Electric propulsion is gaining popularity in space industry. This type of propulsion is replacing chemical propulsion for different maneuvers. But it deeply modifies the ambient plasma that surrounds the satellites and can affect the operation of satellites. Modelling the interactions arising from electric propulsion is then critical. In the frame of SPIS, a simulation software designed to simulate plasma-spacecraft interactions, European Space Agency (ESA) started the AISEPS project which aimed at modelling these interactions. Here, we report the development of new features for SPIS during the last phase of the AISEPS project, how they operate and were tested. Using these developments, a complete spacecraft is modelled and the variation of its floating potential resulting from its solar array rotation is reproduced.

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SMILE (Small Magnetometer In Low-mass Experiment) is a digital fluxgate magnetometer designed with miniaturization as a goal. The instrument is intended asa payload for the Microlink (previously Nanospace) satellite. SMILE operates onsimilar principles as the magnetometer onboard Astrid-2 satellite. The magnetic fieldcomponents are extracted from the pick-up signal by means of digital correlation witha set of reference coefficients. An important difference from the Astrid-2magnetometer is that the digital signal processing previously done in threeprocessors (one for each axis) has been replaced with a single FPGA to achieve asmaller circuit board area. A new miniaturized fluxgate sensor with volumecompensation produced by the Lviv Center of Institute of Space Research is used inthe design. A prototype board was designed and built at the Royal Institute of Technology.Gateware suitable for calibration has been completed. Gateware for the operationalinstrument is still in its final stage of development.

Diamond like carbon (DLC) is a metastable state of amorphous carbon that has very important and wide-ranging thin film applications. DLC has a strong resemblance to pure diamond and exhibits many traits of real diamond, like mechanical hardness and chemical inertness, but with a drastically lower deposition cost. DLC is characterized by a high fraction of sp3 hybridization. To reach a high fraction of sp3 bonding by sputtering of a graphite target, an energetic ion population and a high ionized flux fraction (Fflux) is beneficial. High-power impulse magnetron sputtering (HiPIMS), an ionized physical vapour deposition technique (iPVD) based on magnetron sputtering, has been shown to produce significantly higher ionized fluxes and more energetic ions compared to the industry standard technique of direct current magnetron sputtering (dcMS). For carbon however, the ionized flux fraction is significantly lower than that of common metal targets like titanium and aluminium, even with HiPIMS. In this thesis the ionization region model is applied to experimental carbon-argon 50 µs HiPIMS discharges at peak current densities of 1, 2 and 3 A/cm2 to investigate why the fraction of sputtered carbon reaching the substrate as ions is so low. The ionized flux fraction of the experimental discharges was measured by an ion meter to be lower than 5 %. From the computational modeling we find that the ionization probability of a carbon neutral (α) increases with increased peak discharge current densities from 40 % at 1 A/cm2 to over 60 % at 3 A/cm2. However, the back attraction probability of carbon ions (β) is high or above 90 %. The model predicts a higher Fflux than measured for all cases. The modeled Fflux values were 6-8 %, 10-13 % and 13-15 % for peak discharge current densities of 1, 2 and 3 A/cm2, respectively. By the time evolution of the particle densities, it is clear that most of the ionization takes place at the end of the pulse and thus the afterglow plays a significant role, especially for shorter pulses. The main conclusion is that the HiPIMS carbon discharge is mainly governed by the argon working gas and shares many traits with a typical working gas recycling process

The bow shock current is hypothesized to connect to the Earth's magnetosphere on open field lines and to contribute as a field aligned current to the polar ionospheric currents. In order to investigate this, two years of AMPERE data are used to compute the average region 1 currents, and average currents within the polar cap boundary, under different interplanetary magnetic field (IMF) clock angles and IMF magnitudes. The average currents are studied for stable IMF conditions. Therefore data is selected if the IMF By and Bz components do not change sign in a 30 minutes time interval to ensure sufficiently stable conditions. In addition, the AMPERE current maps are renormalized and recentered such that the region 1 currents have a fixed extent. These averaged current maps are then used to discuss the sources of the currents in the polar cap and their possible connection to the bow shock current. The currents in the polar ionosphere are found to generally agree with the statistical convection pattern. For a strong east-west IMF there are some discrepancies for the region 0 currents which indicates a possible bow shock current closure. Furthermore there are currents in the polar cap of the northern hemisphere for a strong southward IMF, which however do not have the expected polarity for bow shock current closure. Therefore they must have another, but unknown, origin. In addition, SuperDARN data is used to confirm that currents on the dayside of the polar cap and polwards of the Region 1 currents are on open field lines for a strong eastward or westward IMF. Further investigations are needed to confirm the bow shock closure in the ionosphere. Additional investigations are needed to identify the source of the polar cap currents for a strong southward IMF.

Modern advances in sequencing technologies have enabled exploration of molecular biology at unprecedented scale and resolution. Transcriptome sequencing (RNA-seq), in particular, has been widely adopted as a routine cost-effective method for assaying both genetic and functional characteristics of biological systems with resolution down to individual cells. Clinical research and applications leveraging these technologies have largely targeted tumor biology, where transcriptome sequencing can capture tumor genetic and epigenetic characteristics and aid with understanding the etiology or guide treatments. Specialized computational methods and bioinformatic software tools are essential for processing and analyzing RNA-seq to explore various aspects of tumor biology including driver mutations, genome rearrangements, and aneuploidy. With single cell resolution, such methods can yield insights into tumor cellular composition and heterogeneity. Here, we developed methods and tools to support cancer transcriptome studies for bulk and single cell tumor transcriptomes, focusing primarily on fusion transcript detection and predicting large-scale copy number alternations from RNA-seq. These efforts culminated in the development of STAR-Fusion for fast and accurate detection of fusion transcripts, FusionInspector for further characterizing predicted fusion transcripts and discriminating likely artifacts, and TrinityFusion for de novo reconstruction of fusion transcripts and tumor viruses. We also developed advanced methods for predicting copy number alterations and subclonal architecture from tumor and normal single cell RNA-seq data, as incorporated into our InferCNV software. In addition to these bioinformatic method and software developments, we applied our fusion detection methods to thousands of tumor and normal samples and gain novel insights that should further help guide researchers with clinical applications of fusion transcript discovery.

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In this report we present spacecraft and ground-based observations of magnetosheath jets impacting the magnetosphere, both as a case study and a statistical study. In the case study, jets were detected in the magnetosheath by the Magnetospheric MultiScale mission, MMS. By utilizing a data-based magnetosphericmodel (Tsyganenko T96 [29]), we estimated which jets were likely to impact the magnetopause and where they would do so. We examined ground based magnetometers, GMAGs, at the expected foot-point to the affected magnetic fieldline and compared this with the spacecraft observations. Theoretical transfertimes for a jet to be detectable by GMAGs have been estimated and compared with the observed time delay, from detection to GMAG response, and they were in good agreement for all cases. The times found for this geoeffective responsewere found to be around 1-2 min, and the response in the GMAGs was in the form of a pulse with an amplitude of around 50 nT. We suggest that jets of along enough time duration can be geoeffective in a way that they are detectable at ground level by GMAGs. It was also found that GMAGs fluctuate more during periods containing many detected jets. We performed our statistical study with the intention of comparing fluctuations in GMAG observations during Interplanetary Magnetic Field, IMF, configurations which is suggested to be favorable for jet creation. The IMF observationswas provided by the THEMIS (Time History of Events and Macroscale Interactions during Substorms) spacecraft. This was done by selecting periods of steady IMF with different orientations, and examining the GMAGs observed variations. GMAGs were selected based on a region where most of our foot-points were found in our previous case study. We performed this study over a three year interval, and found that GMAGs observe about 2 nT higher variation, according to their standard deviations, during radial IMF compared to northward IMF. During northward IMF we expect less effects from magnetopause phenomena, thus making it suitable to compare with radial IMF. Our statistical investigation support our findings that magnetosheath jets can be geoeffective in a waythat GMAGs can detect them.

This work is part of a bigger project on analyzing the ionospheric dynamics in the equatorial region using simulations. The main objective of this study is to determine and characterize the parameters needed to trigger instabilities and thus the formation of plasma bubbles. An ambition is to keep the calculations as complete as possible by not oversimplifying the process itself as a classic Rayleigh-Taylor instability and by introducing the more realistic Generalized Eccentric Dipole description of the magnetic field. In this way, we aspire to avoid the neglect of convoluted interactions in the ionospheric system as well as the distorted nature of the geomagnetic field. After an in-depth study of the existing literature and getting to know the data generated by IPIM, I derived the equations describing the relevant physical processes based on fundamental plasma physics. In a MATLAB environment, I proceeded to develop the necessary tools for a computation of the quantities needed in the equations to then assemble and interpret the results for a simple study case. The found growth rate values are high enough and thus the characteristic time for the occurrence of instabilities short enough for them to be the principal process in the examined time and altitude range. It has been verified that the computed growth rate is such that instabilities may occur with a higher probability in the Southern Hemisphere due to the elevated amplitudes and the time delay between the foot points. We managed to derive a complete description of the equatorial ionosphere without using unreasonable approximations and the simplicity of the chosen configuration did not hinder the successful computation of instability seeds. The preparations that I undertook during this internship are an important first step for the subsequent development of the ionospheric model.

Measurements are made to investigate the nature of a fast current disruptionappearing in one of the experimental devices at the Alfven Laboratory. Thedisruption appears when we let the induced electric field ( -vxB) in a transverselymagnetized flowing plasma drive a current between two short circuited plasmaprobes. It is the current measured in the circuit connecting the two probes thatshow the disruptive behaviour. The parameters of the typical disruption are a 5 Adrop in 25 ns.The results of the measurements indicate that the disruption is a relatively generalprocess. Instead of being a consequence of some special detail in the probeconfiguration it turns out to be a process appearing whenever we draw a currentbetween two probes in the plasma.The origin of the disruption is located and it turns out to be at, or at least near,the negatively biased probe.Simultaneous current and plasma density measurements indicate that the currentin the probe circuit generally exceeds the theoretical ion saturation current. Forthis to be possible there has to be some sort of electron emission process present atthe surface of the negatively biased probe. The conclusion is that it is this processthat fails when the current disrupts. Cathode spots are sometimes observed on thenegative probe, and they are believed to be the emission process in question.An analysis of the probe circuit gives that the measured current-voltagebehaviour during a disruption in a good way agrees with the assumption that acathode spot is extinguished at the negatively biased probe. When combining themodel of the circuit with a negative current-voltage characteristic for the cathodespot we get an unstable system. The disruption is believed to reflect this instability.The negative current-voltage characteristic needed to make this descriptionsuccessful is well described by curves found in literature on cathode spots.