Self-Evaluation Applied Mathematics 2003-2008 University of Twente

This report contains the self-study for the research assessment of the Department of Applied Mathematics (AM) of the Faculty of Electrical Engineering, Mathematics and Computer Science (EEMCS) at the University of Twente (UT). The report provides the information for the Research Assessment Committee for Applied Mathematics, dealing with mathematical sciences at the three universities of technology in the Netherlands. It describes the state of affairs pertaining to the period 1 January 2003 to 31 December 2008

On the role of pre and post-processing in environmental data mining

The quality of discovered knowledge is highly depending on data quality. Unfortunately real data use to contain noise, uncertainty, errors, redundancies or even irrelevant information. The more complex is the reality to be analyzed, the higher the risk of getting low quality data. Knowledge Discovery from Databases (KDD) offers a global framework to prepare data in the right form to perform correct analyses. On the other hand, the quality of decisions taken upon KDD results, depend not only on the quality of the results themselves, but on the capacity of the system to communicate those results in an understandable form. Environmental systems are particularly complex and environmental users particularly require clarity in their results. In this paper some details about how this can be achieved are provided. The role of the pre and post processing in the whole process of Knowledge Discovery in environmental systems is discussed

Cellular automata : a bridge between building variability and urban form control

In Porto Alegre, a Brazilian town with 1,5 million inhabitants, zoning guidelines assign similar density parameters but fail to be context-specific. As these regulations are linked to individual plot dimensions, physical growth resulted in heterogeneous and unpredictable urban space. The Floor Space Index (FSI) has been used as physical currency which influences the plot value there hence creating a straightjacket to architects wanting to explore new shapes. This research describes a simultaneous top-down and bottom-up strategy to allow urban rules to emulate architectural flexibility and, at the same time, to empower the city with morphological controls over the urban space. A proposed integrated model was set to generate a wide variety of geometries through the association of morpho-types urban blocks (topdown) to bottom-up strategies using cellular automata integrated to Rhinoceros’ Grasshopper as a generative tool. The model includes context sensibility and daylight evaluation but runs with a similar FSI to the existing urban regulations. The proposed model was applied to an existing block in Porto Alegre demonstrating to be an effective tool to support the design of urban rules. It also indicated possible paths for built environment model integration and the creation of innovative perfomative urban indexes as building’s porosity.O Plano Diretor da cidade de Porto Alegre paradoxalmente atribui índices de densidade por região geográfica ao passo que falha ao desconsiderar o contexto imediato. Uma vez que os índices aplicados estão associados às dimensões de cada lote, o crescimento do ambiente construído é restringido pela unidade de divisão territorial (lote) e resulta em um espaço urbano imprevisível e heterogêneo. Nesse contexto, o indicador de intensidade ‘Índice de Aproveitamento’ (IA) é usado como ‘moeda física’ pelos incorporadores, influenciando o valor do lote e limitando a exploração formal dos arquitetos, via de regra, a prismas regulares. Esta pesquisa propõe um modelo alternativo que une estratégias centralizadoras (top-down) e emergentes (bottom-up) a fim de possibilitar a flexibilidade arquitetônica e o controle da forma do espaço urbano simultaneamente. O modelo generativo proposto objetiva gerar geometrias variadas por meio da associação de tipologias morfológicas de quadra (controle) e autômatos celulares (emergente). O modelo gera edificações de IA similar ao existente e aos especificados no plano diretor ao mesmo tempo que é sensível ao contexto e avalia o desempenho de iluminação natural no ambiente de modelagem Rhinoceros 3D e programação visual Grasshopper. O modelo foi aplicado a uma quadra existente em Porto Alegre e os resultados demonstraram a sua eficácia como ferramenta de projeto para a concepção de regras urbanas. Os resultados indicaram a possibilidade de integração com modelos de outras naturezas e da criação de novos índices urbanos performativos como ‘porosidade’

Stochastic analysis of nonlinear dynamics and feedback control for gene regulatory networks with applications to synthetic biology

The focus of the thesis is the investigation of the generalized repressilator model (repressing genes ordered in a ring structure). Using nonlinear bifurcation analysis stable and quasi-stable periodic orbits in this genetic network are characterized and a design for a switchable and controllable genetic oscillator is proposed. The oscillator operates around a quasi-stable periodic orbit using the classical engineering idea of read-out based control. Previous genetic oscillators have been designed around stable periodic orbits, however we explore the possibility of quasi-stable periodic orbit expecting better controllability. The ring topology of the generalized repressilator model has spatio-temporal symmetries that can be understood as propagating perturbations in discrete lattices. Network topology is a universal cross-discipline transferable concept and based on it analytical conditions for the emergence of stable and quasi-stable periodic orbits are derived. Also the length and distribution of quasi-stable oscillations are obtained. The findings suggest that long-lived transient dynamics due to feedback loops can dominate gene network dynamics. Taking the stochastic nature of gene expression into account a master equation for the generalized repressilator is derived. The stochasticity is shown to influence the onset of bifurcations and quality of oscillations. Internal noise is shown to have an overall stabilizing effect on the oscillating transients emerging from the quasi-stable periodic orbits. The insights from the read-out based control scheme for the genetic oscillator lead us to the idea to implement an algorithmic controller, which would direct any genetic circuit to a desired state. The algorithm operates model-free, i.e. in principle it is applicable to any genetic network and the input information is a data matrix of measured time series from the network dynamics. The application areas for readout-based control in genetic networks range from classical tissue engineering to stem cells specification, whenever a quantitatively and temporarily targeted intervention is required

Standard and retrial queueing systems: a comparative analysis

We describe main models and results of a new branch of the queueing theory, theory of retrial queues, which is characterized by the following basic assumption: a customer who cannot get service (due to finite capacity of the system, balking, impatience, etc.)leaves the service area, but after some random delay returns to the system again. Emphasis is done on comparison with standard queues with waiting line and queues with losses. We give a survey of main results for both single server M/G/1 type and multiserver M/M/c type retrial queues and discuss similarities and differences between the retrial queues and their standard counterparts. We demonstrate that although retrial queues are closely connected with these standard queueing models they, however, ossess unique distinguished features. We also mention some open problems.We describe main models and results of a new branch of the queueing theory, theory of retrial queues, which is characterized by the following basic assumption: a customer who cannot get service (due to finite capacity of the system, balking, impatience, etc.)leaves the service area, but after some random delay returns to the system again. Emphasis is done on comparison with standard queues with waiting line and queues with losses. We give a survey of main results for both single server M/G/1 type and multiserver M/M/c type retrial queues and discuss similarities and differences between the retrial queues and their standard counterparts. We demonstrate that although retrial queues are closely connected with these standard queueing models they, however, ossess unique distinguished features. We also mention some open problems

The power-series algorithm applied to the shortest-queue model

Queueing Theory;operations research