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Analysis of biochemical networks using linear programming Simeonidis, Vangelis ; ; et al in Proceedings of the 7th World Congress of Chemical Engineering on CD-ROM (2005, December) The application of mathematical programming methodologies to biochemical systems is demonstrated with the presentation of a linear programming (LP) algorithm for calculating minimal pathway distances in ... [more ▼] The application of mathematical programming methodologies to biochemical systems is demonstrated with the presentation of a linear programming (LP) algorithm for calculating minimal pathway distances in biochemical networks. Minimal pathway distances are identified as the smallest number of steps separating two nodes in the network. Two case studies are examined: 1) the minimal distances for Escherichia coli Small Molecule Metabolism (SMM) enzymes are calculated and their correlations with genome distance and enzyme function are considered; 2) a study of the p53 cell cycle and apoptosis control network is performed in order to assess the survivability of the network to both random node failures and a directed assault, by studying the modification of the network’s diameter for successive protein knockouts. The results verify the applicability of the algorithm to problems of biochemical nature. [less ▲] Detailed reference viewed: 67 (3 UL)Regions of stability for limit cycle oscillations in piecewise linear systems Goncalves, Jorge in IEEE Transactions on Automatic Control (2005), 50(11), 1877-1882 Oscillations appear in numerous applications from biology to technology.However, besides local results, rigorous stability and robustness analysis of oscillations are rarely done due to their intrinsic ... [more ▼] Oscillations appear in numerous applications from biology to technology.However, besides local results, rigorous stability and robustness analysis of oscillations are rarely done due to their intrinsic nonlinear behavior. Poincarémaps associated with the system cannot typically be found explicitly and stability is estimated using extensive simulations and experiments. This paper gives conditions in the form of linear matrix inequalities (LMIs) that guarantee asymptotic stability in a reasonably large region around a limit cycle for a class of systems known as piecewise linear systems (PLS). Such conditions, based on recent results on impact maps and surface Lyapunov functions (SuLF), allow a systematic and efficient analysis of oscillations of PLS or arbitrarily close approximations of nonlinear systems by PLS. The methodology applies to any locally stable limit cycle of a PLS, regardless of the dimension and the number of switching surfaces of the system, and is illustrated with a biological application: a fourth-order neural oscillator, also used in many robotics applications such as juggling and locomotion. [less ▲] Detailed reference viewed: 84 (0 UL)Eine adaptive Produktentwicklungsmethodik als Beitrag zur Prozessgestaltung in der Produktentwicklung ; Gericke, Kilian ; et al in Proceedings of 16th Symposium Design for X (2005) In den letzen Jahrzehnten ist eine Vielzahl von Modellen zur methodischen Unterstützung des Produktentwicklungsprozesses (PEP) entstanden. Diese präskriptiven Modelle beinhalten oft den impliziten ... [more ▼] In den letzen Jahrzehnten ist eine Vielzahl von Modellen zur methodischen Unterstützung des Produktentwicklungsprozesses (PEP) entstanden. Diese präskriptiven Modelle beinhalten oft den impliziten Anspruch, in jeder Branche und auf die Entwicklung jeder Art von Produkten anwendbar zu sein. Um dem gerecht zu werden, beschreiben die Modelle den PEP auf einem relativ abstrakten Niveau. Eine Anpassung an den Kontext der Produktentwicklung erfolgt in der Regel nicht. Existierende Ansätze ermöglichen eine Analyse des Kontexts aus verschiedenen Blickwinkeln, bieten jedoch keine konkreten Vorschläge, wie diese Analyse in den Prozess der Produktentwicklung einfließen kann. Welche Auswirkungen ausgewählte Kontextfaktoren auf tatsächliche PEP haben, geht aus einer schriftlichen Befragung von 1000 deutschen Unternehmen des produzierenden Gewerbes hervor. Es werden die Grundlagen einer Vorgehensweise beschrieben, welche basierend auf dem Kontext der Produktentwicklung die Gestaltung effektiver, effizienter, transparenter und methodisch unterstützter Produktentwicklungsprozesse ermöglichen soll. [less ▲] Detailed reference viewed: 114 (0 UL)How companies learn from design flaws: results from an empirical study of the german manufacturing industry ; Gericke, Kilian ; Blessing, Lucienne in Proceedings of the 15th International Conference on Engineering Design (2005) Design flaws often become apparent at a time when the product is already in use and its development process, which in many cases includes extensive testing of parts, components and prototypes, is ... [more ▼] Design flaws often become apparent at a time when the product is already in use and its development process, which in many cases includes extensive testing of parts, components and prototypes, is considered complete. Such flaws may reach from poor ergonomics to the total failure of the product. Often, especially when user safety is at risk, design flaws are so severe that companies are forced to announce a product callback. Petroski suggests that many (if not most) products, which we are familiar with today, have a long history of previously flawed designs [3]. This implies that designers did indeed learn from design flaws in both senses of the word “learn”: discovering the flaw and utilizing the knowledge gained about it to find a solution. As far as discovering a design flaw is concerned, it can be assumed that the feedback from those who interact with the physical products in practice – the individuals who maintain, repair, recycle but essentially use the products – plays an important role. In their previous work, the authors pointed out hat this feedback information could not only be vital for identifying potential product hazards but helps designers to review the effects of their design measures and therefore to improve their products from generation to generation [4]. In order to obtain a better understanding of how designers learn from design flaws, a mail survey was conducted that aimed at investigating company-, process- and product-related factors of this phenomenon and to answer (among others) the following research questions: • To what extent are design flaws of a company’s (or a competitor’s) product a driving force in the development of new products? • How do the designers of a company become aware of design flaws of their products? • How successful are companies in correcting design flaws? • How do successful and unsuccessful companies differ in terms of size, activity profile of their designers and characteristics of their products? • What are possible factors that influence the success in correcting a design fault? [less ▲] Detailed reference viewed: 77 (2 UL)Tradeoffs in networks with positive and negative feedback Goncalves, Jorge ; ; Scientific Conference (2005) Detailed reference viewed: 43 (0 UL)Reachability analysis of continuous time piecewise linear systems ; Goncalves, Jorge in Proceedings of the 44th IEEE Conference on Decision and Control and European Control Conference (2005) This paper presents a new approach to the reachability problem for a class of hybrid systems called Piecewise Linear Systems (PLS). The principal tool used is the impact map between switching surfaces ... [more ▼] This paper presents a new approach to the reachability problem for a class of hybrid systems called Piecewise Linear Systems (PLS). The principal tool used is the impact map between switching surfaces. The method consists of specifying a ellipsoidal set on the initial switching surface and finding upper- and lower-bound estimates of the possible reach sets using tools such as the S-procedure to set up linear matrix inequalities, of which numerical solutions are then computed. [less ▲] Detailed reference viewed: 52 (0 UL)Student's Perception of a Semantic Search Engine Reichert, Monique ; Linckels, Serge ; Scientific Conference (2005) Detailed reference viewed: 29 (0 UL)Application of robust model validation using SOSTOOLS to the study of G-Protein signalling in yeast ; ; et al Scientific Conference (2005) Two major methodological challenges in modeling biological systems are model (in)validation and parameter estimation. The traditional approach is to fit the model parameters to data. An alternative ... [more ▼] Two major methodological challenges in modeling biological systems are model (in)validation and parameter estimation. The traditional approach is to fit the model parameters to data. An alternative approach pioneered by Packard, Frenklach, Seiler and colleagues (Frenklach et al., 2002) defines the range of parameter values that is consistent with the data while taking into account parametric and data uncertainty. If an invalidation certificate is found, the feasible parameter space is proved empty; otherwise, attempts to describe the feasible parameter space are carried out. We refer to this methodology as Robust Model Validation (RMV). Here we perform RMV using sum of squares (SOS) programs implemented by the MATLAB toolbox SOSTOOLS (Prajna et al., 2002). The principal advantage of SOS over conventional semidefinite programming (SDP) techniques such as the Sprocedure is the possibility of using higher-order multipliers to obtain tighter parameter bounds. We applied SOSTOOLS to a simple model of the yeast heterotrimeric G-protein cycle. We were able to invalidate the model based on real experimental data. Furthermore, using synthetic data that did not invalidate the model, we explored different techniques for representing the feasible parameter space. [less ▲] Detailed reference viewed: 54 (1 UL)Mobile Satellite Broadcast and Multichannel Communications Analysis and Design Martin, Cristoff Book published by KTH (2005) In this thesis, analytical analysis and design techniques for wireless communications with diversity are studied. The impact of impairments such as correlated fading is analyzed using statistical models ... [more ▼] In this thesis, analytical analysis and design techniques for wireless communications with diversity are studied. The impact of impairments such as correlated fading is analyzed using statistical models. Countermeasures designed to overcome, or even exploit, such effects are proposed and examined. In particular two applications are considered, satellite broadcast to vehicular terminals and communication using transmitters and receivers equipped with multiple antennas. Mobile satellite broadcast systems offer the possibility of high data rate services with reliability and ubiquitous coverage. The design of sys- tem architectures providing such services requires complex trade-offs involving technical, economical, and regulatory aspects. A satisfactory availability can be ensured using space, terrestrial, and time diversity techniques. The amount of applied diversity affects the spectral efficiency and system performance. Also, dedicated satellite and terrestrial networks represent significant investments and regulatory limitations may further complicate system design. The work presented in this thesis provides insights to the technical aspects of the trade-offs above. This is done by deriving an efficient method for estimating what resources in terms of spectrum and delay are required for a broadcast service to reach a satisfactory number of end users using a well designed system. The results are based on statistical models of the mobile satellite channel for which efficient analytical design and error rate estimation methods are derived. We also provide insight to the achievable spectral efficiency using different transmitter and receiver configurations. Multiple-element antenna communication is a promising technology for future high speed wireless infrastructures. By adding a spatial dimension, radio resources in terms of transmission power and spectrum can be used more efficiently. Much of the design and analysis work has focused on cases where the transmitter either has access to perfect channel state information or it is blind and the spatial channels are uncorrelated. Herein, systems where the fading of the spatial channels is correlated and/or the transmitter has access to partial channel state information are considered. While maintaining perfect channel knowledge at the transmitter may prove difficult, updating parameters that change on a slower time scale could be realistic. Here we formulate analysis and design techniques based on statistical models of the multichannel propagation. Fundamental properties of the multi-element antenna channel and limitations given by information theory are investigated under an asymptotic assumption on the number of antennas on either side of the system. For example, limiting normal distributions are derived for the squared singular values of the channel matrix and the mutual information. We also propose and examine a practical scheme capable of exploiting partial channel state information. In both applications outlined above, by using statistical models of the channel characteristics in the system design, performance can be improved. The main contribution of this thesis is the development of efficient techniques for estimating the system performance in different scenarios. Such techniques are vital to obtain insights to the impact of different impairments and how countermeasures against these should be designed. [less ▲] Detailed reference viewed: 38 (2 UL) |
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