Conventional MRI techniques are not convenient when it comes to study cerebral microvascularization due to the length of the scans needed. A technique called Magnetic Resonance Fingerprinting (MRF) is an excellent candidate to solve this problem as it requires much shorter scan durations. It relies on the ability to simulate a large amount of MR signals coming from virtual voxels of controlled parameters. This thesis addresses this simulation aspect. Coding implements were made on a simulation tool called MRVox2D to improve its realism and flexibility. In particular, the voxel geometry generation algorithm was reworked to allow simulations in line with what can be obtained from a scanner. Having a variable vessel size within a simulated voxel is now possible and the Vessel Size Index can be computed accordingly. MRF applications were made on mice data using these implementations, showing encouraging but perfectible results. / Konventionella MR-tekniker är inte praktiska när det gäller att studera cerebral mikrovaskularisering på grund av längden på de skanningar som krävs. En teknik som kallas Magnetic Resonance Fingerprinting (MRF) är en utmärkt kandidat för att lösa detta problem eftersom den kräver mycket kortare skanningsvaraktigheter. Metoden baseras på förmågan att simulera en stor mängd MR-signaler som kommer från virtuella voxels av kontrollerade parametrar. Det här examensarbetet behandlar denna simuleringsaspekt. Kodningsredskap gjordes på ett simuleringsverktyg som heter MRVox2D för att förbättra dess realism och flexibilitet. I synnerhet omarbetades algoritmen för generering av voxelgeometri för att tillåta simuleringar i linje med vad som kan erhållas från en skanner. Att ha en variabel kärlstorlek inom en simulerad voxel är nu möjligt och Vessel Size Index kan beräknas i enlighet därmed. MRF-applikationer gjordes på mössdata med användning av dessa implementationer, vilket visade uppmuntrande men ännu inte perfekta resultat.

Radar sounders (RS) are active instruments that have proved to be able to profile the subsurface of planetary bodies. The design of RS instruments, as well as the interpretation of the acquired data, is a non-trivial task due to the complexity of the scenario of acquisition and the limited amount of information on the targets (especially in planetary exploration). In this context, data simulations are necessary to support the design of the radar, the development of the related processing chain, and the definition of algorithms for the automatic analysis of data. However, state-of-the-art RS simulation methods are characterized by different trade-offs between simulation accuracy and computational costs. On the one hand, numerical methods, such as the Finite-Difference Time-Domain (FDTD) technique, allow to accurately model the wave-target interaction by exactly solving Maxwell's equations at the cost of very high computational requirements. On the other hand, optical methods, such as the ray-tracing based Multi-layer Coherent Simulator (MCS), rely on approximated solution of Maxwell's equations that allow for a better usage of computational resources at the cost of a less accurate modeling. Moreover, simulators produce raw or range-compressed only data, making it difficult to interpret and analyze them via direct comparison with the real data, which are typically processed also for azimuth compression. In this thesis, we present four main contributions related to the simulation of RS data to address the above-mentioned limitations. The first and second contributions thus present 3D simulations of selected targets of two new RS instruments, i.e., the Radar for Icy Moon Exploration (RIME) and the EnVision Subsurface Radar Sounder (SRS). The simulations are performed with the FDTD and MCS simulators. Despite producing good results in terms of detection probability of the selected targets, these two contributions highlight the above-mentioned gaps in the literature of simulation of RS data. The first main limitation is the lack of methods that can accurately model both large and small-scale scattering phenomena at relatively low computational costs. This problem is addressed by the third contribution of this thesis, which presents a novel integrated simulation technique that models both large and small-scale surface scattering phenomena by combining the advantages of the FDTD and MCS techniques, in an accurate and computationally efficient way. The second problem identified is the lack of SAR processing techniques to be applied to the simulated radargrams. This is addressed in the fourth contribution which presents a range-Doppler method for focusing raw radar sounder data simulated with 3D coherent electromagnetic simulators. The method is general and can be applied to any electromagnetic simulator, and is demonstrated for both the FDTD and MCS methods. The results presented throughout the thesis indicate that the proposed methods advance the state-of-the-art of techniques for both generating and processing simulated RS data.

<p> The various criteria and methods suggested in the literature for choosing the optimum sequence of calculation are compared. They are then analysed using the results of runs on three different simulations. Two techniques of convergence are used, and it is found that Geometric Convergence Promotion will improve the rate of convergence compared to Direct Substitution for any feasible sequence. It is also shown that the optimal sequences of calculation are different for the two techniques. </p> <p> It is concluded that the Minimum Cut Streams criterion is the best to use for Direct Substitution, but that the use of the feasible Set criterion and Convergence Promotion will yield better convergence. The iterative improvement of convergence is discussed, and it is concluded that the available time is best spent on improving the starting point and the Convergence Promotion technique rather than on changing the sequence of calculation. </p> / Thesis / Master of Engineering (MEngr)

Part A of 2 parts. / <p> This report is a study of the dynamic properties of semiconductor laser diodes. The measurement of some important laser diode parameters necessary for dynamic behaviour prediction is described. The relaxation oscillation behaviour for laser diodes pumped with nanosecond time scale current pulses is predicted using both an approximate analytic solution and computer simulations. This predicted behaviour is compared with experimental results. Dynamic experiments with an external cavity for extra optical feedback and a regenerative loop for optoelectronic feedback are also described and discussed. Details of the experimental setups and techniques used are given. </p> / Thesis / Master of Engineering (MEngr)

Indiana University-Purdue University Indianapolis (IUPUI) / Bacterial endospores have been a topic of research interest over the last several decades given their high resistance to ultraviolet (UV) damage. Unlike vegetative bacterial cells, which form cyclobutane pyrimidine dimers (CPD) and pyrimidine 6-4 pyrimidone photoproducts (6-4PPs) as the major product upon UV irradiation, endospore bacteria form a spore photoproduct (5-(R-thyminyl)-5,6-dihydrothymine or SP) as the major product. Vegetative bacteria cells are subject to regular cell activities and processes such as division and deoxyribonucleic acid (DNA) replication, which are prone to damage from UV exposure. However, in endospores, which have a largely anhydrous inner environment, the DNA remains dormant when bound to spore-specific small acid-soluble proteins (SASP) and dipicolinic acid, making spores highly resistant to radiation, heat, desiccation, and chemical harm. During spore germination, SP lesions in DNA are repaired by a distinctive repair enzyme, spore photoproduct lyase (SPL). In this thesis, molecular dynamics (MD) simulations were carried out to (i) examine how the formation of the SP lesion in DNA affects the global and local structural properties of duplex DNA and (ii) study how this lesion is recognized and repaired in endospore. The first part of this work was focused on designing and developing a structurally and dynamically stable model for dinucleotide SP molecule (TpT), which was subsequently used as an SP patch incorporated into duplex DNA. Computationally, this requires modifications of the bond and nonbonded force field parameters. The stability of the patch and developed parameters was tested via solution-phase MD simulations for the SP lesion incorporated within the B-DNA dodecamer duplex (PDB 463B). The second part involved applying the new SP patch to simulate the crystallographic structure of the DNA oligomer containing SP lesions. Solution-phase MD simulations were performed for the SP-containing DNA oligomers (modeled based on PDB 4M94) and compared to the simulations of the native structure (PDB 4M95). Our analysis of the MD trajectories revealed a range of SP-induced structural and dynamical changes, including the weakened hydrogen bonds at the SP sites, increased DNA bending, and distinct conformational stability and distribution. In the third part of this thesis project, we carried out MD simulations of SP-containing DNA bound with SASPs to examine how the DNA interacts differently with SASP in the presence and absence of the SP lesion. The simulation results suggested decreased electrostatic and hydrogen bonding interactions between SASP and the damaged DNA at the SP site compared to the undamaged DNA-protein complex. In addition, decreased helicity percentage was observed in the SASPs that directly interact with the SP lesion. The last part of this this thesis work focused on the SP-dimer flipping mechanism, as the lesion is likely flipped out to its extrahelical state to be recognized and repaired by SPL. Using steered molecular dynamic (SMD) simulations and a pseudo-dihedral angle reaction coordinate, we obtained possible SP flipping pathways both in the presence and absence of SASP. Collectively, these simulation results lend new perspectives toward understanding the unique behavior of the SP lesion within the DNA duplex and the nucleoprotein complex. They also provide new insights into how the SP lesion is efficiently recognized and repaired during spore germination.

The universal traits of cellular expression and replication in modern life point to the existence of an ancient RNA world. Leading up to the origin of life, this stage of evolution utilized RNA as the genetic material, and as a catalyst in the form of ribozymes. Although it is expected that a polymerase ribozyme was required for the efficient replication of RNA, it is also likely that the earliest form of replication took place under non-enzymatic conditions. There are several problems with the current scenarios depicting non-enzymatic RNA replication, thus we aim to examine them in more detail using computational models. We first consider the relationship between the thermodynamics of RNA base pairing and non-enzymatic nucleotide addition in an attempt to model the rate of primer extension. Our predicted rates reveal the model parameters to be too simple to produce reliably accurate results. For now, we should simply use available experimental rate data, until we have access to more data and less unknown parameters. Nevertheless, the model indicates that the primer extension rate does depend on thermodynamics of base pairing, and a more accurate model can be of great use when creating realistic complex models of RNA world scenarios. In chapter 3, we investigate non-enzymatic RNA replication under temperature cycling using computer simulations. When starting with a diverse mixture of sequences, partially matching sequences can reanneal in configurations that allow continued strand growth. This is in contrast to the case of having multiple copies of matching sequences, where reannealing occurs quickly upon cooling. We find that, starting with short oligomers, strands can grow over multiple cycles to produce long sequences over 100 nucleotides in length. The small strand extension per cycle does not produce replicates of any one specific sequence. This relates to the work done in chapter 4, where we look for the presence of a virtual circular genome within our simulations. In a virtual circle, short overlapping RNA sequences will make up a mutually catalytic set. Within the diversity of our simulation, virtual circles are rare, and require a specific level of starting mixture diversity along with no input of new sequences. Continued replication of the diverse sequence mixture and emergence of long strands may eventually lead to the creation of rolling circles and ribozymes. / Thesis / Master of Science (MSc) / The origin of biological life can be traced back by looking at the common themes between modern cellular processes. The role of RNA polymers seems to be of great importance, making us believe that an RNA world existed leading up to life’s origin. During this time, RNA would act as both a genetic material and a catalyst. To examine this theory in more detail, we use computational modeling to recreate and explore the various potential chemistries and conditions on the early Earth. Specifically, we explore the problems that exist for the replication and production of RNA polymers. Our results can be used to guide future theoretical and experimental research of the RNA world.

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