Genetic algorithm based indicator sequence method for exon prediction

Considerable research effort has been devoted in predicting the exon regions of genes. The binary indicator (BI), Electron ion interaction pseudo potential (EIIP), Filter method are some of the methods. All these methods make use of the period three behavior of the exon region. Even though the method suggested in this paper is similar to above mentioned methods , it introduces a set of sequences for mapping the nucleotides selected by applying genetic algorithm and found to be more promising

Ground state correlation energy of the Be-sequence for Z = 4-20 in MCDF approximation

The ground state (J = 0) electronic correlation energy of the 4-electron Be-sequence is calculated in the Multi-Configuration Dirac-Fock approximation for Z = 4-20. The 4 electrons were distributed over the configurations arising from the 1s, 2s, 2p, 3s, 3p and 3d orbitals. Theoretical values obtained here are in good agreement with experimental correlation energies.

Protein Folding Simulations: Confinement, External Fields and Sequence Design

The present Thesis looks at the problem of protein folding using Monte Carlo and Langevin simulations, three topics in protein folding have been studied: 1) the effect of confining potential barriers, 2) the effect of a static external field and 3) the design of amino acid sequences which fold in a short time and which have a stable native state (global minimum). Regarding the first topic, we studied the confinement of a small protein of 16 amino acids known as 1NJ0 (PDB code) which has a beta-sheet structure as a native state. The confinement of proteins occurs frequently in the cell environment. Some molecules called Chaperones, present in the cytoplasm, capture the unfolded proteins in their interior and avoid the formation of aggregates and misfolded proteins. This mechanism of confinement mediated by Chaperones is not yet well understood. In the present work we considered two kinds of potential barriers which try to mimic the confinement induced by a Chaperon molecule. The first kind of potential was a purely repulsive barrier whose only effect is to create a cavity where the protein folds up correctly. The second kind of potential was a barrier which includes both attractive and repulsive effects. We performed Wang-Landau simulations to calculate the thermodynamical properties of 1NJ0. From the free energy landscape plot we found that 1NJ0 has two intermediate states in the bulk (without confinement) which are clearly separated from the native and the unfolded states. For the case of the purely repulsive barrier we found that the intermediate states get closer to each other in the free energy landscape plot and eventually they collapse into a single intermediate state. The unfolded state is more compact, compared to that in the bulk, as the size of the barrier decreases. For an attractive barrier modifications of the states (native, unfolded and intermediates) are observed depending on the degree of attraction between the protein and the walls of the barrier. The strength of the attraction is measured by the parameter $\epsilon$. A purely repulsive barrier is obtained for $\epsilon=0$ and a purely attractive barrier for $\epsilon=1$. The states are changed slightly for magnitudes of the attraction up to $\epsilon=0.4$. The disappearance of the intermediate states of 1NJ0 is already observed for $\epsilon =0.6$. A very high attractive barrier ($\epsilon \sim 1.0$) produces a completely denatured state. In the second topic of this Thesis we dealt with the interaction of a protein with an external electric field. We demonstrated by means of computer simulations, specifically by using the Wang-Landau algorithm, that the folded, unfolded, and intermediate states can be modified by means of a field. We have found that an external field can induce several modifications in the thermodynamics of these states: for relatively low magnitudes of the field ($<2.06 \times 10^8$ V/m) no major changes in the states are observed. However, for higher magnitudes than ($6.19 \times 10^8$ V/m) one observes the appearance of a new native state which exhibits a helix-like structure. In contrast, the original native state is a $\beta$-sheet structure. In the new native state all the dipoles in the backbone structure are aligned parallel to the field. The design of amino acid sequences constitutes the third topic of the present work. We have tested the Rate of Convergence criterion proposed by D. Gridnev and M. Garcia ({\it work unpublished}). We applied it to the study of off-lattice models. The Rate of Convergence criterion is used to decide if a certain sequence will fold up correctly within a relatively short time. Before the present work, the common way to decide if a certain sequence was a good/bad folder was by performing the whole dynamics until the sequence got its native state (if it existed), or by studying the curvature of the potential energy surface. There are some difficulties in the last two approaches. In the first approach, performing the complete dynamics for hundreds of sequences is a rather challenging task because of the CPU time needed. In the second approach, calculating the curvature of the potential energy surface is possible only for very smooth surfaces. The Rate of Convergence criterion seems to avoid the previous difficulties. With this criterion one does not need to perform the complete dynamics to find the good and bad sequences. Also, the criterion does not depend on the kind of force field used and therefore it can be used even for very rugged energy surfaces.

Konzeption von Entwicklungspfaden für Zulieferparks in der Automobilindustrie

Die Automobilindustrie reagiert mit Modularisierungsstrategien auf die zunehmende Produktkomplexität, getrieben durch die wachsenden Individualisierungsanforde-rungen auf der Kundenseite und der Modellpolitik mit neuen Fahrzeuganläufen. Die Hersteller verlagern die Materialbereitstellungskomplexität durch Outsourcing an die nächste Zulieferebene, den First Tier Suppliern, die seit Beginn der 90er Jahre zunehmend in Zulieferparks in unmittelbarer Werknähe integriert werden. Typische Merkmale eines klassischen Zulieferparks sind: Bereitstellung einer Halleninfrastruktur mit Infrastrukturdienstleistungen, Anlieferung der Teileumfänge im JIS-Verfahren (Just-in-Sequence = reihenfolgegenaue Synchronisation), lokale Wertschöpfung (Vormontagen, Sequenzierung) des Zulieferers, Vertragsbindung der First Tier Zulieferer für die Dauer eines Produktlebenszyklus und Einbindung eines Logistikdienstleisters. Teilweise werden zur Finanzierung Förderprojekte des öffent-lichen Sektors initiiert. Bisher fehlte eine wissenschaftliche Bearbeitung dieses Themas "Zulieferpark". In der Arbeit werden die in Europa entstandenen Zulieferparks näher untersucht, um Vor- und Nachteile dieses Logistikkonzeptes zu dokumentieren und Entwicklungs-trends aufzuzeigen. Abgeleitet aus diesen Erkenntnissen werden Optimierungs-ansätze aufgezeigt und konkrete Entwicklungspfade zur Verbesserung der Chancen-Risikoposition der Hauptakteure Automobilhersteller, Zulieferer und Logistikdienst-leister beschrieben. Die Arbeit gliedert sich in vier Haupteile, einer differenzierten Beschreibung der Ausgangssituation und den Entwicklungstrends in der Automobilindustrie, dem Vorgehensmodell, der Dokumentation der Analyseergebnisse und der Bewertung von Zulieferparkmodellen. Im Rahmen der Ergebnisdokumentation des Analyseteils werden vier Zulieferparkmodelle in detaillierten Fallstudien anschaulich dargestellt. Zur Erarbeitung der Analyseergebnisse wurde eine Befragung der Hauptakteure mittels strukturierten Fragebögen durchgeführt. Zur Erhebung von Branchentrends und zur relativen Bewertung der Parkmodelle wurden zusätzlich Experten befragt. Zur Segmentierung der Zulieferparklandschaft wurde die Methode der Netzwerk-analyse eingesetzt. Die relative Bewertung der Nutzenposition basiert auf der Nutzwertanalyse. Als Ergebnisse der Arbeit liegen vor: · Umfassende Analyse der Zulieferparklandschaft in Europa, · Segmentierung der Parks in Zulieferparkmodelle, Optimierungsansätze zur Verbesserung einer Win-Win-Situation der beteiligten Hauptakteure, · Relative Nutzenbewertung der Zulieferparkmodelle, · Entwicklungspfade für klassische Zulieferparks.

Mobile P2Ping: A Super-Peer based Structured P2P System Using a Fleet of City Buses

Recently, researchers have introduced the notion of super-peers to improve signaling efficiency as well as lookup performance of peer-to-peer (P2P) systems. In a separate development, recent works on applications of mobile ad hoc networks (MANET) have seen several proposals on utilizing mobile fleets such as city buses to deploy a mobile backbone infrastructure for communication and Internet access in a metropolitan environment. This paper further explores the possibility of deploying P2P applications such as content sharing and distributed computing, over this mobile backbone infrastructure. Specifically, we study how city buses may be deployed as a mobile system of super-peers. We discuss the main motivations behind our proposal, and outline in detail the design of a super-peer based structured P2P system using a fleet of city buses.

Vision-based localization of an underwater robot in a structured environment

This paper presents a vision-based localization approach for an underwater robot in a structured environment. The system is based on a coded pattern placed on the bottom of a water tank and an onboard down looking camera. Main features are, absolute and map-based localization, landmark detection and tracking, and real-time computation (12.5 Hz). The proposed system provides three-dimensional position and orientation of the vehicle along with its velocity. Accuracy of the drift-free estimates is very high, allowing them to be used as feedback measures of a velocity-based low-level controller. The paper details the localization algorithm, by showing some graphical results, and the accuracy of the system

Estimating the motion of an underwater robot from a monocular image sequence

When underwater vehicles perform navigation close to the ocean floor, computer vision techniques can be applied to obtain quite accurate motion estimates. The most crucial step in the vision-based estimation of the vehicle motion consists on detecting matchings between image pairs. Here we propose the extensive use of texture analysis as a tool to ameliorate the correspondence problem in underwater images. Once a robust set of correspondences has been found, the three-dimensional motion of the vehicle can be computed with respect to the bed of the sea. Finally, motion estimates allow the construction of a map that could aid to the navigation of the robot

Detection of matchings in a sequence of underwater images through texture analysis

This paper presents an approach to ameliorate the reliability of the correspondence points relating two consecutive images of a sequence. The images are especially difficult to handle, since they have been acquired by a camera looking at the sea floor while carried by an underwater robot. Underwater images are usually difficult to process due to light absorption, changing image radiance and lack of well-defined features. A new approach based on gray-level region matching and selective texture analysis significantly improves the matching reliability

Calibration of a Structured Light-Based Stereo Catadioptric Sensor

Catadioptric sensors are combinations of mirrors and lenses made in order to obtain a wide field of view. In this paper we propose a new sensor that has omnidirectional viewing ability and it also provides depth information about the nearby surrounding. The sensor is based on a conventional camera coupled with a laser emitter and two hyperbolic mirrors. Mathematical formulation and precise specifications of the intrinsic and extrinsic parameters of the sensor are discussed. Our approach overcomes limitations of the existing omni-directional sensors and eventually leads to reduced costs of production

Robust decoupled visual servoing based on structured light

This paper focuses on the problem of realizing a plane-to-plane virtual link between a camera attached to the end-effector of a robot and a planar object. In order to do the system independent to the object surface appearance, a structured light emitter is linked to the camera so that 4 laser pointers are projected onto the object. In a previous paper we showed that such a system has good performance and nice characteristics like partial decoupling near the desired state and robustness against misalignment of the emitter and the camera (J. Pages et al., 2004). However, no analytical results concerning the global asymptotic stability of the system were obtained due to the high complexity of the visual features utilized. In this work we present a better set of visual features which improves the properties of the features in (J. Pages et al., 2004) and for which it is possible to prove the global asymptotic stability

Plane-to-plane positioning from image-based visual servoing and structured light

In this paper we face the problem of positioning a camera attached to the end-effector of a robotic manipulator so that it gets parallel to a planar object. Such problem has been treated for a long time in visual servoing. Our approach is based on linking to the camera several laser pointers so that its configuration is aimed to produce a suitable set of visual features. The aim of using structured light is not only for easing the image processing and to allow low-textured objects to be treated, but also for producing a control scheme with nice properties like decoupling, stability, well conditioning and good camera trajectory

A new optimised De Bruijn coding strategy for structured light patterns

Coded structured light is an optical technique based on active stereovision that obtains the shape of objects. One shot techniques are based on projecting a unique light pattern with an LCD projector so that grabbing an image with a camera, a large number of correspondences can be obtained. Then, a 3D reconstruction of the illuminated object can be recovered by means of triangulation. The most used strategy to encode one-shot patterns is based on De Bruijn sequences. In This work a new way to design patterns using this type of sequences is presented. The new coding strategy minimises the number of required colours and maximises both the resolution and the accuracy