I projektet har i huvudsak förslag på tre tekniker tagits fram som skulle kunna användas för resistensbestämning hos H. contortus. Dessa tre metoder är allelspecifik PCR, RT-PCR och MALDI-TOF. Slutsatsen i detta projekt är att samtliga av dessa tre metoder har potential som molekylär diagnostikmetod. Dock krävs mer forskning kring H. contortus resistensmekanismer, storskalig sekvensering samt kartläggning av transkriptom och proteomikstudier innan teknikerna kan appliceras som standardiserade diagnostikmetoder.

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Affibody® molecules are small affinity proteins with great opportunities in the application of biotechnological areas. Their popularity as biomolecules in pharmaceutical applications and research entails that the purity of Affibody® molecules is essential for their use as safe medical drugs. Hydrophobic Interaction Chromatography (HIC) is a purification technique that separates molecules based on their inherent difference in hydrophobicity, and the application as a purification strategy for Affibody® molecules may be possible. This thesis investigates the implementation of HIC on Affibody® molecules by screening for differences in binding, recovery, and purity influenced by different parameters, such as resin, pH, salt type, and salt concentration, have on binding, recovery, and purity. HIC presents as a viable purification method where an approximate 97% reduction in Host Cell Proteins was obtained. The yield of the purified product also presented as promising with a recovery of approximately 82%. These results indicate that further investigation and optimization of this technique may benefit the downstream process of the investigated Affibody® molecule.

Molecular electronics is an active research area for the future information technology. The fabrication of basic electronic elements with molecules as the core-operators has been made experimentally in the laboratory in recent years. However, the underlying electron or charge transport mechanisms for most devices are still under debate, Theoretical modelling based on the first-principles methods are expected to play an important role in this field. A generalized quantum chemical approach based on Green's function scattering theory has been developed and applied to two- and three-terminal molecular devices. It allows to study both elastic and inelastic electron scattering at hybrid density functional theory levels. It can treat molecular devices where the metal electrodes and the molecule are either chemically or physically bonded on equal footing. As one of the applications, we have studied the length dependence of electron transport in gold-oligophenylene-gold junctions. We have shown that the experimental results for molecular junctions of oligophenylene with di erent lengths can be well reproduced by hybrid density functional theory calculations. It is also found that the current-voltage characteristics of the junctions depend strongly on the metal-molecule bonding distances. With the help of the calculations, the possible gold-molecule bonding distances in the experimental devices are identi ed. The central focus of this thesis is to study the three-terminal molecular devices, namely the eld e ect transistor (FET). An extension of our quantum chemical approach to FET devices has been made and successfully applied to different FET devices constructed with polymer, small and middle sized conjugated molecules. The experimentally observed conductance oscillation in polymer FET and three orders of magnitude enhancement of the current in electrochemical gated molecular FET have been verified by the calculations. The electron transport mechanisms of these devices are revealed. / QC 20101129

The report examines how the market, as well as purification conditions, forpeptide-oligonucleotide conjugates look like today. These conjugates are intended to be usedin drugs to treat otherwise incurable diseases but so far these types of molecules are still intest-phases and no finished conjugate is on the market yet. However, the drug SRP-5051 is inclinical phase II and it is expected to be seen on the market no earlier than May 2022. Thedrug consists of a phosphorodiamidate morpholino oligomer conjugated to a cationiccell-penetrating peptide. The aim of the project was to gain an understanding of what currentresearch looks like, what types of conjugates seem to be the most promising and whatchallenges there are with these. In addition, various purification possibilities for the mostpromising conjugates were also investigated. The report is a literature study and containsinterviews with experts in the field. The oligonucleotide most likely to occur in a futureconjugate consists of a charge-neutral phosphorodiamidate morpholino oligomer (PMO) orpeptide nucleic acid (PNA), which are spinal modifications that increase stability and affinity.The peptide in such a conjugate needs to perform endocytosis and is therefore expected to becationic. The amount of arginine in the peptide is correlated with both efficiency and toxicity,which is the major challenge of the conjugates today. The purification is performed with acation exchanger where the cationic charge of the peptide is utilized. Elution takes place witha salt gradient, if necessary a secondary purification step in the form of size exclusion is used.

The work presented in the thesis concerned theoretical study of light-matter nonlinear interactions. Two important aspects of such interactions have been examined, namely the nonlinear optical properties of a series of organic charge transfer molecules in solutions induced by the laser light and the propagation of the ultrafast high power laser through the nonlinear molecular medium. Special attention has been paid to understand the solvent effects on the two-photon absorption of a symmetrical diamino substituted distyrylbenzene chromophore, for which time-dependent density functional theory in combination with polarizable continuum model (PCM) have been employed. The dielectric medium alone has a rather small effect both on the bond length alternation and on the one-photon absorption spectrum, but noticeable effects on the two-photon absorption cross section. Both one- and two-photon absorptions are found to be extremely sensitive to the planarity of the molecule. Our calculations indicate that the experimentally observed anomalous solvent effect on the two-photon absorption of dialkylamino substituted distyrylbenzene chromophores can not be attributed to the intrinsic properties of a single molecule and its interaction with solvents. With the same theoretical approaches, two-photon absorption properties of interacting polar chromophores have been investigated to examine the validity of the widely used exciton model. Our first principles calculations have shown that the exciton model offers a conceptually simple interpretation for experimental observations, but is lack of predictability. The second part of the thesis is to investigate the propagation of ultrashort laser pulse through a one-dimensional asymmetric organic molecular medium by solving full Maxwell-Bloch equations using predictor-corrector finite-difference time-domain method. It focuses on the supercontinuum generation of spectra and the formation of attosecond pulses. It is shown that the supercontinuum generation is strongly modulated by both area and width of the pulse, which results from the interference between the splitting pulses in time-domain and is the implication of the time-energy uncertainty relation. The presence of permanent dipole moment in molecular medium has noticeable effects on the supercontinuum generation. Our calculations show that a well-shaped 132 attosecond pulse can be generated from a two femtosecond incoming pulse under certain conditions. Influences of carrier-envelope phase and time-dependent ionization on the spectral and temporal evolutions of the ultrashort pulses have also been discussed. / QC 20101122

The development of computational models for predicting drug solubility has increased drastically during the last decades. Nevertheless these models still have diffculties to estimate the aqueous solubility as accurate as desired. In this thesis di erent aspects that are known to have a large impact on the aqueous solubility of a molecule have been studied in detail using various theoretical methods with intension to provide microscopic view on drug solubility. The rst aspect studied is the hydrogen bond energies. Eight drug molecules have been calculated using density functional theory and the validity of additive model that has often been used in solubility models is examined. The impact of hydrogen bonds in Infrared and Raman spectra of three commonly used drug molecules has also been demonstrated. The calculated spectra are found to be in good agreement with the experimental data. Another aspect that is important in solubility models is the volume that a molecule occupies when it is dissolved in water. The volume term and its impact on the solvation energy has therefore also been calculated using three di erent methods. It was shown that the calculated volume di ered signi cantly dependent on which method that had been used, especially for larger molecules. Most of the solubility models assume the solute molecule to be in the bulk of the solvent. The molecular behavior at the water/gas interface has been investigated to see how it di ers from bulk. It was seen that the concentration close to the interface was almost three times higher than in the bulk. The increase in concentration close to the surface depends on the larger gap between the interface energy and the gas phase energy than between the bulk energy and the gas phase energy. / QC 20101109

In this thesis, quantum chemical methods are used to investigate enzymatic reaction mechanisms. The Density functional theory, in particular the hybrid B3LYP functional, is used to model two enzymes belonging to the tautomerase superfamily; 4-Oxalocrotonate Tautomerase (4-OT) and cis-Chloroacrylic Acid Dehalogenase (cis-CAAD). The methodology is presented and new mechanistic insights for the two enzymes are discussed. For 4-OT, two different models are built and the potential energy curves are computed. This allows the methodology to be evaluated. The results give new insight into the energetics of the 4-OT reaction, indicating that the charge-separated intermediate is quite close in energy to the reactant species. The models also make it possible to perform in silico mutations to investigate the role of active site groups. Excellent agreement is found between the calculations and site-directed mutagenesis experiments, further substantiating the validity of the models. For cis-CAAD, the uncatalyzed reaction is first considered and excellent agreement is found between the calculated barrier and the measured rate constant. The enzymatic reaction is then studied with a quite large active site model and a reaction mechanism is proposed. / QC 20101123

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