In the field of Computational Fluid Dynamics, several types of mesh adaptation strategies are used to enhance a mesh’s quality, thereby improving simulation speed and accuracy. Mesh smoothing (r-refinement) is a simple and effective technique, where nodes are repositioned to increase or decrease local mesh resolution. Mesh partitioning divides a mesh into sections, for use on distributed-memory parallel machines. As a more abstract form of modeling, graph theory can be used to simulate many real-world problems, and has applications in the fields of computer science, sociology, engineering and transportation, to name a few. One of the more important graph analysis tasks involves moving through the graph to evaluate and calculate nodal connectivity. The basic structures of meshes and graphs are the same, as both rely heavily on connectivity information, representing the relationships between constituent nodes and edges. This research examines the parallelization of these algorithms using commodity graphics hardware; a low-cost tool readily available to the computing community. Not only does this research look at the benefits of the fine-grained parallelism of an individual graphics processor, but the use of Message Passing Interface (MPI) on large-scale GPU-based supercomputers is also studied.

Inspired by a planar partitioning problem involving multiple unbounded chambers, this thesis investigates using classical techniques what can be said of the existence, uniqueness, and regularity of minimizers in a certain free-endpoint isoperimetric problem. In two cases, a full existence-uniqueness-regularity result is proved using a convexity technique inspired by work of Talenti. The problem studied here can be interpreted physically as the identification of the equilibrium shape of a sessile liquid drop in half-space (in the absence of gravity). This is a well-studied variational problem whose full resolution requires the use of geometric measure theory, in particular the theory of sets of finite perimeter. A crash course on the theory required for the modern statement of the equilibrium shape theorem is presented in an appendix. / Thesis / Master of Science (MSc)

The distribution of male and female plants was examined in five dioecious, wind pollinated species representing five plant families and two classes (gymnosperms and angiosperms). The arid to semiarid habitats occupied by these species in northern Utah were stratified for sampling into two categories: chronically xeric and seasonally moist. Results show that for all species, males prevail on xeric microsites, while females dominate the more moist parts of each local environment. Habitat partitioning between the sexes is a strategy that maximizes seedset of females and pollen dispersal of males; it also tends to minimize intraspecific competition between the sexes.

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Forecasting is an important analysis technique used in many application domains such as electricity management, sales and retail and, traffic predictions. The employed statistical models already provide very accurate predictions, but recent developments in these domains pose new requirements on the calculation speed of the forecast models. Especially, the often used multi-equation models tend to be very complex and their estimation is very time consuming. To still allow the use of these highly accurate forecast models, it is necessary to improve the data processing capabilities of the involved data management systems. For this purpose, we introduce a partitioning approach for multi-equation forecast models that considers the specific data access pattern of these models to optimize the data storage and memory access. With the help of our approach we avoid the redundant reading of unnecessary values and improve the utilization of the CPU cache. Furthermore, we utilize the capabilities of modern multi-core hardware and parallelize the model estimation. Our experimental results on real-world data show speedups of up to 73x for the initial model estimation. Thus, our partitioning and parallelization approach significantly increases the efficiency of multi-equation models.

An analysis of the presence or absence of black melanin in broiler chickens as affected by the presence of different traits is studied in the following project. The purpose of this analysis is to show that the simple partitioning of chi-square method is as good as any method. This project also shows the equivalence of different statistical methods. / Thesis / Master of Science (MSc)

Eukaryotic cells are characterized by having a clearly defined nucleus that encloses genetic material, separating it from the rest of the cell. The regulation of protein partitioning between the nucleus and cytoplasm is crucial for controlling specific cellular functions; any imbalance in protein partitioning can lead to a range of diseases, highlighting its significance in cellular physiology. The major mechanism for establishing nuclear composition is the trafficking of proteins in and out of the nucleus by karyopherins after the formation of the nuclear envelope. Regulating protein partitioning is particularly challenging during early embryonic development due to the rapid and successive cell divisions that lead to a dramatic reduction in cell size. Further, the embryo is maternally deposited with vast quantities of proteins that must be appropriately incorporated into an exponentially increasing number of nuclei. How such large quantities of proteins are robustly partitioned into the nucleus during these dynamic developmental processes remains unclear. During my Ph.D., I studied the nuclear partitioning of the Xenopus laevis embryonic linker histone H1.8, a protein that alters the chromatin structure in a concentration-dependent manner. By using quantitative microscopy of Xenopus laevis egg extract, I provide evidence H1.8 is partitioned into the nucleus through a mechanism independent of nuclear import. H1.8 has already been shown to be one of the earliest proteins to partition within the nucleus during embryonic development. However, I demonstrate that the import kinetics of H1.8 is insufficient to account for its rapid nuclear partitioning. Further, I discovered that H1.8 is present in the nucleus and cytoplasm as liquid condensates. As the nucleus expands and grows in interphase, the nuclear condensates dissolve, suggesting that they act as reservoirs of proteins, potentially for DNA replication. The dissolution also suggests that most nuclear H1.8 is already present during the nuclear assembly, thus indicating that the partition of H1.8 inside the nucleus is not solely dependent on its import. Prior to the formation of the nucleus, I observe that the surface of the chromatid nucleates H1.8 as condensates similar to the formation of dew droplets on a cold surface. These condensates are then sequestered into the nucleus as the cell cycle progresses, leading to the protein reservoirs we observe in the nucleus. Such a mechanism allows for instantaneous enrichment of excess H1.8 inside the nucleus. Furthermore, I demonstrate that the cytoplasmic H1.8 condensates modulate the nucleation of H1.8 on the chromatid surface by buffering the soluble concentration of H1.8. This ensures that the amount of surface condensates is independent of the nucleus-to-cytoplasmic ratio, thus potentially allowing for a fixed enrichment of proteins despite the reduction in cell size during embryonic development. Such a mechanism would be crucial for key structural proteins, like H1.8, that maintain DNA packaging and structure in a concentration-dependent manner. Taken together, I propose that the nucleation of condensates on the surface of mitotic chromatids and subsequent wetting can provide an alternative mechanism to nuclear trafficking in regulating nuclear composition.:1) Introduction 2) This work – aim and scope 3) The dynamics of H1.8 nuclear localization 4) H1.8 undergoes liquid-liquid phase separation in Xenopus laevis egg extract. 5) H1.8 condenses on the surface of chromatids. 6) Cytoplasmic condensates buffer the amount of surface condensates on chromatids. 7) Summary. 8) Future perspectives. 9) Methods

Cyber-physical systems are computers equipped with sensors and actuators that enable them to interact with their surrounding environments. Ground vehicles, drones, and manufacturing robots are examples of such systems that require timing guarantees in addition to functional correctness to achieve their mission objectives. These systems often use multiple microcontroller boards for workload distribution and physical redundancy. The emergence of PC-class embedded systems featuring high processing capabilities and abundant resources presents an opportunity to consolidate separate microcontroller boards as software-defined functions into fewer computer systems. For instance, current automotive systems utilize upwards of 100 electronic control units (ECUs) for chassis, body, power-train, infotainment, and vehicle control services. Consolidation saves manufacturing costs, reduces wiring, simplifies packaging in space-limited situations, and streamlines software update delivery to end-users. However, consolidating functions on PC-class hardware does not address the real-time I/O challenges. A fundamental problem in such real-time solutions is the handling of device input and output in a timely manner. For example, a control system might require input data from a sensor to be sampled and processed regularly so that output signals to actuators occur within specific delay bounds. Input/output (I/O) devices connect to the host computer using different types of bus interfaces not necessarily supported by PC-class hardware natively. Examples of such interfaces include Controller Area Network (CAN) and FlexRay, which are prominent in the automotive world, but are not found in PC-class embedded systems. Universal Serial Bus (USB) is now ubiquitous in the PC-class domain, in part due to its support for many classes of devices with simplified hardware needed to connect to the host, and can be utilized to bridge this gap. USB provides the throughput and delay capabilities for next-generation high bandwidth sensors to be integrated with actuators in control area networks. However, typical USB host controller drivers suffer from potential timing delays that affect the delivery of data between tasks and devices. This Ph.D. thesis examines the use of Universal Serial Bus (USB) as the physical fabric for host-to-device and host-to-host communication, without special switching hardware or protocol translation logic, and through a unified programming interface. Combined with the real-time scheduling framework of the Quest RTOS, this work investigates how to form networks of I/O devices and computing nodes over USB with end-to-end timing guarantees. The main contribution of this thesis is a USB-centric design solution for real-time cyber-physical systems with distributed computing nodes.

京都大学 / 新制・課程博士 / 博士(情報学) / 甲第25023号 / 情博第855号 / 新制||情||143(附属図書館) / 京都大学大学院情報学研究科社会情報学専攻 / (主査)教授 大手 信人, 教授 土居 秀幸, 教授 三田村 啓理 / 学位規則第4条第1項該当 / Doctor of Informatics / Kyoto University / DGAM

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