QoS Support in the X11 Window Systems

Abstract In this paper, we consider the problem of providing QoS guarantees to the execution of applications using the X11 window system. In particular, we offer a system level analysis of the issues encountered when using X11 to serve realtime applications. By using a tracer developed for the purpose we analyse in depth the internal behaviour of the system

Communication in Microkernel-Based Operating Systems

Communication in microkernel-based systems is much more frequent than system calls known from monolithic kernels. This can be attributed to the placement of system services into their own protection domains. Communication has to be fast to avoid unnecessary overhead. Also, communication channels in microkernel-based systems are used for more than just remote procedure calls. In distributed systems, which also have a componentized design, it is state of the art to use tools to generate stubs for the communication between components. The communication interfaces of components are described in an interface definition language (IDL). In contrast to distributed systems, components of a microkernel-based system run on the same architecture and message delivery is guaranteed. In this Thesis, I explore the different kinds of communication, which can be used in microkernel-based systems, as well as their possible representation in IDL. Specifically, I introduce the syntax to describe kernel objects in IDL. I discuss the complexity of IDL compilers and its relation to the complexity of the IDL. Furthermore, I evaluate the performance of the communication stubs generated by different IDL compilers and discuss techniques to minimize performance overhead in generated stubs. I validated these techniques by implementing the Drops IDL Compiler - Dice. Finally, this Thesis presents a mechanism to measure the frequency and performance of invocations of generated communication code. I used this technique to conduct measurements in highly complex systems and introducing the least possible overhead

Communication in Microkernel-Based Operating Systems

Communication in microkernel-based systems is much more frequent than system calls known from monolithic kernels. This can be attributed to the placement of system services into their own protection domains. Communication has to be fast to avoid unnecessary overhead. Also, communication channels in microkernel-based systems are used for more than just remote procedure calls. In distributed systems, which also have a componentized design, it is state of the art to use tools to generate stubs for the communication between components. The communication interfaces of components are described in an interface definition language (IDL). In contrast to distributed systems, components of a microkernel-based system run on the same architecture and message delivery is guaranteed. In this Thesis, I explore the different kinds of communication, which can be used in microkernel-based systems, as well as their possible representation in IDL. Specifically, I introduce the syntax to describe kernel objects in IDL. I discuss the complexity of IDL compilers and its relation to the complexity of the IDL. Furthermore, I evaluate the performance of the communication stubs generated by different IDL compilers and discuss techniques to minimize performance overhead in generated stubs. I validated these techniques by implementing the Drops IDL Compiler - Dice. Finally, this Thesis presents a mechanism to measure the frequency and performance of invocations of generated communication code. I used this technique to conduct measurements in highly complex systems and introducing the least possible overhead

STRUCTURAL CHARACTERIZATION OF GEMINI-BASED NANOPARTICLES FOR DELIVERY OF DNA

Cationic gemini surfactants have been used for delivery of DNA into cells. These cationic surfactants are known to strongly bind to DNA to form a complex. In the dilute regimen, when the gemini-DNA complexes are mixed with helper neutral lipids, they undergo spontaneous assembly to form particles that are able to transfect DNA into the cells. In this study, the structure of several gemini surfactants, gemini-DNA complexes and gemini-DNA-neutral lipids complexes were systematically examined by small angle x-ray scattering (SAXS). The gemini surfactants were found to form micelles of varying shapes and arrangements modulated by the nature of spacer region and tail lengths. This includes ellipsoidal and worm-like micelles (as in the case of the 12- s-12 series) and disk-shaped hexagonally packed micelles (as in the case of 16-3-16). In addition to the study of the gemini surfactants, the effect of varying the DNA: gemini charge ratio on the DNA-gemini assembly was studied. The scattering pattern has shown that in the presence of excess gemini surfactants, free unbound surfactants exist in the solution. Upon the addition of neutral lipids, DNA-gemini-neutral lipid complexes are formed. The scattering patterns of the latter showed evidence of a strong interaction of the neutral lipids with the free gemini surfactants and the overcharged DNA-gemini complexes. Effectively, overcharging DNA-gemini complexes seem to aid in its incorporation into the neutral lipid matrix. These findings shed the light on the structure of DNA-gemini-neutral lipid systems and provide insights into the factors that influence the spontaneity of the self-assembly process. More importantly, the presented work provides a general strategy that can be applied to the study of similar systems using small angle x-ray scattering. A helium and vacuum chambers were made to enable testing the feasibility of the technique at the Canadian Light Source. Further, a pipeline was written to automate the reduction and analysis of SAXS data

Communication in Microkernel-Based Operating Systems

Communication in microkernel-based systems is much more frequent than system calls known from monolithic kernels. This can be attributed to the placement of system services into their own protection domains. Communication has to be fast to avoid unnecessary overhead. Also, communication channels in microkernel-based systems are used for more than just remote procedure calls. In distributed systems, which also have a componentized design, it is state of the art to use tools to generate stubs for the communication between components. The communication interfaces of components are described in an interface definition language (IDL). In contrast to distributed systems, components of a microkernel-based system run on the same architecture and message delivery is guaranteed. In this Thesis, I explore the different kinds of communication, which can be used in microkernel-based systems, as well as their possible representation in IDL. Specifically, I introduce the syntax to describe kernel objects in IDL. I discuss the complexity of IDL compilers and its relation to the complexity of the IDL. Furthermore, I evaluate the performance of the communication stubs generated by different IDL compilers and discuss techniques to minimize performance overhead in generated stubs. I validated these techniques by implementing the Drops IDL Compiler - Dice. Finally, this Thesis presents a mechanism to measure the frequency and performance of invocations of generated communication code. I used this technique to conduct measurements in highly complex systems and introducing the least possible overhead

Role of asynchronous awareness in digital art creation

Thesis (S.M.)--Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2008.Includes bibliographical references (p. 83-85).The majority of visitors to sites on the World Wide Web (WWW) have traditionally been only passive observers; consumers of previously created content. More recently, however, these users have been encouraged to contribute to these sites, opening the door to new forms of creative self expression. As we enter this new era of widespread collaboration and sharing made possible by the WWW, one question that remains is how to build appropriate communication channels to and from this new medium with respect to the tools used for digitally mediated creative expression. In this thesis, I will attempt to formulate a coherent set of characteristics that both creative programming environments and their associated WWW sites must possess to help improve, inspire, and support the work of creative individuals using these systems, which I will refer to as architectures for web-based collectivity.by Kyle Matthew Buza.S.M

Membrane mediated toppling mechanism of the folate energy coupling factor transporter

Energy coupling factor (ECF) transporters are responsible for the uptake of micronutrients in bacteria and archaea. They consist of an integral membrane unit, the S-component, and a tripartite ECF module. It has been proposed that the S-component mediates the substrate transport by toppling over in the membrane when docking onto an ECF module. Here, we present multi-scale molecular dynamics simulations and in vitro experiments to study the molecular toppling mechanism of the S-component of a folate-specific ECF transporter. Simulations reveal a strong bending of the membrane around the ECF module that provides a driving force for toppling of the S-component. The stability of the toppled state depends on the presence of non-bilayer forming lipids, as confirmed by folate transport activity mea- surements. Together, our data provide evidence for a lipid-dependent toppling-based mechanism for the folate-specific ECF transporter, a mechanism that might apply to other ECF transporters

The COMQUAD Component Container Architecture and Contract Negotiation

Component-based applications require runtime support to be able to guarantee non-functional properties. This report proposes an architecture for a real-time-capable, component-based runtime environment, which allows to separate non-functional and functional concerns in component-based software development. The architecture is presented with particular focus on three key issues: the conceptual architecture, an approach including implementation issues for splitting the runtime environment into a real-time-capable and a real-time-incapable part, and details of contract negotiation. The latter includes selecting component implementations for instantiantion based on their non-functional properties

Computational studies on Membrane Proteins (bovine CNGA1 & mouse TSPO)

Around thirty percent of total proteins are present in the membrane and play an important role to communicate intracellular and extracellular region. Their presence in the membrane is one of the limiting steps to determine protein structure and to understand their mechanisms. Hence bioinformatics techniques and computational tools play an important role to overcome these issues in characterizing the structural/functional mechanism of membrane proteins. In this thesis, I have developed and used state of the art computational techniques applied to two different pharmaceutically relevant membrane proteins, Cyclic nucleotide-gated channels (CNG) and translocator membrane protein (TSPO). CNG ion channels are embedded into the neuronal membrane. Till date, the structure and their gating mechanism are subject to interest. Different approaches like electrophysiology, single molecule force spectroscopy, biophysics, etc. have been employed to study these channels. Here I studied the gating mechanism of the CNGA1 ion channel by use of homology modeling and coarse-grained molecular dynamics. TSPO is a key biomarker for the diagnostics of inflammation in the brain. Limited Structural and functional information available on mammalian TSPOs homodimers. Computational studies suggested that the NMR-solved structure is not prone to dimer formation and is not stable in a membrane environment and has been an object of vivid criticism. To address this issue we use homology modeling technique and molecular dynamics approach. Principle results are: 1. I have successfully created homology models for CNGA1 homotetramer and performed coarse-grained simulation in the presence and absence of cGMP molecule and developed the coarse-grained force-field parameters for cGMP. 2. I have proposed a new model of the functionally relevant dimeric form of mTSPO. The model is fully consistent with solid-state NMR spectral data. Our predictions provide for the first time structural insights on this pharmaceutically important target fully consistent with experimental data. 3. During these studies, and in order to optimize the preparation of the systems it was necessary to develop an automated tool for creating the input files for doing coarse-grained simulations. These tools are shared with the community through a publically available online web-server that simplifies the task of generating input files which help in performing simulation and retrieving the result data for small simulations. The web-server, MERMAID is available at MERMAID (http://molsim.sci.univr.it/mangesh/). The application of novel computational approaches in this thesis allowed me to characterize extensively both systems by offering a rational to a huge amount of experimental data on biological relevant systems

Relieving the cognitive load of constructing molecular biological ontology based queries by means of visual aids.

Thesis (M.Comp.Sc.)-Universty of KwaZulu-Natal, Pietermaritzburg, 2007.The domain of molecular biology is complex and vast. Bio-ontologies and information visualisation have arisen in recent years as means to assist biologists in making sense of this information. Ontologies can enable the construction of conceptual queries, but existing systems to do this are too technical for most biologists. OntoDas, the software developed as part of this thesis work, demonstrates how the application of techniques from information visualisation and human computer interaction can result in software which enables biologists to construct conceptual queries