Current ASIC only designs which interface with a general purpose processor are fairly restricted as far as their ability to be upgraded after fabrication. The primary intent of the research documented in this thesis is to determine if the inclusion of FPGAs in existing ASIC designs can be considered as an option for alleviating this constraint by analyzing the performance of such a framework as a replacement for the parsing logic in a typical network switch. This thesis also covers an ancilliary goal of the research which is to compare the various methods used to reconfigure modern FPGAs, including the use of self initiated dynamic partial reconfiguration, in regards to the degree in which they interrupt the operation of the device in which an FPGA is embedded. This portion of the research is also conducted in the context of a network switch and focuses on the ability of the network switch to reconfigure itself dynamically when presented with a new type of network traffic.

Peptide-membrane interactions play an important role in a number of biological processes, such as antimicrobial defence mechanisms, viral translocation, membrane fusion and functions ofmembrane proteins. In particular, amphipathic α-helical peptides comprise a large family of membrane-active peptides that could exhibit a broad range of biological activities. A membrane, interacting with an amphipathic α-helical peptide, may experience a number of possible structural transitions, including stretching, reorganization of lipid molecules, formation of defects, transient and stable pores, formation of vesicles, endo- and pinocytosis and other phenomena. Naturally, theoretical and experimental studies of these interactions have been an intense on-going area of research. However, complete understanding of the relationship between the structure of the peptide and themechanismof interaction it induces, as well asmolecular details of this process, still remain elusive. Lack of this knowledge is a key challenge in our efforts to elucidate some of the biological functions of membrane active peptides or to design peptides with tailored functionalities that can be exploited in drug delivery or antimicrobial strategies. In principle,molecular dynamics is a powerful research tool to study peptide-membrane interactions, which can provide a detailed description of these processes on molecular level. However, a model operating on the appropriate time and length scale is imperative in this description. In this study, we adopt a coarse-grained approach where the accessible simulation time and length scales reach microseconds and tens of nanometers, respectively. Thus, the two key objectives of this study are to validate the applicability of the adopted coarse-grained approach to the study of peptide-membrane interactions and to provide a systematic description of these interactions as a function of peptide structure and surface chemistry. We applied the adopted strategy to a range of peptide systems, whose behaviour has been well established in either experiments or detailed atomistic simulations and outlined the scope and applicability of the coarse-grained model. We generated some useful insights on the relationship between the structure of the peptides and themechanism of peptide-membrane interactions. Particularly interesting results have been obtained for LS3, a membrane spanning peptide, with a propensity to self-assembly into ion-conducting channels. Firstly, we captured, for the first time, the complete process of self-assembly of LS3 into a hexameric ion-conducting channel and explored its properties. The channel has structure of a barrel-stave pore with peptides aligned along the lipid tails. However, we discovered that a shorter version of the peptide leads to a more disordered, less stable structure often classified as a toroidal pore. This link between two types of pores has been established for the first time and opens interesting opportunities in tuning peptide structures for a particular pore-inducing mechanism. We also established that different classes of peptides can be uniquely characterized by the distinct energy profile as they cross the membrane. Finally, we extended this investigation to the internalization mechanisms of more complex entities such as peptide complexes and nanoparticles. Coarse-grained steered molecular dynamics simulations of these model systems are performed and some preliminary results are presented in this thesis. To summarize, in this thesis, we demonstrate that coarse-grained models can be successfully used to underpin peptide interaction and self-assembly processes in the presence of membranes in their full complexity. We believe that these simulations can be used to guide the design of peptides with tailored functionalities for applications such as drug delivery vectors and antimicrobial systems. This study also suggests that coarse-grained simulations can be used as an efficient way to generate initial configurations for more detailed atomistic simulations. These multiscale simulation ideas will be a natural future extension of this work.

Coarse-grained beaches, such as pure gravel (PG), mixed sand-gravel (MSG) and composite (CSG) beaches, can be considered as one of the most resilient non-cohesive morpho-sedimentary coastal environments to energetic wave forcing (e.g., storms). The hydraulically-rough and permeable nature of gravel (D50 > 2 mm), together with the steep (reflective) beach face, provide efficient mechanisms of wave energy dissipation in the swash zone and provide a natural means of coastal defence. Despite their potential for shore protection very little is known about the response of these environments during high energetic wave conditions. Field measurements of sediment transport and hydrodynamics on coarse-grained beaches are difficult, because there are few instruments capable of taking direct measurements in an energetic swash zone in which large clasts are moving, and significant morphological changes occur within a short period of time. Remote sensing methods emerge in this context as the most appropriate solution for these types of field measurement. A new remote sensing method, based around a mid-range (~ 50 m) 2D laser-scanner was developed, which allows the collection of swash zone hydrodynamics (e.g., vertical and horizontal runup position, swash depth and velocity) and bed changes on wave-by-wave time scale. This instrument allowed the complete coverage of the swash zone on several coarse-grained beaches with a vertical accuracy of approximately 0.015 m and an average horizontal resolution of 0.07 m. The measurements performed with this new methodology are within the accuracy of traditional field techniques (e.g. video cameras, ultrasonic bed-level sensors or dGPS). Seven field experiments were performed between March 2012 and January 2014 on six different coarse-grained beaches (Loe Bar, Chesil, Slapton, Hayling Island, Westward Ho! and Seascale), with each deployment comprising the 2D laser-scanner together with complementary in-situ instrumentation (e.g., pressure transducer, ADV current meter). These datasets were used to explore the hydrodynamics and morphological response of the swash zone of these different environments under different energetic hydrodynamic regimes, ranging from positive, to zero, to negative freeboard regimes. With reference to the swash zone dynamics under storms with positive freeboard regimes (when runup was confined to the foreshore) it was found that extreme runup has an inverse relationship with the surf scaling parameter (=2Hs /gTptan2). The highest vertical runup excursions were found on the steepest beaches (PG beaches) and under long-period swell, while lower vertical runup excursions where linked to short-period waves and beaches with intermediate and dissipative surf zones, thus demonstrating that the contrasting degree of wave dissipation observed in the different types of surf zones is a key factor that control the extreme runup on coarse-grained beaches. Contrasting morphological responses were observed on the different coarse-grained beaches as a result of the distinct swash\surf zone hydrodynamics. PG beaches with narrow surf zone presented an asymmetric morphological response during the tide cycle (accretion during the rising and erosion during the falling tide) as a result of beach step adjustments to the prevailing hydrodynamics. On dissipative MSG and CSG beaches the morphological response was limited due to the very dissipative surf zone, while on an intermediate CSG beach significant erosion of the beach face and berm was observed during the entire tide cycle as a result of the absence of moderate surf zone wave dissipation and beach step dynamics. Fundamental processes related to the link between the beach step dynamics and the asymmetrical morphological response during the tidal cycle were for the first time measured under energetic wave conditions. During the rising tide the onshore shift of the breaking point triggers the onshore translation of the step and favors accretion (step deposit development), while during the falling tide the offshore translation of the wave breaking point triggers retreat of the step and favours backwash sediment transport (erosion of the step deposit). Under zero and negative freeboard storm regimes (when runup exceeds the crest of the barrier or foredune), field measurements complimented by numerical modelling (Xbeach-G) provide clear evidence that the presence of a bimodal wave spectrum enhances the vertical runup and can increase the likelihood of the occurrence of overtopping and overwash events over a gravel barrier. Most runup equations (e.g., Stockdon et al., 2006) used to predict the thresholds for storm impact regime (e.g., swash, overtopping and overwash) on barriers lack adequate characterisation of the full wave spectra; therefore, they may miss important aspects of the incident wave field, such as wave bimodality. XBeach-G allows a full characterization of the incident wave field and is capable of predicting the effect of wave spectra bimodality on the runup, thus demonstrating that is a more appropriate tool for predicting the storm impact regimes on gravel barriers. Regarding the definition of storm impact regimes on gravel barriers, it was found that wave period and wave spectra bimodality are key parameters that can affect significantly the definition of the thresholds for these different regimes. While short-period waves dissipate most of their energy before reaching the swash zone (due to breaking) and produce short runup excursions, long-period waves arrive at the swash zone with enhanced heights (due to shoaling) and break at the edge of the swash, thus promoting large runup excursions. When offshore wave spectrum presents a bimodal shape, the wave transformation on shallow waters favours the long period peak (even if the short-period peak is the most energetic offshore) and large runup excursions occur. XBeach-G simulations show that the morphological response of fine gravel barriers is distinct from coarse gravel barriers under similar overtopping conditions. While on coarser barriers overtopping regimes are expected to increase the crest elevation and narrow the barrier, on fine barriers sedimentation occurs on the back of the barrier and in the lower beach face. Such different sedimentation patterns are attributed to the different hydraulic conductivity of the different sediment sizes which control the amount of flow dissipation (due to infiltration) and, therefore, the capacity of the flow to transport sediment across and over the barrier crest. The present findings have significantly improved our conceptual understanding of the response of coarse-grained beaches during storms. A new field technique to measure swash dynamics in the field was developed during this thesis and has great potential to become widely used in a variety of coastal applications.

Coarse-Grained Reconfigurable Architectures (CGRAs) are promising in developing high performance low-power portable applications. In this research, we crowdsource a mapping problem using gamification to harnass human intelligence. A scientific puzzle game, Untangled, was developed to solve a mapping problem by encapsulating architectural characteristics. The primary motive of this research is to draw insights from the mapping solutions of players who possess innate abilities like decision-making, creative problem-solving, recognizing patterns, and learning from experience. In this dissertation, an extensive analysis was conducted to investigate how players' computational skills help to solve an open-ended problem with different constraints. From this analysis, we discovered a few common strategies among players, and subsequently, a library of dictionaries containing identified patterns from players' solutions was developed. The findings help to propose a better version of the game that incorporates these techniques recognized from the experience of players. In the future, an updated version of the game that can be developed may help low-performance players to provide better solutions for a mapping problem. Eventually, these solutions may help to develop efficient mapping algorithms, In addition, this research can be an exemplar for future researchers who want to crowdsource such electrical engineering problems and this approach can also be applied to other domains.

No description available.

Proteínas desempenham uma grande variedade de funções biológicas. O conhecimento da estrutura tridimensional proteica pode ajudar no entendimento da função desempenhada. De acordo com a hipótese de Anfisen, a estrutura terciária nativa de uma proteína pode ser determinada a partir da informação contida na sequência primária, o que permitiria que métodos computacionais poderiam ser usados para predizer estruturas terciárias quando a primária estiver disponível. No entanto, ainda não existe uma ferramenta computacional capaz de predizer a estrutura tridimensional para uma grande variedade de proteínas. Desse modo, o problema de Predição de Estruturas de Proteínas (PEP) permanece como um desafio para a Biologia Molecular. A conformação nativa de uma proteína é frequentemente a configuração termodinamicamente mais estável, ou seja, que possui menor energia livre. Assim, PEP pode ser vista como um problema de otimização, onde a estrutura com menor energia livre deve ser encontrada dentre todas as possíveis. Entretanto, este é um problema NP-completo, no qual métodos tradicionais de otimização, em geral, não apresentam um bom desempenho. Algoritmos Genéticos (AGs), devido às suas características, são interessantes para essa classe de problemas. O principal objetivo desse trabalho é verificar se a adição de informação pode ser útil aos AGs aplicados em PEP, valendo-se dede modelos moleculares simplificados. Cada indivíduo do AG representa uma solução que, neste caso, é uma possível conformação que será avaliada por um campo de força. Dessa forma, o indivíduo é codificado por um conjunto de ângulos de torção de cada aminoácido. Para auxiliar no processo de busca, bases de dados compostas de ângulos determinados por cristalografia e RNM são utilizadas. Com o objetivo de guiar o processo de busca e manter a diversidade nos AGs, duas estratégias são aqui testadas: Imigrantes Aleatórios e Imigrantes por Similaridade. A última delas foi criada baseando-se na similaridade da sequência primária. Além disso, é investigado neste trabalho o uso de um campo de força coarse grained, que utiliza os átomos de carbono- para representar a cadeia proteica, para avaliar os indivíduos do AG. / Proteins exhibit an enormous variety of biology functions. The knowledge of tertiary structures can help the understanding of the proteins function. According to Anfisen, the native tertiary structure of a protein can be determined by its primary structure information, what could allow that computational methods could be used to predict the tertiary structure when the primary structure is available. However, there is still not a computational tool to solve the structure prediction problem for a large range of proteins. In this way, Protein Structure Prediction (PSP) has been a challenge to Molecular Biology. The conformation of native protein is usually the thermodynamically most stable configuration, i.e., the one having the lowest free energy. Hence, PSP can be viewed as a problem of optimization, where the structure with the lowest free energy should be found among all possible structures. However, this is an NP-problem, where traditional optimization methods, in general, do not have good performance. Genetic algorithms (GAs), due to their characteristics, are interesting for this class of problems. In recent years, there is a growing interest in using GAs for the protein structure prediction problem. The main objective of this work is to verify the addition of useful information to GAs employed in PSP. Each individual of the GA represents a solution for the optimization problem which is, in this case, a possible conformation that will be evaluated by a force field function. Thus, an individual is encoded by a set of torsion angles of each amino acid. In order to reduce the search space, a database composed of angles, determined by crystallography and NMR, is used. With the aim to guide the final search process and maintain diversity in GAs, two strategies were employed here: Random Immigrants and Similarity-based Immigrants. The last strategy was based on similarity of primary amino acid sequence. Furthermore, in this work, a coarse-grained force field, which uses -carbon to represent the protein backbone was employed to evaluate the individuals of GA.

Proteínas desempenham uma grande variedade de funções biológicas. O conhecimento da estrutura tridimensional proteica pode ajudar no entendimento da função desempenhada. De acordo com a hipótese de Anfisen, a estrutura terciária nativa de uma proteína pode ser determinada a partir da informação contida na sequência primária, o que permitiria que métodos computacionais poderiam ser usados para predizer estruturas terciárias quando a primária estiver disponível. No entanto, ainda não existe uma ferramenta computacional capaz de predizer a estrutura tridimensional para uma grande variedade de proteínas. Desse modo, o problema de Predição de Estruturas de Proteínas (PEP) permanece como um desafio para a Biologia Molecular. A conformação nativa de uma proteína é frequentemente a configuração termodinamicamente mais estável, ou seja, que possui menor energia livre. Assim, PEP pode ser vista como um problema de otimização, onde a estrutura com menor energia livre deve ser encontrada dentre todas as possíveis. Entretanto, este é um problema NP-completo, no qual métodos tradicionais de otimização, em geral, não apresentam um bom desempenho. Algoritmos Genéticos (AGs), devido às suas características, são interessantes para essa classe de problemas. O principal objetivo desse trabalho é verificar se a adição de informação pode ser útil aos AGs aplicados em PEP, valendo-se dede modelos moleculares simplificados. Cada indivíduo do AG representa uma solução que, neste caso, é uma possível conformação que será avaliada por um campo de força. Dessa forma, o indivíduo é codificado por um conjunto de ângulos de torção de cada aminoácido. Para auxiliar no processo de busca, bases de dados compostas de ângulos determinados por cristalografia e RNM são utilizadas. Com o objetivo de guiar o processo de busca e manter a diversidade nos AGs, duas estratégias são aqui testadas: Imigrantes Aleatórios e Imigrantes por Similaridade. A última delas foi criada baseando-se na similaridade da sequência primária. Além disso, é investigado neste trabalho o uso de um campo de força coarse grained, que utiliza os átomos de carbono- para representar a cadeia proteica, para avaliar os indivíduos do AG. / Proteins exhibit an enormous variety of biology functions. The knowledge of tertiary structures can help the understanding of the proteins function. According to Anfisen, the native tertiary structure of a protein can be determined by its primary structure information, what could allow that computational methods could be used to predict the tertiary structure when the primary structure is available. However, there is still not a computational tool to solve the structure prediction problem for a large range of proteins. In this way, Protein Structure Prediction (PSP) has been a challenge to Molecular Biology. The conformation of native protein is usually the thermodynamically most stable configuration, i.e., the one having the lowest free energy. Hence, PSP can be viewed as a problem of optimization, where the structure with the lowest free energy should be found among all possible structures. However, this is an NP-problem, where traditional optimization methods, in general, do not have good performance. Genetic algorithms (GAs), due to their characteristics, are interesting for this class of problems. In recent years, there is a growing interest in using GAs for the protein structure prediction problem. The main objective of this work is to verify the addition of useful information to GAs employed in PSP. Each individual of the GA represents a solution for the optimization problem which is, in this case, a possible conformation that will be evaluated by a force field function. Thus, an individual is encoded by a set of torsion angles of each amino acid. In order to reduce the search space, a database composed of angles, determined by crystallography and NMR, is used. With the aim to guide the final search process and maintain diversity in GAs, two strategies were employed here: Random Immigrants and Similarity-based Immigrants. The last strategy was based on similarity of primary amino acid sequence. Furthermore, in this work, a coarse-grained force field, which uses -carbon to represent the protein backbone was employed to evaluate the individuals of GA.

No description available.

Electrostatic interactions between charged species play a prominent role in determining structures and states of physical system, leading to important technological and biological applications. In coarse-grained simulations, accurate description of electrostatic interactions is crucial in addressing physical phenomena at larger spatial and longer temporal scales. In this thesis, we implement ENUF method, an abbreviation for Ewald summation based on non-uniform fast Fourier transform technique, into dissipative particle dynamics (DPD) scheme. With determined suitable parameters, the computational complexity of ENUF-DPD method is approximately described as O(N logN). The ENUF-DPD method is further validated by investigating dependence of polyelectrolyte conformations on charge fraction of polyelectrolyte and counterion valency of added salts, and studying of specific binding structures of dendrimers on amphiphilic membranes. In coarse-grained simulations, electrostatic interactions are either explicitly calculated with suitable methods, or implicitly included in effective potentials. The effect of treatment fashion of electrostatic interactions on phase behavior of [BMIM][PF6] ionic liquid (IL) is systematically investigated. Our systematic analyses show that electrostatic interactions should be incorporated explicitly in development of effective potentials, as well as in coarse-grained simulations to improve reliability of simulation results. Detailed image of microscopic structures and orientations of [BMIM][PF6] at graphene and vacuum interfaces are investigated by using atomistic simulations. Imidazolium rings and alkyl side chains of [BMIM] lie preferentially flat on graphene surface. At IL-vacuum interface, ionic groups pack closely together to form polar domains, leaving alkyl side chains populated at interface and imparting hydrophobic character. With the increase of IL filmthickness, orientations of [BMIM] change gradually from dominant flat distributions along graphene surface to orientations where imidazolium rings are either parallel or perpendicular to IL-vacuum interface with tilted angles. The interfacial spatial ionic structural heterogeneity formed by ionic groups also contributes to heterogeneous dynamics in interfacial regions.

Digital image processing and compression technologies have significant market potential, especially the JPEG2000 standard which offers outstanding codestream flexibility and high compression ratio. Strong demand for high performance digital image processing and compression system solutions is forcing designers to seek proper architectures that offer competitive advantages in terms of all performance metrics, such as speed and power. Traditional architectures such as ASIC, FPGA and DSPs have limitations in either low flexibility or high power consumption. On the other hand, through the provision of a degree of flexibility similar to that of a DSP and performance and power consumption advantages approaching that of an ASIC, coarse-grained dynamically reconfigurable architectures are proving to be strong candidates for future high performance digital image processing and compression systems. This thesis investigates dynamically reconfigurable architectures and especially the newly emerging RICA paradigm. Case studies such as Reed- Solomon decoder and WiMAX OFDM timing synchronisation engine are implemented in order to explore the potential of RICA-based architectures and the possible optimisation approaches such as eliminating conditional branches, reducing memory accesses and constructing kernels. Based on investigations in this thesis, a novel customised dynamically reconfigurable architecture targeting digital image processing and compression applications is devised, which can be tailored to adopt different applications. A demosaicing engine based on the Freeman algorithm is designed and implemented on the proposed architecture as the pre-processing module in a digital imaging system. An efficient data buffer rotating scheme is designed with the aim of reducing memory accesses. Meanwhile an investigation targeting mapping the demosaicing engine onto a dual-core RICA platform is performed. After optimisation, the performance of the proposed engine is carefully evaluated and compared in aspects of throughput and consumed computational resources. When targeting the JPEG2000 standard, the core tasks such as 2-D Discrete Wavelet Transform (DWT) and Embedded Block Coding with Optimal Truncation (EBCOT) are implemented and optimised on the proposed architecture. A novel 2-D DWT architecture based on vector operations associated with RICA paradigm is developed, and the complete DWT application is highly optimised for both throughput and area. For the EBCOT implementation, a novel Partial Parallel Architecture (PPA) for the most computationally intensive module in EBCOT, termed Context Modeling (CM), is devised. Based on the algorithm evaluation, an ARM core is integrated into the proposed architecture for performance enhancement. A Ping-Pong memory switching mode with carefully designed communication scheme between RICA based architecture and ARM is proposed. Simulation results demonstrate that the proposed architecture for JPEG2000 offers significant advantage in throughput.