# Coming theses from other universities

Please note that the date and time given on these pages is the time of electronic publication, and not the date of the public defense. To find the time and venue of the public defense, please follow the link to DiVA of the thesis in question.
• #### Uptake signalling of PepFect 14

Author: Maxime Gestin
Publication date: 2019-01-17 13:41

Cell-penetrating peptides are able to bind and carry various therapeutic agents including oligonucleotides into cells for a therapeutic effect. The aim of the cell-penetrating peptide research field is to produce a simple, safe and potent delivery platform for intracellular therapy and more especially for gene therapy.

More than twenty five years after their discovery, numerous sequences of cell penetrating peptides have been designed based on natural substances, chimeric strategy or entirely synthetic products. The precise interactions leading to the uptake of cell-penetrating peptides is as of today still not entirely clear. Global mechanisms of direct penetration and endocytosis are proposed, but little is known about actual molecular interactions building the signalling pathway of cell-penetrating peptides.

In this thesis, with the help of the cell-penetrating peptide PepFect 14, we study the signalling of the uptake of cell-penetrating peptides either by transcriptome analysis or ligand interfering. We demonstrate the involvement of autophagy in the uptake of both PepFect 14 and the complex formed by PepFect 14 and oligonucleotides. We also present the use of a high throughput assay aimed at identifying new signalling pathways affected by the delivery of oligonucleotides using PepFect 14.

• #### Parametric design with Visual programming in Dynamo with Revit : The conversion from CAD models to BIM and the design of analytical applications

Author: Darwn Nezamaldin
Publication date: 2019-01-16 12:47

Nowadays, there is a big strive to achieve faster and more accurate results of designing buildings in construction companies. Construction companies that work with the design part are continuously searching for methods to increase efficiency in the working process. Autodesk have introduced a software that uses parametric design to provide input to Revit models and to retrieve and manipulate the outcomes of Revit models. The Dynamo software uses visual programming and is connected directly to Revit where the user can gain access to Revit’s data structure where parameters can be controlled and manipulated.

This research consists of two parts. The first part shows how 2D Autocad drawing can be converted into 3D Revit models. This is done by using the 2D geometry as reference lines for placing BIM objects. The second part shows how the BIM model can then be used to analyze different elements with Dynamo. The calculations of element cost, weight and thermal transmission losses of floors, walls and roofs are used to illustrate this possibility.

All the main goals were achieved and are presented in the report for engineers to utilize. The report illustrates the basics of Dynamo, shows examples of how to it can be used while sharing the scripts that were used for this research. The report also encourages other competent students to continue where this thesis ended. Even though several tasks were achieved in this thesis, there are still much more to learn about parametric design and visual programming.

• #### Radio emission from supernovae

Author: Esha Kundu
Publication date: 2019-01-16 08:00

This thesis presents the modeling of radio and X-ray emissions from supernova (SN) shock fronts and hydrodynamical simulations of SN-circumstellar medium (CSM) interaction. The interaction of SN ejecta with the CSM drives a strong shock wave into the CSM. These shocks are ideal places where effective particle acceleration and magnetic field amplification can take place. The accelerated relativistic particles, in the presence of magnetic field, could emit part of their energy via synchrotron radiation in radio wavelengths. The flux of this radiation, when compared with observations, gives an estimate of the CSM density. This could either be the particle density (nISM) in case of the SN exploding in a constant density medium, characteristic of interstellar medium, or pre-SN mass loss rate (dM/dt) of the progenitor system for a wind medium. In Paper I we have modeled the synchrotron emission and compared that with the radio upper limits measured for the Type Ia SNe 2011fe and 2014J. Assuming equipartition of energy between electric and magnetic fields, with 10% of the thermal shock energy in each field, we obtain a very low density medium, having nISM <~ 0.35 cm-3, around both the SNe. In terms of dM/dt this implies an upper limit of 10-9 Msun yr-1 for a wind velocity, vw, of 100 km s-1. This study suggests that in SN shocks it is more likely that the amplification efficiency of magnetic fields is less than that for the electric fields. In Paper II, we carry out the hydrodynamical simulations of the interaction between SN ejecta and CSM for SN 1993J and SN 2011dh. Subsequently, the radio and X-ray emission have been calculated from the shocked gas encapsulated between the forward and reverse shocks. Considering the ejecta profile of these SNe from multi-group radiation hydrodynamics simulation (STELLA), it is found from our investigation that for a wind velocity of 10 km/s around 6500 years prior to the explosion of SN 1993J a change in mass loss rate occurred in the system. For a binary system this may imply that the change in dM/dt could be due to a change in the mass accretion efficiency of the companion star. In case of SN 2011dh the late time emission is turned up to be consistent with a wind medium with (dM/dt)/vw = 4 × 10-6 Msun yr-1/10 km s-1. Paper III focuses on the radio emission from four young SNe Type Ia, SN 2013dy, SN 2016coj, SN 2018pv and SN 2018gv. Using the same model for radio emission as in Paper I, the upper limits on dM/dt and nISM are estimated. We found tenuous media around these SNe, which put tight constrain on their progenitor systems.

• #### Unraveling the structures of complex nanocrystalline materials by combining TEM and XRPD – development and application

Author: Magdalena Ola Cichocka
Publication date: 2019-01-16 08:00

Knowledge of the three-dimensional (3D) atomic structure of materials is essential to a fundamental understanding of their properties. The key to understanding the functionality of many materials, particularly those of commercial and industrial interest, is often hidden in the details at the nanoscale. For this reason, it is very important to choose the right strategy to analyze the structure of challenging materials with complex disordered framework structures, or of the layered materials that are the subject of this thesis. Structure analysis of beam-sensitive or uniquely disordered materials can be complicated. Although there are already existing methods such as X-ray powder diffraction (XRPD), the data may exhibit reflection overlap or other problems that make structure determination difficult. To overcome these limitations for nanocrystalline materials, complementary characterization techniques can be used. Here, I will focus on 3D electron crystallography (continuous rotation electron diffraction and high-resolution electron microscopy) methods that have grown during the past years as hybrid methods for structure determination. Based on the presented materials, I will also emphasize that any kind of challenges can be a driving force for method development.  Furthermore, some of the insights gained lead to better understanding of how to collect and process 3D electron diffraction data, which could be applied to make data collection of challenging samples easier and obtain higher quality structure refinements from the data. Finally, I will try to describe the general procedures for ab initio structure elucidation of disordered nanocrystals and layered materials.

• #### Aqueous Exfoliation of Transition Metal Oxides for Energy Storage and Photocatalysis Applications : Vanadium Oxide and Molybdenum Oxide Nanosheets

Author: Ahmed S. Etman
Publication date: 2019-01-14 08:00

Two-dimensional (2D) transition metal oxides (TMOs) are a category of materials which have unique physical and chemical properties compared to their bulk counterparts. However, the synthesis of 2D TMOs commonly includes the use of environmental threats such as organic solvents. In this thesis, we developed environmentally friendly strategies to fabricate TMO nanosheets from the commercially available bulk oxides. In particular, hydrated vanadium pentoxide (V2O5∙nH2O) nanosheets and oxygen deficient molybdenum trioxide (MoO3-x) nanosheets were prepared.  The V2O5∙nH2O nanosheets were drop-cast onto multi-walled carbon nanotube (MWCNT) paper and applied as a free-standing electrode (FSE) for a lithium battery. The accessible capacity of the FSE was dependent on the electrode thickness; the thickest electrode delivered the lowest accessible capacity.  Alternatively, a composite material of V2O5∙nH2O nanosheets with 10% MWCNT (VOx-CNT composite) was prepared and two types of electrodes, FSE and conventionally cast electrode (CCE), were employed as cathode materials for lithium batteries. A detailed comparison between these electrodes was presented. In addition, the VOx-CNT composite was applied as a negative electrode for a sodium-ion battery and showed a reversible capacity of about 140 mAh g-1. On the other hand, the MoO3-x nanosheets were employed as binder-free electrodes for supercapacitor application in an acidified Na2SO4 electrolyte. Furthermore, the MoO3-x nanosheets were used as photocatalysts for organic dye degradation. The simple eco-friendly synthesis methods coupled with the potential application of the TMO nanosheets reflect the significance of this thesis in both the synthesis and the energy-related applications of 2D materials.

• #### The synthetic chromosphere : Results and techniques with a numerical approach

Author: Johan Pires Bjørgen
Publication date: 2019-01-09 08:00

Realistic numerical simulations of the solar atmosphere can be used to interpret different phenomena observed on the solar surface. To gain insight into the atmospheric physical conditions, we compare the observations with 3D radiative magnetohydrodynamic models combined with forward modeling (radiative transfer). This thesis focuses particularly on the less understood chromospheric layer between the photosphere and the transition region. Only a few and complex spectral lines can probe the chromosphere making its observations a real challenge.The chromospheric environment is strongly influenced by departures from local thermodynamic equilibrium (non-LTE), horizontal radiative transfer (3D effects), and partially-coherent scattering of photons (partial redistribution effects). All these effects make the detailed 3D non-LTE radiative transfer very computationally demanding.In paper I, we focus on increasing the efficiency of non-LTE modeling of spectral lines in realistic solar models. We implemented a non-linear multigrid solver into the Multi3D code and showed that the method can handle realistic model atmospheres produced by radiative-MHD simulations. We obtained a speed-up of a factor 4.5-6 compared to multilevel accelerated lambda iteration.In paper II, we studied the chromospheric resonance lines Ca \textsc{ii} H\&K. Understanding their formation is crucial to interpreting the observations from the new imaging spectrometer CHROMIS, recently installed at the Swedish 1-m Solar Telescope. We investigated how the synthetic observables of Ca \textsc{ii} H\&K lines are related to atmospheric parameters.In paper III, we investigated a simulated active region including flux emergence that produced a flare. We modeled strong chromospheric lines, such as Ca \textsc{ii} H\&K, 8542 \AA, Mg \textsc{ii} h\&k, and H-$\alpha$, to investigate how it appears in synthetic images and spectra.

• #### Understanding and manipulating primary cell walls in plant cell suspension cultures

Author: Felicia Leijon
Publication date: 2019-01-07 13:34

The cell wall is required for many aspects of plant function and development. It is also an accessible and renewable resource utilized both in unrefined forms and as raw material for further development. Increased knowledge regarding cell wall structure and components will contribute to better utilization of plants and the resources they provide. In this thesis aspects of the primary cell wall of Populus trichocarpa and Nicotiana tabacum are explored.

In Publication I a method for isolation and biochemical characterization of plant glycosyltransferases using a spectrophotometric or a radiometric assay was optimized. The radiometric assay was applied in Publication II where the proteome of the plasmodesmata isolated from P. trichocarpa was analyzed. Proteins identified belonged to functional classes such as "transport", "signalling" and "stress responses". Plasmodesmata-enriched fractions had high levels of callose synthase activity under ion depleted conditions as well as with calcium present.

The second part of the thesis comprises the alteration of the cell wall of N. tabacum cells and A. thaliana plants through in vivo expression of a carbohydrate binding module (CBM) (Publication III). In tobacco this resulted in cell walls with loose ultrastructure containing an increased proportion of 1,4-β-glucans. The cell walls were more susceptible to saccharification, possibly due to changes in the structure of cellulose or xyloglucan. Arabidopsis plants showed increased saccharification after mild pretreatment, suggesting that heterologous expression of CBMs is a promising method for cell wall engineering. In Publication IV cellulose microfibrils (CMFs) and nanocrystals (CNCs) were extracted from the transgenic cells. CNC preparation resulted in higher yields and longer CNCs. Nanopapers prepared from the CMFs of the CBM line demonstrated enhanced strength and toughness. Thus, changes to the ordered regions of cellulose were suggested to take place due to CBM expression.

• #### Efficient Memory Access and Synchronization in NoC-based Many-core Processors

Author: Xiaowen Chen
Publication date: 2019-01-07 10:13

In NoC-based many-core processors, memory subsystem and synchronization mechanism are always the two important design aspects, since mining parallelism and pursuing higher performance require not only optimized memory management but also efficient synchronization mechanism. Therefore, we are motivated to research on efficient memory access and synchronization in three topics, namely, efficient on-chip memory organization, fair shared memory access, and efficient many-core synchronization.

One major way of optimizing the memory performance is constructing a suitable and efficient memory organization. A distributed memory organization is more suitable to NoC-based many-core processors, since it features good scalability. We envision that it is essential to support Distributed Shared Memory (DSM) because of the huge amount of legacy code and easy programming. Therefore, we first adopt the microcoded approach to address DSM issues, aiming for hardware performance but maintaining the flexibility of programs. Second, we further optimize the DSM performance by reducing the virtual-to-physical address translation overhead. In addition to the general-purpose memory organization such as DSM, there exists special-purpose memory organization to optimize the performance of application-specific memory access. We choose Fast Fourier Transform (FFT) as the target application, and propose a multi-bank data memory specialized for FFT computation.

In 3D NoC-based many-core processors, because processor cores and memories reside in different locations (center, corner, edge, etc.) of different layers, memory accesses behave differently due to their different communication distances. As the network size increases, the communication distance difference of memory accesses becomes larger, resulting in unfair memory access performance among different processor cores. This unfair memory access phenomenon may lead to high latencies of some memory accesses, thus negatively affecting the overall system performance. Therefore, we are motivated to study on-chip memory and DRAM access fairness in 3D NoC-based many-core processors through narrowing the round-trip latency difference of memory accesses as well as reducing the maximum memory access latency.

Barrier synchronization is used to synchronize the execution of parallel processor cores. Conventional barrier synchronization approaches such as master-slave, all-to-all, tree-based, and butterfly are algorithm oriented. As many processor cores are networked on a single chip, contended synchronization requests may cause large performance penalty. Motivated by this, different from the algorithm-based approaches, we choose another direction (i.e., exploiting efficient communication) to address the barrier synchronization problem. We propose cooperative communication as a means and combine it with the master-slave algorithm and the all-to-all algorithm to achieve efficient many-core barrier synchronization. Besides, a multi-FPGA implementation case study of fast many-core barrier synchronization is conducted.

• #### Manufacturing and Characterization of Cellulose Nanofibers

Author: Carl Moser
Publication date: 2018-12-23 06:36

The usage of wood has been a dominant driving force during the evolution of the human species. It allowed us to cook food, build tools, put roofs over our head and explore the world. The fibers making up the tree has been the most important way to store and transmit knowledge in the form of paper for centuries. It may not be considered as the most interesting or hi-tech of fields, although, nothing could be further from the truth. One of society's most significant issue is how to live sustainably, which is coincidentally exactly what trees can solve. We can live in tall buildings made from wood, locking up vast amounts of carbon dioxide - we can replace many of the plastics we use today with sustainable alternative from the components making up the tree - we could even make clothes from our trees and stop being reliant on the untenable cotton production - only our imagination is holding us back from what can be made from trees.

Cellulose is the structural component in trees, the molecule arranges itself in a complex hierarchical structure that forms the wood-cells, or fibers. Breaking down this hierarchical structure down to its smallest structural units leaves us with tiny fibers, no longer than a few micrometers and with a width of merely four nanometers. These are cellulose nanofibers, and this work has aimed to understand how and what it takes to liberate these fine fibers from the larger fiber that they make up. Two main pathways exist to liberate the nanofibers, either chemically by introducing negatively charged groups on the surface of the cellulose, making the fibrils repel each other, or mechanically, simply by intense processing of the fibers. However, these processes are associated with certain flaws in that (i) vast amount of energy is required unless the fibers are pretreated, (ii) disintegration is performed in instruments that do not scale well, (iii) disintegration is carried out at a low concentration of fibers, typically below 5%. Additionally, what comes out of a process is difficult to characterize in terms of quality due to an inherent inhomogeneity and the small size of the nanofibers.

These issues in combination with a greater understanding of the processes are the foundation of this thesis.

Decreased energy consumption and scalability was explored via the steam explosion concept Nanopulp. In order to avoid issues associated with the low concentration, a method was developed for drying cellulose nanofibers to a paste without causing hornification using glycerol. A variety of cellulose nanofibers from different sources were prepared and characterization techniques were compared and expanded upon, including the development of a method for better describing the surface area of cellulose nanofibers. Finally, an environmentally friendly composite was made using cheap and available resources in combination with cellulose nanofibers.

• #### Modelling the Production and Propagation of Sound in Individual Human Vocal Tracts

Author: Lukas Schickhofer
Publication date: 2018-12-21 11:20

Voice generation and the expression through speech are of vital importance for communication. The human upper airways are the origin of the process of speech production, which involves a modulation of the periodically pulsed pressure from the lungs by the vocal tract volume. In this work, phonation and voiced speech are investigated through both low- and high-order models, which are applied to vocal tract geometries of increasing complexity. Initially, the effect of variations of vocal fold closure, fundamental frequency, and vocal tract length on the computed acoustic signal is examined through parameter studies based on one-dimensional wave reflection analogues. Eventually, unsteady large eddy simulations based on the compressible Navier-Stokes equations are carried out to compute the pressure fluctuations and the associated distribution of resonance modes as a result of the interaction with the static vocal tract. Thus it is possible to calculate tonalities from the entire audible range of frequencies from 20 to 20000 Hz. In particular the inharmonic broadband sound component produced predominantly by coherent structures in the upper airways and at frequencies above 2 kHz is resolved in the current study, which is not captured by low-order models based on wave equations. Furthermore, three-dimensional numerical meshes based on surface representations of the human upper airways under voiced speech from magnetic resonance imaging (MRI) data of a healthy male subject are applied. These are necessary to resolve high-order acoustic modes that would not be represented by simplified geometries. Validation and verification of the chosen methods are achieved through comparison with experimentally obtained speech data, as well as Helmholtz eigenfrequencies of the considered vowel pronunciations. The main scope of this work is the assessment of acoustic sources and the conditions for aerodynamic sound being produced and propagated in the upper airways during phonation. The distribution of acoustic sources involved in the generation of the dominant frequencies are identified by application of acoustic analogies as well as surface Fourier transformation of the acoustic pressure fluctuations. However, the human upper airways do not only embrace the source of phonation and affect the modulation of the voice. Moreover, unwanted sounds may be generated in the upper airways due to elastic, collapsible parts that are susceptible to flow-induced vibration and resonance. The sound resulting from fluid-structure interaction in the upper respiratory tract, commonly known as snoring, can be an important indicator for underlying breathing disorders, such as obstructive sleep apnea (OSA). In a smaller part of this project, the flow structures and acoustic sources as a result of the interaction of shear flow of various Reynolds numbers with an elastic element are computed. The geometric dimensions are chosen to be representative of average physical values of the upper respiratory tract. Onset of tissue vibrations and resonance effects are investigated for a range of parameters of both solid and fluid. The obtained results of this work are aimed to contribute also to the development of a computational tool that assists physicians in the assessment of the airway function and the effectiveness of treatment plans prior to their application.