Effective routing is critical in mobile ad hoc networks (MANETs). In recent years, many hierarchical routing protocols have been proposed to build a backbone structure for supporting MANET routing, especially for large scalability. The clustering approach is seen as the first step in providing a flat network with a hierarchical architecture. The clusterheads become the backbone nodes (BNs), which use greater power to transmit packets, forming the backbone network. Backbone network routing can reduce the number of data-packet forwarding hops throughout the entire network. However, previous protocols have focused on clustering schemes. Fault tolerance in a backbone structure has not been considered. In this paper, we propose a backup routing scheme that can repair broken links locally without activating a route re-discovery procedure. The backup route is piggybacked in the data packet header to achieve the most durable route. The proposed method can improve the packet delivery ratio and reduce control overhead, compared to general hierarchical routing protocols.

Com o aumento no uso de aglomerados e grades de computadores, cresce o interesse no estudo de comunicações entre processadores. Em um computador paralelo dedicado, ou em uma rede local homogênea, o tempo de comunicação é geralmente modelado de forma similar, independente de quais processadores estão se comunicando. Em uma rede onde os links entre os computadores são heterogêneos, computadores mais próximos tendem a apresentar menor latência e maior largura de banda do que computadores distantes. Além disso, a largura de banda agregada é diferente dependendo do número de conexões simultâneas existentes entre dois aglomerados distantes. Neste trabalho estudaremos a troca completa de mensagens de tamanhos diferentes entre aglomerados interligados por backbones. Proporemos um novo algoritmo de comunicação baseado em algoritmos conhecidos, apresentaremos simulações de escalonamentos dos algoritmos estudados para esta rede multi-aglomerado e analisaremos os resultados destas simulações. / The growth in popularity of clusters and computational grids caused an increase in the interest in studying interprocessors communications. The comunication time in a dedicated parallel computer or in a local homogeneous network is modeled in a similar way, regardless of which processors are communicating. In a network with heterogeneous links, closer computers generally have lower latency and larger bandwidth than wide area computers. Besides, the aggregated bandwidth depends on the number of simultaneous connections between two wide area clusters. In this work we study the complete exchange of messages of different sizes between interconnected clusters using a backbone. We propose a new comunication algorithm based on known algorithms, we present some scheduling simulations of the studied algorithms in this multi-cluster network and we present the results analysis of these simulations.

The increasing number of nucleic acid-based therapeutics demonstrates the potential to treat diseases at the genetic level. Although oligonucleotides show clinical potential, challenges remain including nuclease degradation, rapid clearance when administered systemically, low cell permeability, and limited distribution to tissues of interest. This is largely imparted by the polyanionic phosphate backbone, which produces unfavourable electrostatic interactions at cell membranes. As a result, their clinical translation is dependent on delivery technologies that improve stability, facilitate cell entry, and increase target affinity. Spherical nucleic acids (SNAs) consist of radially orienting linear nucleic acids onto a nanoparticle core, conferring them a three-dimensional, spherical architecture. These structures enter cells readily and display distinct properties that are independent of their nanoparticle core. Accordingly, we decided to replace the intrinsically anionic phosphodiester linkage of DNA with a phosphoramidate linkage (P-N), allowing us to incorporate new functionality at the phosphate backbone. With this handle, we inserted cationic and hydrophobically modified functional groups that were compatible with nanoscale architectures, giving rise to new properties relevant in biological contexts. Specifically, amine and guanidinium derivatized functional groups provided SNAs with a ~10-fold increase in cell uptake at early incubation times compared with unmodified SNAs. This demonstrates that we can tune the behaviour of SNAs with phosphate backbone modifications in a highly controlled manner. We hypothesize that the stringent control over location and placement of functional groups within the SNA framework will afford them favourable interactions at cell membranes, not only increasing their cell uptake, but also access to alternative uptake mechanisms and potency as therapeutics. / Thesis / Master of Science (MSc) / Oligonucleotides are short synthetic sequences of DNA or RNA that have the capacity to treat diseases at the genetic level. However, they face challenges such as degradation, low cell uptake, and poor tissue distribution. To overcome this issue, we plan to incorporate chemical modifications at the phosphate backbone of oligonucleotides to make them more stable and facilitate more favourable interactions at cell membranes. Conferring oligonucleotides into a 3D arrangement further enhances their stability and cell uptake relative to linear oligonucleotides. By densely functionalizing them onto a nanoparticle core, we can create spherical nucleic acids (SNAs). We hypothesize that the modifications imparted onto the phosphate backbone of linear oligonucleotides will translate their properties into SNAs. The new properties afforded to the SNAs will provide increased cell uptake, alternative uptake mechanisms, and access to cytosolic and nuclear targets, highlighting their potency and therapeutic potential.

Zugl.: Rostock, Univ., Diss., 2009

One of the protocols used for communication between coaches inside a train is the National Train Bus (NTB). The result of this work is support for diagnostics on the NTB - mainly watching the process data-flow and monitoring of chosen variables distributed along the train, with consideration to their character and validity.

Large-amplitude vibration of thin plates and shells has been critical design issues for many engineering structures. The increasingly more stringent safety requirements and the discovery of new materials with amazingly superior properties have further focused the attention of research on this area. This thesis deals with the vibration problem of rectangular, circular and angle-ply composite plates. This vibration can be triggered by an initial vibration amplitude, or an initial velocity, or both. Four types of boundary conditions including simply supported and clamped combined with in-plane movable/immovable are considered. To solve the differential equation generated from the vibration problem, Lindstedt's perturbation technique and Runge-Kutta method are applied. In previous works, this problem was solved by Lindstedt's Perturbation Technique. This technique can lead to a quick approximate solution. Yet based on mathematical assumptions, the solution will no longer be accurate for large amplitude vibration, especially when a significant amount of imperfection is considered. Thus Runge-Kutta method is introduced to solve this problem numerically. The comparison between both methods has shown the validity of the Lindstedt's Perturbation Technique is generally within half plate thickness. For a structure with a sufficiently large geometric imperfection, the vibration can be represented as a well-known backbone curve transforming from soften-spring to harden-spring. By parameter variation, the effects of imperfection, damping ratio, boundary conditions, wave numbers, young's modulus and a dozen more related properties are studied. Other interesting research results such as the dynamic failure caused by out-of-bound vibration and the change of vibration mode due to damping are also revealed.

ABSTRACT   Context: Many websites today are very interactive and the users are getting used to sites that change hundreds of elements every second. Often a JavaScript framework is used to build the web site and with many changing elements on the site the need for a JavaScript framework that can handle the fast changes are needed. Each frameworks do it differently to achieving this but most of them do some manipulation with the Document Object Model (DOM).     Objectives: This research will show how fast the selected MCV like JavaScript frameworks (AngularJs, AngularJs 2.0, Aurelia, Backbone, Ember, Knockout, Mithril, Vue) can create, delete and update HTML elements on the screen.     Methods: This research have used Google Chromes TimeLine tool to measure the speed of the frameworks. The test involves creating a HTML table and fill it with a thousand rows of data with six columns. The tables content are tested to see how fast the frameworks can create, update and remove the elements.       Conclusions: Angular 2.0 almost achieved first place in all tests. Angular 1.5 did very good in the update tests and was good in the create elements test. Backbone and Ember did not do so well in the create and update tests but Backbone was the best framework in one of the delete tests. Aurelia got very good results and so did Vue which almost had the same values as Aurelia throughout the tests. Mithril and Knockout performed well in the create test which placed them in the middle among all the selected frameworks. When it came to the update tests Mithril and Knockout also found them self in the middle positions of all the frameworks.          Key Words: JavaScript, Framework, performance, Angular, Aurelia, Backbone,  Ember, Knockout, Mithril, Vue.

Proteins are chemically simple molecules, being unbranched polymers of uncomplicated organic compounds. Nonetheless, they fold up into a dazzling variety of complex and beautiful configurations with a dizzying array of structural, regulatory, and catalytic functions. Despite great progress, we still have very limited ability to predict the folded conformation of an amino acid sequence, and limited understanding of its dynamics and motions. Thus, this work presents a quartet of interrelated studies that address some aspects of the detailed local conformations and motions of protein backbone. First, I used a density-dependent smoothing algorithm and a high-quality, B-filtered data set to construct highly accurate conformational distributions for protein backbone (Ramachandran plots) and sidechains (rotamers). These distributions are the most accurate and restrictive produced to date, with improved discrimination between rare-but-real conformations and artifactual ones. Second, I analyzed hundreds of alternate conformations in atomic resolution crystal structures, and discovered that dramatic conformational change in a protein sidechain is often coupled to a subtle but very common mode of conformational change in its backbone -- the backrub motion. Examination of other biophysical data further supports the ubiquity of this motion. Third, I applied a model of backrub motion to protein design calculations. Although experimental characterization of the designs showed them to be unstable and/or inactive, the computational results proved to be very sensitive to changes in the backbone. Finally, I describe how MolProbity uses my conformational distributions together with all-atom contacts and other tools to validate protein structures, and how those quality metrics can be combined visually or analytically to provide "multi-criterion" validation summaries. / dissertation

Given a protein sequence and the C£\ coordinates on its backbone, the all-atom protein backbone reconstruction problem (PBRP) is to reconstruct the backbone by its 3D coordinates of N, C and O atoms. In the past few decades, many methods have been proposed for solving PBRP, such as ab initio, homology modeling, SABBAC, Wang¡¦s method, Chang¡¦s method, BBQ (Backbone Building from Quadrilaterals) and Chen¡¦s method. Chen found that, if they can choose the correct prediction tool to build the 3D coordinates of the desired atoms, the RMSD may be improved. In this thesis, we propose a method for solving PBRP based on Chen¡¦s method. We use tool preference classification on each atom of the residue, where the classification model is generated by SVM (Support Vector Machine). We rebuild the backbone by combing the prediction results of all atoms in all residues. The data sets used in our experiments are CASP7, CASP8 and CASP9, which have 65, 52 and 63 proteins, respectively. These data sets contain nonstandard amino acids as well as standard ones. We improve the average RMSDs of Chen¡¦s results in some cases. The average RMSDs of our method are 0.3496 in CASP7, 0.3084 in CASP8 and 0.3286 in CASP9.

Zugl.: Stuttgart, Univ., Diss., 2006.