08221 Abstracts Collection -- Geometric Modeling

From May 26 to May 30 2008 the Dagstuhl Seminar 08221 ``Geometric Modeling\u27\u27 was held in the International Conference and Research Center (IBFI), Schloss Dagstuhl. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available

Computer-Aided Geometry Modeling

Techniques in computer-aided geometry modeling and their application are addressed. Mathematical modeling, solid geometry models, management of geometric data, development of geometry standards, and interactive and graphic procedures are discussed. The applications include aeronautical and aerospace structures design, fluid flow modeling, and gas turbine design

In conversation with simulation: The application of numerical simulation to the design of structural nodal connections

The thesis explores methods for integration of structural analysis, design and production in a digital design environment. The somewhat ambiguous title implies the ambition to make such integration in relation to the explorative phase of the design process which is described by Donald Sch\uf6n as having a conversational character. A conversation between the designer and the representation by the means of the tool. The tool is in this context a simulation and instead of exploring the potential of automatic optimisation, the simulation is used for designer driven exploration. The aim of the thesis is to give an overview of how this type of integration is currently being approached and to contribute with new tools and methods in that pursuit. The motivation behind the work is to lower the threshold for the application of structural analysis in early-stage design, with an ambition of architectural qualities and resource efficiency in mind. An overview of the historical context is portrayed with broad brush strokes, followed by a more precise account of the mathematical and physical context, which is complemented by an attempt to describe how our tools and roles tend to interplay in the composition of the design process. Methods such as the finite element method, isogeometric analysis, smoothed particle hydrodynamics and peridynamics, including their related geometrical representations are introduced in relation to this context. A variety of production techniques are also discussed in relation to material mechanical properties for conventional building materials such as steel, concrete and wood.The method development is approached through the use of numerical and physical experiments which are applied for design of material-efficient structural components, with a particular design process perspective. The nodal connection is chosen as an application because it combines geometrical and structural complexity in an element that is of crucial importance for a holistic spatial setting, while often being produced in a material inefficient way, with poor attention to detail.The three articles that are included follow a trajectory from large to small, from the holistic to the particular. The first article is a description of the computational design work with the roof for the new international airport of Mexico City. The second article aims to address one of the challenges that were faced in that project with material inefficiency for nodal connections, with a critical perspective on optimisation. The final article presents an extension/modification for the peridynamics theory enabling variable particle sizes and an irregular particle distribution through the introduction of a concept called force flux density. The development is motivated by limitations found in the present theory through numerical experiments. The method enables simulation of phenomena such as brittle fracture, for which correlation with Griffith\u27s theory of fracture is shown. Further work includes an extension of the force flux method from 2D to 3D, including calibration of material a model for 3D printed steel. Other possibilities involve the exploration of how such a method can adapt to the various stages of the design process, where requirements of accuracy, speed and interactivity will vary

Antimicrobial Peptides against Listeria monocytogenes : omic approaches and potential biotechnological applications

A Listeria monocytogenes representa uma ameaça, especialmente para pessoas com sistema imunológico fraco, crianças e mulheres grávidas. A Nisina é utilizada na indústria alimentar para comparar surtos de bactérias Gram-positivas que podem pôr em risco a saúde dos consumidores. No entanto, a pesquisa de novos compostos antimicrobianos (AMPs) tornou-se fundamental para contrastar a detecção cada vez mais frequente da resistência à nisina por L. monocytogenes. Neste trabalho, Bacillus velezensis P34 produtor de fengicina um lipopeptídeos cíclicos foi estudado como possível alternativa de AMPs para uso contra L. monocytogenes. O genoma completo de B. velezensis P34 foi investigado quanto à presença de aglomerados de genes de compostos antimicrobianos. Os compostos secretados foram identificados como fengicina A e B, e em menores quantidades bacilomicina L, por meio de análise de espectrometria de massas. A análise proteômica foi realizada para estudar o "proteosurfactoma", incluindo a proteína moonlight de L. monocytogenes tratada com uma concentração subletal de nisina, detectando a inibição do processo de virulência, além da promoção do biofilme como estratégia de resistência bacteriana. Um estudo proteômico adicional permitiu pela primeira vez a reação fisiológica em L. monocytogenes tratada com os AMPs secretados por Bacillus velezensis P34. Neste estudo, uma nanoencapsulação em lipossomas foi avaliada como aplicação biotecnológica. Dentre os principais resultados deste último trabalho, foi observada forte desregulação dos transportadores de manganês com intensa regulação de outros transportadores de metais para a homeostase de íons metálicos, além de forte regulação negativa de proteínas relacionadas com os principais fatores de virulência Prfa, σB e virR. Além disso, foi realizado um estudo de comparação proteômica e lipidômica adicional, no qual os AMPs de nisina e fengicina foram considerados nesta pesquisa. A forte regulação negativa de proteínas e a variação quantitativa dos ácidos graxos do lipidoma da membrana sugeriram fortemente a inibição do biofilme quando tratado com uma concentração subletal de lipopeptídeos de fengicina; enquanto um grupo de proteínas de membrana foi investigado por sua ação na manutenção da possível resistência de membrana aos AMPs. Os resultados sugeriram a estrutura multicelular do biofilme como a principal preocupação quando pequenas quantidades de nisina podem ser utilizadas, além de que o estudo da ação de compostos secretados de Bacillus velezensis P34 sobre L. monocytogenes pode representar um importante ponto de partida para estudos mais aprofundados de fengicina para uso contra Gram-bactérias positivas, incluindo cepas multirresistentes.Listeria monocytogenes poses a threat especially to people with weak immune systems, children, and pregnant women. Nisin is employed in food industries to contrast Gram positive bacteria outbreaks, which could endanger the health of consumers. However, the research of new antimicrobial compounds (AMPs) has become pivotal to contrast the always more frequent detection of L. monocytogenes nisin resistance. In this doctoral dissertation, the Bacillus velezensis P34, producer of fengycin cyclic lipopeptides as possible alternative AMPs, to use against L. monocytogenes, was studied. Bacillus velezensis P34 whole genome was investigated because of the presence of antimicrobial compound gene clusters, and the secreted compounds were identified as fengycin A and B and, in smaller quantities, bacillomycin L through mass spectrometric analysis. Proteomics analysis was carried out to study the “proteosurfactome” including moonlight protein of L. monocytogenes treated with a sub-lethal concentration of nisin detecting the inhibition of the virulence process besides the biofilm promotion as a bacterial resistance strategy. An additional proteomic study permitted, for the first time, to detect the physiological reaction on L. monocytogenes treated with the AMPs secreted by Bacillus velezensis P34; in the latter, a biotechnological application, specifically a liposome nanoencapsulation, was evaluated. Among the main results of this latter work, strong deregulation of the manganese transporters was observed with intense regulation of others metals transporters for the metal ions homeostasis, besides a strong downregulation of proteins related with the main virulence factors Prfa, σB and virR Moreover, an additional proteomic and lipidomic comparison study was performed, nisin and fengycin AMPs were considered in the experimental drawing of this latter. The strong downregulation of proteins and, quantitatively, the variation of membrane lipidome fatty acids strongly suggested the inhibition of biofilm when treated with a sub-lethal concentration of fengycin lipopeptides; whereas a group of membrane proteins was investigated for their action on the maintaining of the possible membrane resistance to AMPs. The results suggested the promotion of biofilm multicellular organization as the main concern when sub-lethal concentration of nisin was used, besides to that the L. monocytogenes responses to the CLPs synthesized by Bacillus velezensis P34 may represent an important start for deeper studies involving the antimicrobial action of fengycin to use against Gram-positive bacteria, including multiresistant strains

A Partially Randomized Approach to Trajectory Planning and Optimization for Mobile Robots with Flat Dynamics

Motion planning problems are characterized by huge search spaces and complex obstacle structures with no concise mathematical expression. The fixed-wing airplane application considered in this thesis adds differential constraints and point-wise bounds, i. e. an infinite number of equality and inequality constraints. An optimal trajectory planning approach is presented, based on the randomized Rapidly-exploring Random Trees framework (RRT*). The local planner relies on differential flatness of the equations of motion to obtain tree branch candidates that automatically satisfy the differential constraints. Flat output trajectories, in this case equivalent to the airplane's flight path, are designed using Bézier curves. Segment feasibility in terms of point-wise inequality constraints is tested by an indicator integral, which is evaluated alongside the segment cost functional. Although the RRT* guarantees optimality in the limit of infinite planning time, it is argued by intuition and experimentation that convergence is not approached at a practically useful rate. Therefore, the randomized planner is augmented by a deterministic variational optimization technique. To this end, the optimal planning task is formulated as a semi-infinite optimization problem, using the intermediate result of the RRT(*) as an initial guess. The proposed optimization algorithm follows the feasible flavor of the primal-dual interior point paradigm. Discretization of functional (infinite) constraints is deferred to the linear subproblems, where it is realized implicitly by numeric quadrature. An inherent numerical ill-conditioning of the method is circumvented by a reduction-like approach, which tracks active constraint locations by introducing new problem variables. Obstacle avoidance is achieved by extending the line search procedure and dynamically adding obstacle-awareness constraints to the problem formulation. Experimental evaluation confirms that the hybrid approach is practically feasible and does indeed outperform RRT*'s built-in optimization mechanism, but the computational burden is still significant.Bewegungsplanungsaufgaben sind typischerweise gekennzeichnet durch umfangreiche Suchräume, deren vollständige Exploration nicht praktikabel ist, sowie durch unstrukturierte Hindernisse, für die nur selten eine geschlossene mathematische Beschreibung existiert. Bei der in dieser Arbeit betrachteten Anwendung auf Flächenflugzeuge kommen differentielle Randbedingungen und beschränkte Systemgrößen erschwerend hinzu. Der vorgestellte Ansatz zur optimalen Trajektorienplanung basiert auf dem Rapidly-exploring Random Trees-Algorithmus (RRT*), welcher die Suchraumkomplexität durch Randomisierung beherrschbar macht. Der spezifische Beitrag ist eine Realisierung des lokalen Planers zur Generierung der Äste des Suchbaums. Dieser erfordert ein flaches Bewegungsmodell, sodass differentielle Randbedingungen automatisch erfüllt sind. Die Trajektorien des flachen Ausgangs, welche im betrachteten Beispiel der Flugbahn entsprechen, werden mittels Bézier-Kurven entworfen. Die Einhaltung der Ungleichungsnebenbedingungen wird durch ein Indikator-Integral überprüft, welches sich mit wenig Zusatzaufwand parallel zum Kostenfunktional berechnen lässt. Zwar konvergiert der RRT*-Algorithmus (im probabilistischen Sinne) zu einer optimalen Lösung, jedoch ist die Konvergenzrate aus praktischer Sicht unbrauchbar langsam. Es ist daher naheliegend, den Planer durch ein gradientenbasiertes lokales Optimierungsverfahren mit besseren Konvergenzeigenschaften zu unterstützen. Hierzu wird die aktuelle Zwischenlösung des Planers als Initialschätzung für ein kompatibles semi-infinites Optimierungsproblem verwendet. Der vorgeschlagene Optimierungsalgorithmus erweitert das verbreitete innere-Punkte-Konzept (primal dual interior point method) auf semi-infinite Probleme. Eine explizite Diskretisierung der funktionalen Ungleichungsnebenbedingungen ist nicht erforderlich, denn diese erfolgt implizit durch eine numerische Integralauswertung im Rahmen der linearen Teilprobleme. Da die Methode an Stellen aktiver Nebenbedingungen nicht wohldefiniert ist, kommt zusätzlich eine Variante des Reduktions-Ansatzes zum Einsatz, bei welcher der Vektor der Optimierungsvariablen um die (endliche) Menge der aktiven Indizes erweitert wird. Weiterhin wurde eine Kollisionsvermeidung integriert, die in den Teilschritt der Liniensuche eingreift und die Problemformulierung dynamisch um Randbedingungen zur lokalen Berücksichtigung von Hindernissen erweitert. Experimentelle Untersuchungen bestätigen, dass die Ergebnisse des hybriden Ansatzes aus RRT(*) und numerischem Optimierungsverfahren der klassischen RRT*-basierten Trajektorienoptimierung überlegen sind. Der erforderliche Rechenaufwand ist zwar beträchtlich, aber unter realistischen Bedingungen praktisch beherrschbar