Design and analysis of distributed utility maximization algorithm for multihop wireless network with inaccurate feedback

Distributed network utility maximization (NUM) is receiving increasing interests for cross-layer optimization problems in multihop wireless networks. Traditional distributed NUM algorithms rely heavily on feedback information between different network elements, such as traffic sources and routers. Because of the distinct features of multihop wireless networks such as time-varying channels and dynamic network topology, the feedback information is usually inaccurate, which represents as a major obstacle for distributed NUM application to wireless networks. The questions to be answered include if distributed NUM algorithm can converge with inaccurate feedback and how to design effective distributed NUM algorithm for wireless networks. In this paper, we first use the infinitesimal perturbation analysis technique to provide an unbiased gradient estimation on the aggregate rate of traffic sources at the routers based on locally available information. On the basis of that, we propose a stochastic approximation algorithm to solve the distributed NUM problem with inaccurate feedback. We then prove that the proposed algorithm can converge to the optimum solution of distributed NUM with perfect feedback under certain conditions. The proposed algorithm is applied to the joint rate and media access control problem for wireless networks. Numerical results demonstrate the convergence of the proposed algorithm. © 2013 John Wiley & Sons, Ltd.

Using genetic programming and decision trees for generating structural descriptions of four bar mechanisms

Four bar mechanisms are basic components of many important mechanical devices. The kinematic synthesis of four bar mechanisms is a difficult design problem. A novel method that combines the genetic programming and decision tree learning methods is presented. We give a structural description for the class of mechanisms that produce desired coupler curves. Constructive induction is used to find and characterize feasible regions of the design space. Decision trees constitute the learning engine, and the new features are created by genetic programming.

Automated Problem Domain Cognition Process in Information Systems Design

An automated cognitive approach for the design of Information Systems is presented. It is supposed to be used at the very beginning of the design process, between the stages of requirements determination and analysis, including the stage of analysis. In the context of the approach used either UML or ERD notations may be used for model representation. The approach provides the opportunity of using natural language text documents as a source of knowledge for automated problem domain model generation. It also simplifies the process of modelling by assisting the human user during the whole period of working upon the model (using UML or ERD notations).

Editorial overview:new protein production tools for structural biology

Full text: The idea of producing proteins from recombinant DNA hatched almost half a century ago. In his PhD thesis, Peter Lobban foresaw the prospect of inserting foreign DNA (from any source, including mammalian cells) into the genome of a λ phage in order to detect and recover protein products from Escherichia coli [ 1 and 2]. Only a few years later, in 1977, Herbert Boyer and his colleagues succeeded in the first ever expression of a peptide-coding gene in E. coli — they produced recombinant somatostatin [ 3] followed shortly after by human insulin. The field has advanced enormously since those early days and today recombinant proteins have become indispensable in advancing research and development in all fields of the life sciences. Structural biology, in particular, has benefitted tremendously from recombinant protein biotechnology, and an overwhelming proportion of the entries in the Protein Data Bank (PDB) are based on heterologously expressed proteins. Nonetheless, synthesizing, purifying and stabilizing recombinant proteins can still be thoroughly challenging. For example, the soluble proteome is organized to a large part into multicomponent complexes (in humans often comprising ten or more subunits), posing critical challenges for recombinant production. A third of all proteins in cells are located in the membrane, and pose special challenges that require a more bespoke approach. Recent advances may now mean that even these most recalcitrant of proteins could become tenable structural biology targets on a more routine basis. In this special issue, we examine progress in key areas that suggests this is indeed the case. Our first contribution examines the importance of understanding quality control in the host cell during recombinant protein production, and pays particular attention to the synthesis of recombinant membrane proteins. A major challenge faced by any host cell factory is the balance it must strike between its own requirements for growth and the fact that its cellular machinery has essentially been hijacked by an expression construct. In this context, Bill and von der Haar examine emerging insights into the role of the dependent pathways of translation and protein folding in defining high-yielding recombinant membrane protein production experiments for the common prokaryotic and eukaryotic expression hosts. Rather than acting as isolated entities, many membrane proteins form complexes to carry out their functions. To understand their biological mechanisms, it is essential to study the molecular structure of the intact membrane protein assemblies. Recombinant production of membrane protein complexes is still a formidable, at times insurmountable, challenge. In these cases, extraction from natural sources is the only option to prepare samples for structural and functional studies. Zorman and co-workers, in our second contribution, provide an overview of recent advances in the production of multi-subunit membrane protein complexes and highlight recent achievements in membrane protein structural research brought about by state-of-the-art near-atomic resolution cryo-electron microscopy techniques. E. coli has been the dominant host cell for recombinant protein production. Nonetheless, eukaryotic expression systems, including yeasts, insect cells and mammalian cells, are increasingly gaining prominence in the field. The yeast species Pichia pastoris, is a well-established recombinant expression system for a number of applications, including the production of a range of different membrane proteins. Byrne reviews high-resolution structures that have been determined using this methylotroph as an expression host. Although it is not yet clear why P. pastoris is suited to producing such a wide range of membrane proteins, its ease of use and the availability of diverse tools that can be readily implemented in standard bioscience laboratories mean that it is likely to become an increasingly popular option in structural biology pipelines. The contribution by Columbus concludes the membrane protein section of this volume. In her overview of post-expression strategies, Columbus surveys the four most common biochemical approaches for the structural investigation of membrane proteins. Limited proteolysis has successfully aided structure determination of membrane proteins in many cases. Deglycosylation of membrane proteins following production and purification analysis has also facilitated membrane protein structure analysis. Moreover, chemical modifications, such as lysine methylation and cysteine alkylation, have proven their worth to facilitate crystallization of membrane proteins, as well as NMR investigations of membrane protein conformational sampling. Together these approaches have greatly facilitated the structure determination of more than 40 membrane proteins to date. It may be an advantage to produce a target protein in mammalian cells, especially if authentic post-translational modifications such as glycosylation are required for proper activity. Chinese Hamster Ovary (CHO) cells and Human Embryonic Kidney (HEK) 293 cell lines have emerged as excellent hosts for heterologous production. The generation of stable cell-lines is often an aspiration for synthesizing proteins expressed in mammalian cells, in particular if high volumetric yields are to be achieved. In his report, Buessow surveys recent structures of proteins produced using stable mammalian cells and summarizes both well-established and novel approaches to facilitate stable cell-line generation for structural biology applications. The ambition of many biologists is to observe a protein's structure in the native environment of the cell itself. Until recently, this seemed to be more of a dream than a reality. Advances in nuclear magnetic resonance (NMR) spectroscopy techniques, however, have now made possible the observation of mechanistic events at the molecular level of protein structure. Smith and colleagues, in an exciting contribution, review emerging ‘in-cell NMR’ techniques that demonstrate the potential to monitor biological activities by NMR in real time in native physiological environments. A current drawback of NMR as a structure determination tool derives from size limitations of the molecule under investigation and the structures of large proteins and their complexes are therefore typically intractable by NMR. A solution to this challenge is the use of selective isotope labeling of the target protein, which results in a marked reduction of the complexity of NMR spectra and allows dynamic processes even in very large proteins and even ribosomes to be investigated. Kerfah and co-workers introduce methyl-specific isotopic labeling as a molecular tool-box, and review its applications to the solution NMR analysis of large proteins. Tyagi and Lemke next examine single-molecule FRET and crosslinking following the co-translational incorporation of non-canonical amino acids (ncAAs); the goal here is to move beyond static snap-shots of proteins and their complexes and to observe them as dynamic entities. The encoding of ncAAs through codon-suppression technology allows biomolecules to be investigated with diverse structural biology methods. In their article, Tyagi and Lemke discuss these approaches and speculate on the design of improved host organisms for ‘integrative structural biology research’. Our volume concludes with two contributions that resolve particular bottlenecks in the protein structure determination pipeline. The contribution by Crepin and co-workers introduces the concept of polyproteins in contemporary structural biology. Polyproteins are widespread in nature. They represent long polypeptide chains in which individual smaller proteins with different biological function are covalently linked together. Highly specific proteases then tailor the polyprotein into its constituent proteins. Many viruses use polyproteins as a means of organizing their proteome. The concept of polyproteins has now been exploited successfully to produce hitherto inaccessible recombinant protein complexes. For instance, by means of a self-processing synthetic polyprotein, the influenza polymerase, a high-value drug target that had remained elusive for decades, has been produced, and its high-resolution structure determined. In the contribution by Desmyter and co-workers, a further, often imposing, bottleneck in high-resolution protein structure determination is addressed: The requirement to form stable three-dimensional crystal lattices that diffract incident X-ray radiation to high resolution. Nanobodies have proven to be uniquely useful as crystallization chaperones, to coax challenging targets into suitable crystal lattices. Desmyter and co-workers review the generation of nanobodies by immunization, and highlight the application of this powerful technology to the crystallography of important protein specimens including G protein-coupled receptors (GPCRs). Recombinant protein production has come a long way since Peter Lobban's hypothesis in the late 1960s, with recombinant proteins now a dominant force in structural biology. The contributions in this volume showcase an impressive array of inventive approaches that are being developed and implemented, ever increasing the scope of recombinant technology to facilitate the determination of elusive protein structures. Powerful new methods from synthetic biology are further accelerating progress. Structure determination is now reaching into the living cell with the ultimate goal of observing functional molecular architectures in action in their native physiological environment. We anticipate that even the most challenging protein assemblies will be tackled by recombinant technology in the near future.

Mathematical Modeling of the Weaving Structure Design

Красимир Йорджев, Христина Костадинова - В работата се разглежда една релация на еквивалентност в множеството от всички квадратни бинарни матрици. Обсъдена е комбинаторната задача за намиране мощността и елементите на фактормножеството относно тази релация. Разгледана е и възможността за получаване на някои специални елементи на това фактормножество. Предложен е алгоритъм за решаване на поставените задачи. Получените в статията резултати намират приложение при описанието топологията на различните тъкачни структури.

Practical design considerations of cascaded hybrid battery storage systems

The high cost of batteries has led to investigations in using second-life ex-transportation batteries for grid support applications. Vehicle manufacturers currently all have different specifications for battery chemistry, arrangement of cells, capacity and voltage. With anticipated new developments in battery chemistry which could also affect these parameters, there are, as yet, no standards defining parameters in second life applications. To overcome issues relating to sizing and to prevent future obsolescence for the rest of the energy storage system, a cascaded topology with an operating envelope design approach has been used to connect together modules. This topology offers advantages in terms of system reliability. The design methodology is validated through a set of experimental results resulting in the creation of surface maps looking at the operation of the converter (efficiency and inductor ripple current). The use of a pre-defined module operating envelope also offers advantages for developing new operational strategies for systems with both hybrid battery energy systems and also hybrid systems including other energy sources such as solar power.

Design of a modular, high step-up ratio DC–DC converter for HVDC applications integrating offshore wind power

High-power and high-voltage gain dc-dc converters are key to high-voltage direct current (HVDC) power transmission for offshore wind power. This paper presents an isolated ultra-high step-up dc-dc converter in matrix transformer configuration. A flyback-forward converter is adopted as the power cell and the secondary side matrix connection is introduced to increase the power level and to improve fault tolerance. Because of the modular structure of the converter, the stress on the switching devices is decreased and so is the transformer size. The proposed topology can be operated in column interleaved modes, row interleaved modes, and hybrid working modes in order to deal with the varying energy from the wind farm. Furthermore, fault-tolerant operation is also realized in several fault scenarios. A 400-W dc-dc converter with four cells is developed and experimentally tested to validate the proposed technique, which can be applied to high-power high-voltage dc power transmission.

Refinement methods for software architecture design using the software architecture model

Modern software systems are often large and complicated. To better understand, develop, and manage large software systems, researchers have studied software architectures that provide the top level overall structural design of software systems for the last decade. One major research focus on software architectures is formal architecture description languages, but most existing research focuses primarily on the descriptive capability and puts less emphasis on software architecture design methods and formal analysis techniques, which are necessary to develop correct software architecture design. ^ Refinement is a general approach of adding details to a software design. A formal refinement method can further ensure certain design properties. This dissertation proposes refinement methods, including a set of formal refinement patterns and complementary verification techniques, for software architecture design using Software Architecture Model (SAM), which was developed at Florida International University. First, a general guideline for software architecture design in SAM is proposed. Second, specification construction through property-preserving refinement patterns is discussed. The refinement patterns are categorized into connector refinement, component refinement and high-level Petri nets refinement. These three levels of refinement patterns are applicable to overall system interaction, architectural components, and underlying formal language, respectively. Third, verification after modeling as a complementary technique to specification refinement is discussed. Two formal verification tools, the Stanford Temporal Prover (STeP) and the Simple Promela Interpreter (SPIN), are adopted into SAM to develop the initial models. Fourth, formalization and refinement of security issues are studied. A method for security enforcement in SAM is proposed. The Role-Based Access Control model is formalized using predicate transition nets and Z notation. The patterns of enforcing access control and auditing are proposed. Finally, modeling and refining a life insurance system is used to demonstrate how to apply the refinement patterns for software architecture design using SAM and how to integrate the access control model. ^ The results of this dissertation demonstrate that a refinement method is an effective way to develop a high assurance system. The method developed in this dissertation extends existing work on modeling software architectures using SAM and makes SAM a more usable and valuable formal tool for software architecture design. ^

An innovative approach to teaching structural induction for computer science

Proofs by induction are central to many computer science areas such as data structures, theory of computation, programming languages, program efficiency-time complexity, and program correctness. Proofs by induction can also improve students’ understanding and performance of computer science concepts such as programming languages, algorithm design, and recursion, as well as serve as a medium for teaching them. Even though students are exposed to proofs by induction in many courses of their curricula, they still have difficulties understanding and performing them. This impacts the whole course of their studies, since proofs by induction are omnipresent in computer science. Specifically, students do not gain conceptual understanding of induction early in the curriculum and as a result, they have difficulties applying it to more advanced areas later on in their studies. The goal of my dissertation is twofold: (1) identifying sources of computer science students’ difficulties with proofs by induction, and (2) developing a new approach to teaching proofs by induction by way of an interactive and multimodal electronic book (e-book). For the first goal, I undertook a study to identify possible sources of computer science students’ difficulties with proofs by induction. Its results suggest that there is a close correlation between students’ understanding of inductive definitions and their understanding and performance of proofs by induction. For designing and developing my e-book, I took into consideration the results of my study, as well as the drawbacks of the current methodologies of teaching proofs by induction for computer science. I designed my e-book to be used as a standalone and complete educational environment. I also conducted a study on the effectiveness of my e-book in the classroom. The results of my study suggest that, unlike the current methodologies of teaching proofs by induction for computer science, my e-book helped students overcome many of their difficulties and gain conceptual understanding of proofs induction.

Study of carbon nanotube film and shape memory alloys treatment for sensing and structural vibration control

Structural vibration control is of great importance. Current active and passive vibration control strategies usually employ individual elements to fulfill this task, such as viscoelastic patches for providing damping, transducers for picking up signals and actuators for inputting actuating forces. The goal of this dissertation work is to design, manufacture, investigate and apply a new type of multifunctional composite material for structural vibration control. This new composite, which is based on multi-walled carbon nanotube (MWCNT) film, is potentially to function as free layer damping treatment and strain sensor simultaneously. That is, the new material integrates the transducer and the damping patch into one element. The multifunctional composite was prepared by sandwiching the MWCNT film between two adhesive layers. Static sensing test indicated that the MWCNT film sensor resistance changes almost linearly with the applied load. Sensor sensitivity factors were comparable to those of the foil strain gauges. Dynamic test indicated that the MWCNT film sensor can outperform the foil strain gage in high frequency ranges. Temperature test indicated the MWCNT sensor had good temperature stability over the range of 237 K-363 K. The Young’s modulus and shear modulus of the MWCNT film composite were acquired by nanoindentation test and direct shear test, respectively. A free vibration damping test indicated that the MWCNT composite sensor can also provide good damping without adding excessive weight to the base structure. A new model for sandwich structural vibration control was then proposed. In this new configuration, a cantilever beam covered with MWCNT composite on top and one layer of shape memory alloy (SMA) on the bottom was used to illustrate this concept. The MWCNT composite simultaneously serves as free layer damping and strain sensor, and the SMA acts as actuator. Simple on-off controller was designed for controlling the temperature of the SMA so as to control the SMA recovery stress as input and the system stiffness. Both free and forced vibrations were analyzed. Simulation work showed that this new configuration for sandwich structural vibration control was successful especially for low frequency system.

Structural Characterization of Metal Hydrides for Energy Applications

Hydrogen can be an unlimited source of clean energy for future because of its very high energy density compared to the conventional fuels like gasoline. An efficient and safer way of storing hydrogen is in metals and alloys as hydrides. Light metal hydrides, alanates and borohydrides have very good hydrogen storage capacity, but high operation temperatures hinder their application. Improvement of thermodynamic properties of these hydrides is important for their commercial use as a source of energy. Application of pressure on materials can have influence on their properties favoring hydrogen storage. Hydrogen desorption in many complex hydrides occurs above the transition temperature. Therefore, it is important to study the physical properties of the hydride compounds at ambient and high pressure and/or high temperature conditions, which can assist in the design of suitable storage materials with desired thermodynamic properties. ^ The high pressure-temperature phase diagram, thermal expansion and compressibility have only been evaluated for a limited number of hydrides so far. This situation serves as a main motivation for studying such properties of a number of technologically important hydrides. Focus of this dissertation was on X-ray diffraction and Raman spectroscopy studies of Mg2FeH6, Ca(BH4) 2, Mg(BH4)2, NaBH4, NaAlH4, LiAlH4, LiNH2BH3 and mixture of MgH 2 with AlH3 or Si, at different conditions of pressure and temperature, to obtain their bulk modulus and thermal expansion coefficient. These data are potential source of information regarding inter-atomic forces and also serve as a basis for developing theoretical models. Some high pressure phases were identified for the complex hydrides in this study which may have better hydrogen storage properties than the ambient phase. The results showed that the highly compressible B-H or Al-H bonds and the associated bond disordering under pressure is responsible for phase transitions observed in brorohydrides or alanates. Complex hydrides exhibited very high compressibility suggesting possibility to destabilize them with pressure. With high capacity and favorable thermodynamics, complex hydrides are suitable for reversible storage. Further studies are required to overcome the kinetic barriers in complex hydrides by catalytic addition. A comparative study of the hydride properties with that of the constituting metal, and their inter relationships were carried out with many interesting features.^

Pressure induced structural changes and gas diffusion pathways in monomeric fluorescent proteins

Fluorescent proteins (FPs) are extremely valuable biochemical markers which have found a wide range of applications in cellular and molecular biology research. The monomeric variants of red fluorescent proteins (RFPs), known as mFruits, have been especially valuable for in vivo applications in mammalian cell imaging. Fluorescent proteins consist of a chromophore caged in the beta-barrel protein scaffold. The photophysical properties of an FP is determined by its chromophore structure and its interactions with the protein barrel. Application of hydrostatic pressure on FPs results in the modification of the chromophore environment which allows a systematic study of the role of the protein-chromophore interactions on photophysical properties of FPs. Using Molecular Dynamics (MD) computer simulations, I investigated the pressure induced structural changes in the monomeric variants mCherry, mStrawberry, and Citrine. The results explain the molecular basis for experimentally observed pressure responses among FP variants. It is found that the barrel flexibility, hydrogen bonding interactions and chromophore planarity of the FPs can be correlated to their contrasting photophysical properties at vaious pressures. I also investigated the oxygen diffusion pathways in mOrange and mOrange2 which exhibit marked differences in oxygen sensitivities as well as photostability. Such computational identifications of structural changes and oxygen diffusion pathways are important in guiding mutagenesis efforts to design fluorescent proteins with improved photophysical properties.

Development of physics-based models and design optimization of power electronic conversion systems

The main objective for physics based modeling of the power converter components is to design the whole converter with respect to physical and operational constraints. Therefore, all the elements and components of the energy conversion system are modeled numerically and combined together to achieve the whole system behavioral model. Previously proposed high frequency (HF) models of power converters are based on circuit models that are only related to the parasitic inner parameters of the power devices and the connections between the components. This dissertation aims to obtain appropriate physics-based models for power conversion systems, which not only can represent the steady state behavior of the components, but also can predict their high frequency characteristics. The developed physics-based model would represent the physical device with a high level of accuracy in predicting its operating condition. The proposed physics-based model enables us to accurately develop components such as; effective EMI filters, switching algorithms and circuit topologies [7]. One of the applications of the developed modeling technique is design of new sets of topologies for high-frequency, high efficiency converters for variable speed drives. The main advantage of the modeling method, presented in this dissertation, is the practical design of an inverter for high power applications with the ability to overcome the blocking voltage limitations of available power semiconductor devices. Another advantage is selection of the best matching topology with inherent reduction of switching losses which can be utilized to improve the overall efficiency. The physics-based modeling approach, in this dissertation, makes it possible to design any power electronic conversion system to meet electromagnetic standards and design constraints. This includes physical characteristics such as; decreasing the size and weight of the package, optimized interactions with the neighboring components and higher power density. In addition, the electromagnetic behaviors and signatures can be evaluated including the study of conducted and radiated EMI interactions in addition to the design of attenuation measures and enclosures.

An Innovative Approach to Teaching Structural Induction for Computer Science

Proofs by induction are central to many computer science areas such as data structures, theory of computation, programming languages, program efficiency-time complexity, and program correctness. Proofs by induction can also improve students’ understanding of and performance with computer science concepts such as programming languages, algorithm design, and recursion, as well as serve as a medium for teaching them. Even though students are exposed to proofs by induction in many courses of their curricula, they still have difficulties understanding and performing them. This impacts the whole course of their studies, since proofs by induction are omnipresent in computer science. Specifically, students do not gain conceptual understanding of induction early in the curriculum and as a result, they have difficulties applying it to more advanced areas later on in their studies. The goal of my dissertation is twofold: 1. identifying sources of computer science students’ difficulties with proofs by induction, and 2. developing a new approach to teaching proofs by induction by way of an interactive and multimodal electronic book (e-book). For the first goal, I undertook a study to identify possible sources of computer science students’ difficulties with proofs by induction. Its results suggest that there is a close correlation between students’ understanding of inductive definitions and their understanding and performance of proofs by induction. For designing and developing my e-book, I took into consideration the results of my study, as well as the drawbacks of the current methodologies of teaching proofs by induction for computer science. I designed my e-book to be used as a standalone and complete educational environment. I also conducted a study on the effectiveness of my e-book in the classroom. The results of my study suggest that, unlike the current methodologies of teaching proofs by induction for computer science, my e-book helped students overcome many of their difficulties and gain conceptual understanding of proofs induction.

Analysis and design of tall concrete buildings : an investigation regarding the use of cracked versus un-cracked moment of inertia

A debate is currently prevalent among the structural engineers regarding the use of cracked versus un-cracked moment of inertia of the structural elements in analyzing and designing tall concrete buildings. (The basic definition of a tall building, according to the Journal of Structural Design of Tall Buildings Vol. 13. No. 5, 2004 is a structure that is equal to or greater than 160 feet in height, or 6 stories or greater.) The controversy is the result of differing interpretations of certain ACI (American Concrete Institute) code provisions. The issue is whether designers should use cracked moment of inertia in order to estimate lateral deflection and whether the computed lateral deflection should be used to carry out subsequent second-order analysis (analysis considering the effect of first order lateral deflections on bending moment and shear stresses). On one hand, bending moments and shear forces estimated based on un-cracked moment of inertia of the sections may result in conservative designs by overestimating moments and shears. On the other hand, lateral deflections may be underestimated due to the same analyses resulting in unsafe designs.