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Department of Computer and Systems Sciences

Master thesis.

Master’s programmes at DSV end with a master thesis.

You select and implement relevant scientific methods to write an academic thesis in relation to one of the Department’s research areas. A two-year master thesis consists of 30 credits and a one-year master thesis of 15 credits. You study at a 100 percent study pace for 30 credits work and a 50 percent study pace for a 15 credits work.

• You need to enrol by submitting a project idea before the deadline.
• You need to fulfil the requirements.

It is suggested for master students to write in pairs of two but you are also allowed to work on your own.

Master thesis during the spring semester

• Deadline for your project idea is in the second half of November (submission period starts in the beginning of November and ends in the second half of November).
• The course starts in the middle of January.

Find all information about writing the master thesis, requirements and deadline under "Thesis" in iLearn.

Information about master thesis in iLearn

Writing a thesis in collaboration with companies or orgainsations

Communication with supervisors, reviewers, opposition and examiners is carried out in the SciPro Projects system.

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Thesis support answers questions and helps with everything related to the master thesis and SciPro.

Last updated: June 1, 2023

Source: Department of Computer and Systems Sciences, DSV

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• Fabian Pokorny A microwave dressed Rydberg ion PhD thesis Stockholm University (2020). Download from Diva .
• Chi Zhang Fast and Scalable Entangling Gate in Trapped Ions via Rydberg Interaction PhD thesis Stockholm University (2020). Download from Diva .
• Gerard Higgins A Single Trapped Rydberg Ion PhD thesis Stockholm University and University of Innsbruck (2018) as  cotutelle. Selected for the Springer thesis award as outstanding PhD thesis from around the world and across the physical sciences. Download from Diva or Springer .

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• Shalina Salim Towards a high fidelity Rydberg interaction gate Licentiate thesis Stockholm University (2022). Download from Diva .
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• Fabian Pokorny Microwave dressing of a trapped strontium Rydberg ion Licentiate thesis Stockholm University (2019). Download from Diva .

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Stephan, Katharina

Publications (6 of 6) show all publications, abstract [en].

Mitochondria perform a variety of tasks, but the function they are most prominent for is the energy conversion to form ATP, the universal energy equivalent of the cell. The majority of this ATP is created by the oxidative phosphorylation system, consisting of the respiratory chain and the ATP synthase. These elaborate machineries channel electrons through the respiratory complexes and thereby generate an electrochemical gradient across the inner mitochondrial membrane. This, so called proton motive force, is in turn utilized by the ATP Synthase to produce ATP.

A particularity of the oxidative phosphorylation complexes is that their subunits are derived from two genetic sources. As a result, and the fact that the respiratory chain complexes contain redox cofactors, the biogenesis of these enzymes is challenging and involves multiple, highly coordinated and regulated assembly steps. For the obligate homodimeric bc 1 complex, a handful of assembly factors are known and its assembly can be divided into distinct assembly intermediates. In this work we provided insights into the maturation of the catalytic subunit cytochrome b . We revealed that the insertion of the redox active heme b groups is sequential and that it depends on the interaction with the early assembly factor Cbp4. With successful insertion of both heme b s, the binding of the structural subunit Qcr7 is necessary for stabilization and further assembly.

Furthermore, we were able to delineate the dimerization event in detail. We could establish that the interaction of the two matrix subunits, Cor1 and Cor2, with the bc 1 complex assembly intermediate II, as well as the dissociation of Cbp4, are the triggering point for dimerization.

In our subsequent work we investigated the roles of the fairly uncharacterized assembly factor Bca1 and its interplay with the structural subunit Qcr7. We could demonstrate that Bca1 interacts early and transiently during assembly and is an important factor for efficient assembly. Additionally, we could show that Qcr7 is not only a structural subunit but also serves as an assembly checkpoint for the maturation of the bc 1 complex.

With our work we could illustrate the necessity for basic biochemical research within the model organism yeast, as the fundamental molecular mechanisms are well conserved. This is exemplified by our work on UQCC3, the human orthologue of the bc 1 complex assembly factor Cbp4.

Place, publisher, year, edition, pages

National category, research subject, identifiers, public defence, fernandez-vizarra, erika, supervisors, ott, martin, daley, daniel.

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.

The mitochondrial  bc 1  complex plays an important role in mitochondrial respiration. It transfers electrons from ubiquinol to the soluble electron shuttle cytochrome  c  and thereby contributes to the proton motive force across the inner mitochondrial membrane. In the yeast  Saccharomyces cerevisiae , each monomer consists of three catalytic and seven accessory subunits. The  bc 1  complex is an obligate homo-dimer in all systems. It is currently not known when exactly during the assembly dimerization occurs. In this study, we determined that the dimer formation is an early event. Specifically, dimerization is mediated by the interaction of a stable tetramer formed by the two Cor subunits, Cor1 and Cor2, that joins assembly intermediate II, containing the fully hemylated cytochrome  b  and the two small accessory proteins, Qcr7 and Qcr8. Addition of cytochrome  c 1  and Qcr6 can either occur concomitantly or independently of dimerization. These results reveal a strict order in assembly, where dimerization occurs after stabilization of co-factor acquisition by cytochrome  b . Finally, assembly is completed by addition of the remaining subunits.

Vargas Möller-Hergt, Braulio

Carlström, andreas, imhof, axel.

Mitochondrial gene expression in Saccharomyces cerevisiae is responsible for the production of highly hydrophobic subunits of the oxidative phosphorylation system. Membrane insertion occurs cotranslationally on membrane-bound mitochondrial ribosomes. Here, by employing a systematic mass spectrometry-based approach, we discovered the previously uncharacterized membrane protein Mrx15 that interacts via a soluble C-terminal domain with the large ribosomal subunit. Mrx15 contacts mitochondrial translation products during their synthesis and plays, together with the ribosome receptor Mba1, an overlapping role in cotranslational protein insertion. Taken together, our data reveal how these ribosome receptors organize membrane protein biogenesis in mitochondria.

Wanschers, Bas F. J.

Szklarczyk, radek, van den brand, mariel a. m., jonckheere, an, suijskens, janneke, smeets, roel, rodenburg, richard j., helland, ingrid b., elkamil, areej, rootwelt, terje, van den heuvel, lambert, nijtmans, leo g., huynen, martijn a..

Complex III (cytochrome bc(1)) is a protein complex of the mitochondrial inner membrane that transfers electrons from ubiquinol to cytochrome c. Its assembly requires the coordinated expression of mitochondrial-encoded cytochrome b and nuclear-encoded subunits and assembly factors. Complex III deficiency is a severe multisystem disorder caused by mutations in subunit genes or assembly factors. Sequence-profile-based orthology predicts C11orf83, hereafter named UQCC3, to be the ortholog of the fungal complex III assembly factor CBP4. We describe a homozygous c.59T > A missense mutation in UQCC3 from a consanguineous patient diagnosed with isolated complex III deficiency, displaying lactic acidosis, hypoglycemia, hypotonia and delayed development without dysmorphic features. Patient fibroblasts have reduced complex III activity and lower levels of the holocomplex and its subunits than controls. They have no detectable UQCC3 protein and have lower levels of cytochrome b protein. Furthermore, in patient cells, cytochrome b is absent from a high-molecular-weight complex III. UQCC3 is reduced in cells depleted for the complex III assembly factors UQCC1 and UQCC2. Conversely, absence of UQCC3 in patient cells does not affect UQCC1 and UQCC2. This suggests that UQCC3 functions in the complex III assembly pathway downstream of UQCC1 and UQCC2 and is consistent with what is known about the function of Cbp4 and of the fungal orthologs of UQCC1 and UQCC2, Cbp3 and Cbp6. We conclude that UQCC3 functions in complex III assembly and that the c.59T > A mutation has a causal role in complex III deficiency.

AuthorCount:15;

Hildenbeutel, Markus

Hegg, eric l., gruschke, steffi, meunier, brigitte.

Mitochondrial respiratory chain complexes convert chemical energy into a membrane potential by connecting electron transport with charge separation. Electron transport relies on redox cofactors that occupy strategic positions in the complexes. How these redox cofactors are assembled into the complexes is not known. Cytochrome b, a central catalytic subunit of complex III, contains two henne bs. Here, we unravel the sequence of events in the mitochondrial inner membrane by which cytochrome b is hemylated. Heme incorporation occurs in a strict sequential process that involves interactions of the newly synthesized cytochrome b with assembly factors and structural complex III subunits. These interactions are functionally connected to cofactor acquisition that triggers the progression of cytochrome b through successive assembly intermediates. Failure to hemylate cytochrome b sequesters the Cbp3-Cbp6 complex in early assembly intermediates, thereby causing a reduction in cytochrome b synthesis via a feedback loop that senses hemylation of cytochrome b.

AuthorCount:6;

Singh, Abeer

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Nils Sylvan defends his thesis

Dissertation

Date: Friday 17 December 2021

Time: 15.00 – 17.30

Location: Auditorium 8, Södra huset, hus D

Nils Sylvan defends his thesis on December 17, 15:00–17:30 in Auditorium 8, Södra huset, hus D

Nils Sylvan Academic dissertation for the Degree of Doctor of Philosophy in Philosophy at Stockholm University to be publicly defended on Friday 8 December 2021 at 13.00 in auditorium 8, hus D, Universitetsvägen 10 A.

Faculty opponent : Graham Oddie (CU Boulder)

Value, Fittingness and Partiality: On the Partiality Problem for Fitting Attitude Analyses of Value

This dissertation is about the partiality problem for fitting attitude (FA) analyses of value. More specifically, it is about whether and how the problem might be resolved. In Chapter 1, I set the stage by offering a short introduction to the topic and a rationale for investigating it. I then give a more detailed account of FA analyses of value in Chapter 2, including a brief outline of their history and appeal, before explaining more thoroughly just what the partiality problem is for such analyses in Chapter 3, where I distinguish between several different versions of the problem, identify two broad strategies for resolving it and put forward six evaluation criteria in terms of which the plausibility of a resolution can be assessed.

According to FA analyses of value, what it is for something to have value is, roughly, for it to be fitting to have a certain sort of attitude toward it. To have a positive value, such as being good, is to be something that it is fitting to favor (to have a pro-attitude toward); to have a negative value, such as being bad, is to be something that it is fitting to disfavor (to have a con-attitude toward); and to have a relational or comparative value like being better than, worse than, equally good as or equally bad as something else is to be something that it is fitting to favor more than, disfavor more than, favor equally much as or disfavor equally much as the other thing.

The partiality problem is, roughly, that there are situations in which two things seem to have equal value, which, if things are as they seem and FA analyses of value are correct, means that it is fitting to respond to them equally – to be impartial between them. However, in these situations, there are some people for whom it does not seem fitting to respond in that way because they stand in a certain relationship to one of the bearers of value. For these people, it seems that the fitting response is an unequal or partial response, not an impartial one. If such intuitions about fitting partiality and value are veridical, then how can FA analyses of value be correct?

The rest of the dissertation is then a critical, in-depth study of a wide range of responses to the partiality problem. In Chapter 4, I examine the first of the two response strategies, which is to deny the veracity of at least one of the intuitions that generate the problem without making any changes to the FA analyses themselves. I then turn to the second strategy, which is to try to accommodate the intuitions by revising the FA analyses in some suitable manner. In Chapters 5–13, I consider the possibility and plausibility of solving the problem by revising the FA analyses on the basis of: the distinction between intrinsic and extrinsic properties (Chapter 5), the notion of basic value (Chapter 6), the notion of agent-relative value (Chapter 7), the notion of an impartial observer (Chapter 8), the distinction between moral and non-moral fittingness (Chapter 9), a sui generis notion of fittingness (Chapter 10), the distinction between pro tanto and overall fittingness (Chapter 11), the distinction between actions and attitudes (Chapter 12) and the notions of evaluative distance and perspective (Chapter 13). My assessment is that none of these responses is entirely plausible. Thus, in Chapter 14, I conclude that although the partiality problem may not be irresolvable, it is yet to receive a fully plausible resolution. I also discuss the ramifications of this conclusion.

Last updated: January 19, 2023

Source: Department of Philosophy