In order to better understand the behavior of the human brain, it is very important to perform large scale neural network simulation which may reveal the relationship between the whole network activity and the biophysical dynamics of individual neurons. However, considering the complexity of the network and the large amount of variables, researchers choose to either simulate smaller neural networks or use simple spiking neuron models. Recently, supercomputing platforms have been employed to greatly speedup the simulation of large brain models. However, there are still limitations of these works such as the simplicity of the modeled network structures and lack of biophysical details in the neuron models. In this work, we propose a parallel simulator using biophysically realistic neural models for the simulation of large scale neural networks. In order to improve the performance of the simulator, we adopt several techniques such as merging linear synaptic receptors mathematically and using two level time steps, which significantly accelerate the simulation. In addition, we exploit the efficiency of parallel simulation through three parallel implementation strategies: MPI parallelization, MPI parallelization with dynamic load balancing schemes and Hybrid MPI/OpenMP parallelization. Through experimental studies, we illustrate the limitation of MPI implementation due to the imbalanced workload among processors. It is shown that the two developed MPI load balancing schemes are not able to improve the simulation efficiency on the targeted parallel platform. Using 32 processors, the proposed hybrid approach, on the other hand, is more efficient than the MPI implementation and is about 31X faster than a serial implementation of the simulator for a network consisting of more than 100,000 neurons. Finally, it is shown that for large neural networks, the presented approach is able to simulate the transition from the 3Hz delta oscillation to epileptic behaviors due to the alterations of underlying cellular mechanisms.

This thesis focuses on the enhancement of the IEEE 802.15.4 beaconless-enabled MAC protocol as a solution to overcome the network bottleneck, less flexible nodes, and more energy waste at the centralised wireless sensor networks (WSN). These problems are triggered by mechanism of choosing a centralised WSN coordinator to start communication and manage the resources. Unlike IEEE 802.11 standard, the IEEE 802.15.4 MAC protocol does not include method to overcome hidden nodes problem. Moreover, understanding the behaviour and performance of a large-scale WSN is a very challenging task. A comparative study is conducted to investigate the performance of the proposed ad hoc WSN both over the low data rate IEEE 802.15.4 and the high data rate IEEE 802.11 standards. Simulation results show that, in small-scale networks, ad hoc WSN over 802.15.4 outperforms the WSN where it improves 4-key performance indicators such as throughput, PDR, packet loss, and energy consumption by up to 22.4%, 17.1%, 34.1%, and 43.2%, respectively. Nevertheless, WSN achieves less end-to-end delay; in this study, it introduces by up to 2.0 ms less delay than that of ad hoc WSN. Furthermore, the ad hoc wireless sensor networks work well both over IEEE 802.15.4 and IEEE 802.11 protocols in small-scale networks with low traffic loads. The performance of IEEE 802.15.4 declines for the higher payload size since this standard is dedicated to low rate wireless personal access networks. A deep performance investigation of the IEEE 802.15.4 beaconless-enabled wireless sensor network (BeWSN) in hidden nodes environment has been conducted and followed by an investigation of network overhead on ad hoc networks over IEEE 802.11 protocol. The result of investigation evinces that the performance of beaconless-enabled ad hoc wireless sensor networks deteriorates as indicated by the degradation of throughput and packet reception by up to 72.66 kbps and 35.2%, respectively. In relation to end-to-end delay, however, there is no significant performance deviation caused by hidden nodes appearance. On the other hand, preventing hidden node effect by implementing RTS/CTS mechanism introduces significant overhead on the network that applies low packet size. Therefore, this handshaking method is not suitable for low rate communications protocol such as IEEE 802.15.4 standard. An evaluation study of a 101-node large-scale beaconless-enabled wireless sensor networks over IEEE 802.15.4 protocol has been carried out after the nodes deployment model was arranged. From the experiment, when the number of connection densely increases, then the probability of packet delivery decreases by up to 40.5% for the low payload size and not less than of 44.5% for the upper payload size. Meanwhile, for all sizes of payload applied to the large-scale ad hoc wireless sensor network, it points out an increasing throughput whilst the network handles more connections among sensor nodes. In term of dropped packet, it confirms that a fewer data drops at smaller number of connecting nodes on the network where the protocol outperforms not less than of 34% for low payload size of 30 Bytes. The similar trend obviously happens on packet loss. In addition, the simulation results show that the smaller payload size performs better than the bigger one in term of network latency, where the payload size of 30 Bytes contributes by up to 41.7% less delay compared with the contribution of the payload size of 90 Bytes.

Optical networking has been developing for decades and wavelength-division multiplexing (WDM) is the main technology used to carry signals in fiber-optical communication systems. However, its development has slowed because it is approaching the Shannon limit of nonlinear fiber transmission. Researchers are looking for multi dimensional multiplexing. Space-division multiplexing (SDM) is an ideal way to scale network capacities. The capacity of WDM/SDM network could be expanded to several times the capacity of WDM network but the active hardware devices may also increase by several times. This project aims to answer a practical question: How to construct a WDM/SDM network with less hardware resource? There is no mature research about WDM/SDM network yet. Therefore, the problem can be divided into two parts: (1) how to build a WDM/SDM network and (2) how to allocate resource and compute routes in such a network to minimize hardware resources. First, this thesis proposes a WDM/SDM node which has bypass connections between different fibers and architecture on demand (AoD) to effectively decrease the number of active hardware devices within the node. Then, two types of networks were constructed: one with bypass connections in each node and another one without any bypass connections. These networks were under the control of a software defined network (SDN) controller. The controller knew the wavelength resources within the networks. Several algorithms were applied to these networks to evaluate the effect of a bypass network and to identify the desired characteristics (to find short length path and decrease the probability of spectrum fragmentation) of an algorithm suitable for a network with bypass connections. The results of applying the proposed algorithms in two networks proved that the bypass connections increased the blocking probability in small topology but did not affect the results in large topology. The results in a large-scale network with bypass network were almost the same as the results in a network without bypass connections. Thus, bypass connections are suitable for large-scale network. / Optiskt nätverk har utvecklats i årtionden och våglängdsdelningsmultiplexering (WDM) är den viktigaste tekniken som används för att bära signaler i fiberoptiska kommunikationssystem. Utvecklingen har dock minskat eftersom den närmar sig Shannon-gränsen för olinjär fiberöverföring. Forskare letar efter flerdimensionell multiplexering. Space-division multiplexing (SDM) är ett idealiskt sätt att skala nätverkskapacitet. Kapaciteten för WDM / SDM-nätverk kan utökas till flera gånger WDM-nätverkets kapacitet, men de aktiva hårdvaraenheterna kan också öka med flera gånger. Projektet syftar till att svara på en praktisk fråga: Hur konstruerar jag ett WDM / SDM-nätverk med mindre hårdvara? Det finns ingen mogen forskning om WDM / SDM-nätverk än. Därför kan problemet delas in i två delar: (1) hur man bygger ett WDM / SDM-nätverk och (2) hur man fördelar resurser och beräknar rutter i ett sådant nätverk för att minimera hårdvaruressurser. Först föreslår denna avhandling en WDM / SDM-nod som har förbikopplingsanslutningar mellan olika fibrer och arkitektur på begäran (AoD) för att effektivt minska antalet aktiva hårdvaraenheter inom noden. Sedan konstruerades två typer av nätverk: en med bypass-anslutningar i varje nod och en annan utan några bypass-anslutningar. Dessa nätverk kontrollerades av en mjukvarudefinierad nätverkskontroller (SDN). Styrenheten visste våglängdsresurserna i nätverket. Flera algoritmer applicerades på dessa nätverk för att utvärdera effekten av ett förbikopplingsnätverk och för att identifiera de önskade egenskaperna (för att hitta en kort längdväg och minska sannolikheten för spektrumfragmentering) av en algoritm som är lämplig för ett nätverk med bypass-anslutningar. Resultaten av att tillämpa de föreslagna algoritmerna i två nät visade att förbikopplingsförbindelserna ökade blockeringssannolikheten i liten topologi men inte påverkade resultaten i stor topologi. Resultaten i ett storskaligt nätverk med bypass-nätverk var nästan samma som resultaten i ett nätverk utan bypass-anslutningar. Bypassanslutningar är således lämpliga för storskaliga nätverk.

Der Zellzyklus organisiert die Zellteilung, und kontrolliert die Replikation der DNA sowie die Weitergabe des Genoms an die nächste Zellgeneration. Er unterliegt einer strengen Kontrolle auf molekularer Ebene. Diese molekularen Kontrollmechanismen sind für das Überleben eines Organismus essentiell, da Fehler Krankheiten begüngstigen können. Vor allem Krebs ist assoziiert mit Abweichungen im Ablauf des Zellzyklus. Die Aufklärung solcher Kontrollmechanismen auf molekularer Ebene ermöglicht einerseits das Verständnis deren grundlegender Funktionsweise, andererseits können solche Erkenntnisse dazu beitragen, Methoden zu entwickeln um den Zellzyklus steuern zu können. Um die molekularen Abläufe des Zellzyklus in ihrer Gesamtheit besser zu verstehen, eignen sich computergestützte Analysen. Beim Zellzyklus handelt es sich um einen Signaltransduktionsweg. Die Eigenschaften dieser Prozesse stellen Rekonstruktion und Übersetzung in digital lesbare Formate vor besondere Herausforderungen in Bezug auf Skalierbarkeit, Simulierbarkeit und Parameterschätzung. Diese Studie präsentiert eine großskalige Netzwerkrekonstruktion des Zellzyklus des Modellorganismus Saccharomyces cerevisiae. Hierfür wurde die reaction-contingency Sprache benutzt, die sowohl eine mechanistisch detaillierte Rekonstruktion auf molekularer Ebene zulässt, als auch deren Übersetzung in ein bipartites Boolesches Modell. Für das Boolesche Modell mit 2506 Knoten konnte ein zyklischer Attraktor bestimmt werden, der das Verhalten einer sich teilenden Hefezelle darstellt. Das Boolesche Modell reproduziert zudem das erwartete phänotypische Verhalten bei Aktivierung von vier Zellzyklusinhibitoren, und in 32 von 37 getesteten Mutanten. Die Rekonstruktion des Zellzyklus der Hefe kann in Folgestudien genutzt werden, um Signaltransduktionswege zu integrieren, die mit dem Zellzyklus interferieren, deren Schnittstellen aufzuzeigen, und dem Ziel, die molekularen Mechanismen einer ganzen Zelle abzubilden, näher zu kommen. Diese Studie zeigt zudem, dass eine auf reaction- contingency Sprache basierte Rekonstruktion geeignet ist, um ein biologisches Netzwerk konsistent mit empirischer Daten darzustellen, und gleichzeitig durch Simulation die Funktionalität des Netzwerkes zu überprüfen. / The survival of a species depends on the correct transmission of an intact genome from one generation to the next. The cell cycle regulates this process and its correct execution is vital for survival of a species. The cell cycle underlies a strict control mechanism ensuring accurate cell cycle progression, as aberrations in cell cycle progression are often linked to serious defects and diseases such as cancer. Understanding this regulatory machinery of the cell cycle offers insights into how life functions on a molecular level and also provides for a better understanding of diseases and possible approaches to control them. Cell cycle control is furthermore a complex mechanism and studying it holistically provides for understanding its collective properties. Computational approaches facilitate holistic cell cycle control studies. However, the properties of the cell cycle control network challenge large-scale in silico studies with respect to scalability, model execution and parameter estimation. This thesis presents a mechanistically detailed and executable large-scale reconstruction of the Saccharomyces cerevisiae cell cycle control network based on reaction- contingency language. The reconstruction accounts for 229 proteins and consists of three individual cycles corresponding to the macroscopic events of DNA replication, spindle pole body duplication, and bud emergence and growth. The reconstruction translated into a bipartite Boolean model has, using an initial state determined with a priori knowledge, a cyclic attractor which reproduces the cyclic behavior of a wildtype yeast cell. The bipartite Boolean model has 2506 nodes and correctly responds to four cell cycle arrest chemicals. Furthermore, the bipartite Boolean model was used in a mutational study where 37 mutants were tested and 32 mutants found to reproduce known phenotypes. The reconstruction of the cell cycle control network of S. cerevisiae demonstrates the power of the reaction-contingency based approach, and paves the way for network extension with regard to the cell cycle machinery itself, and several signal transduction pathways interfering with the cell cycle.