Novel Proteins Involved in Dynamics of The Photosynthetic Apparatus

During the past few years, a considerable number of research articles have been published relating to the structure and function of the major photosynthetic protein complexes, photosystem (PS) I, PSII, cytochrome (Cyt) b6f, and adenosine triphosphate (ATP) synthase. Sequencing of the Arabidopsis thaliana (Arabidopsis) genome together with several high-quality proteomics studies has, however, revealed that the thylakoid membrane network of plant chloroplasts still contains a number of functionally unknown proteins. These proteins may have a role as auxiliary proteins guiding the assembly, maintenance, and turnover of the thylakoid protein complexes, or they may be as yet unknown subunits of the photosynthetic complexes. Novel subunits are most likely to be found in the NAD(P)H dehydrogenase (NDH) complex, the structure and function of which have remained obscure in the absence of detailed crystallographic data, thus making this thylakoid protein complex a particularly interesting target of investigation. In this thesis, several novel thylakoid-associated proteins were identified by proteomics-based methods. The major goal of characterization of the stroma thylakoid associated polysome-nascent chain complexes was to determine the proteins that guide the dynamic life cycle of PSII. In addition, a large protein complex of ≥ 1,000 kDa, residing in the stroma thylakoid, was characterized in greater depth and it was found to be a supercomplex composed of the PSI and NDH complexes. A set of newly identified proteins from Arabidopsis thylakoids was subjected to detailed characterization using the reverse genetics approach and extensive biochemical and biophysical analysis. The role of the novel proteins, either as auxiliary proteins or subunits of the photosynthetic protein complexes, was revealed. Two novel thylakoid lumen proteins, TLP18.3 and AtCYP38, function as auxiliary proteins assisting specific steps of the assembly/repair of PSII. The role of the 10-kDa thylakoid lumen protein PsbR is related to the optimization of oxygen evolution of PSII by assisting the assembly of the PsbP protein. Two integral thylakoid membrane proteins, NDH45 and NDH48, are novel subunits of the chloroplast NDH complex. Finally, the thylakoid lumen immunophilin AtCYP20-2 is suggested to interact with the NDH complex, instead of PSII as was hypothesized earlier.

Analysis of electricity distribution network operation business models and capitalization of control room functions with DMS

Electricity distribution network operation (NO) models are challenged as they are expected to continue to undergo changes during the coming decades in the fairly developed and regulated Nordic electricity market. Network asset managers are to adapt to competitive technoeconomical business models regarding the operation of increasingly intelligent distribution networks. Factors driving the changes for new business models within network operation include: increased investments in distributed automation (DA), regulative frameworks for annual profit limits and quality through outage cost, increasing end-customer demands, climatic changes and increasing use of data system tools, such as Distribution Management System (DMS). The doctoral thesis addresses the questions a) whether there exist conditions and qualifications for competitive markets within electricity distribution network operation and b) if so, identification of limitations and required business mechanisms. This doctoral thesis aims to provide an analytical business framework, primarily for electric utilities, for evaluation and development purposes of dedicated network operation models to meet future market dynamics within network operation. In the thesis, the generic build-up of a business model has been addressed through the use of the strategicbusiness hierarchy levels of mission, vision and strategy for definition of the strategic direction of the business followed by the planning, management and process execution levels of enterprisestrategy execution. Research questions within electricity distribution network operation are addressed at the specified hierarchy levels. The results of the research represent interdisciplinary findings in the areas of electrical engineering and production economics. The main scientific contributions include further development of the extended transaction cost economics (TCE) for government decisions within electricity networks and validation of the usability of the methodology for the electricity distribution industry. Moreover, DMS benefit evaluations in the thesis based on the outage cost calculations propose theoretical maximum benefits of DMS applications equalling roughly 25% of the annual outage costs and 10% of the respective operative costs in the case electric utility. Hence, the annual measurable theoretical benefits from the use of DMS applications are considerable. The theoretical results in the thesis are generally validated by surveys and questionnaires.

SME internationalisation from a network perspective : an empirical study on a Finnish-Greek business network

The study examines the internationalisation process of a contemporary SME firm and explores the impact of its business network on this development. The objective of the study is to understand SME internationalisation and its dynamics from a network perspective. The purpose of this research project is to describe and explore the development process of a firm and its business network by identifying the changes, critical events and influence factors that form this development. It is a qualitative case study, which focuses on a Finnish focal firm and its respective business network as it expands into the Greek market. It is a longitudinal research process, which covers a period of time from 1994 to 2004. The empirical study concentrates on the paper trading and converting business. The study builds on the network theory and the framework provided by Johanson and Mattsson's (1988) model on network internationalisation. The incremental internationalisation theories and network theories form the theoretical focus. The research project is organised according to a process view. The focal firm evolves from a domestically-oriented small subsidiary into an internationally experienced company, which has activities in several market areas and numerous business networks in various market segments and product categories. The findings illustrate the importance of both the domestic and foreign business network context in a firm's internationalisation process. The results of the study suggest theoretical modifications on a firm's internationalisation process by broadening the perspective and incorporating the strategic context of a firm. The findings suggest that internationalisation process is a non-linear process, which does not have a deterministic order in its development. The findings emphasise the significance of relational networks, both managerial and entrepreneurial, for establishing position in foreign markets. It implies that a firm's evolution is significantly influenced by its business network and by critical events. Business networks gain coherence due to common goals and they use accumulated capabilities to exploit market opportunities. The business network sets constraints and provides opportunities, which makes the related decision making strategically important. The firm co-evolves with its business network. The research project provides an instrumental case study with a description of an SME internationalisation process. It contributes to existing knowledge by illustrating dynamics in an international business network and by pinpointing the importance of suppliers, customers, partners, ownerships and competition to the internationalisation process.

The Influence of Network Competence on Internationalization of SMEs

This study focuses on the relationship between organizational network competence and the internationalization process of small- and medium sized enterprises (SMEs). Over recent decades, the global business environment has become increasingly conducive to internationalization of small firms. A central facilitating factor in the process has been the emergence of networked business relationships between internationalizing firms. Research on SME internationalization has found that certain types of structures and dynamics of business networks allow SMEs access to the resources they need to enter foreign markets. This consequently means that their internationalization often becomes to depend on the networks they are embedded in. However, research so far has mostly ignored the possibility that the organizational ability to develop and manage business network relationships, network competence, may be a major underlying factor in determining how well SMEs can leverage their network relationships to enter foreign markets and consequently may determine in large part how successful their internationalization process turns out to be. This study aims to respond to those gaps, by empirically examining how the development of network competence in internationalizing SMEs influences the internationalization outcomes that they can expect, and how such network competence is conceptualized and developed. Using a mixed methods approach, survey data collected from 298 Finnish SMEs across five industry sectors is first used to examine how levels of network competence are related to internationalization propensity of SMEs and their subsequent international performance, growth and profitability as internationally operating firms. In order to illustrate in more detail the ways in which network competence is conceptualized and how it develops during the internationalization process of an SME, qualitative data from internationally operating Finnish SMEs are used. Longitudinal interview data of an internationalizing Finnish SME is accompanied by data gathered through a series of semistructured interviews of Finnish and Russian managers involved in mutual business relationship dyads. Structurally, this thesis examines the research issue as an article-based dissertation, consisting of five journal and conference publications. Three of these publications are based on the quantitative data, and the remaining two apply the qualitative interview data. The results find several aspects where network competence has a positive influence on the success of internationalizing SMEs, how it develops and what it entails conceptually in this context. Quantitatively, the level of network competence is found to have a positive relationship to various internationalization outcomes, including the propensity of SMEs to enter foreign markets and on their subsequent international performance, their growth and their profitability. Additionally, the positive relationship is divided between the relationship-specific and cross-relational dimension of network competence, in that the influence of the former is relevant for the propensity to internationalize, while the latter is for the growth and profitability of the already internationalized SMEs. Qualitatively, the results suggest, firstly, that the development process of network competence does not necessarily precede the start of the internationalization process, but may occur through a gradual learning process alongside it. And secondly, the results also imply that the conceptualization of network competence by Finnish managers of internationally operating Finnish SMEs is structurally distinct from that of their culturally distinct partner managers in Russia. This study contributes to the literature on SME internationalization in several ways. Firstly, it introduces operationalized organizational competencies to the literature on internationalization of SMEs, which has so far mainly examined the influence of business networking on the internationalization process without having such an organizational viewpoint. Furthermore, this study provides a multi-level analysis of the determinants of successful SME internationalization, by examining various strategic and performance outcomes across the process. These results also contribute to the literature on organizational strategy of internationalizing SMEs, by clarifying how different dimensions of business networking may be optimal in different phases of the internationalization process. Conceptually, the results of this study contribute to the literature on competence development and SME internationalization, by illustrating how the development process of network competence may occur during internationalization process. Thus, they also contribute to the discussion on how SMEs are able to influence the dynamics and structures of their business networks over time. Finally, this study contributes to the literature on the role of culture in the internationalization process, by implying that the cultural background of the manager of the SME may determine whether business networking and network competence is seen as an organizational-level or an individual level capability. The study also includes some additional contributions to the literature on dynamic capabilities in strategic management, and on that of strategic business networks. These include further clarifying the exact nature and tangibility of dynamic capabilities, and being one of the first studies to introduce constructs from both dynamic capabilities and business network literature to the field of international entrepreneurship. And finally, the study also has some contribution on the two streams of literature, in illustrating how both dyadic and network-level capabilities may be relevant, depending on the current strategic goals and market position of the firm. Keywords: network competence, internationalizatio

A game-theoretic network formation model

We study the dynamics of a game-theoretic network formation model that yields large-scale small-world networks. So far, mostly stochastic frameworks have been utilized to explain the emergence of these networks. On the other hand, it is natural to seek for game-theoretic network formation models in which links are formed due to strategic behaviors of individuals, rather than based on probabilities. Inspired by Even-Dar and Kearns (2007), we consider a more realistic model in which the cost of establishing each link is dynamically determined during the course of the game. Moreover, players are allowed to put transfer payments on the formation of links. Also, they must pay a maintenance cost to sustain their direct links during the game. We show that there is a small diameter of at most 4 in the general set of equilibrium networks in our model. Unlike earlier model, not only the existence of equilibrium networks is guaranteed in our model, but also these networks coincide with the outcomes of pairwise Nash equilibrium in network formation. Furthermore, we provide a network formation simulation that generates small-world networks. We also analyze the impact of locating players in a hierarchical structure by constructing a strategic model, where a complete b-ary tree is the seed network.

Understanding Network Governance: A Case Study Exploration of Active Canada 20/20

Consistent with the governance shift towards network forms of governance, a number of new social movements have formed in response to the declining levels of physical activity in the Western world. One such movement is Active Canada 20/20: A Physical Activity Strategy and Change Agenda for Canada. Network governance is employed as the theoretical framework for this case study exploration of Active Canada 20/20 and the political landscape surrounding its development and implementation. Semi-structured interviews were conducted in addition to document/policy analysis and direct observations. Analysis of the data resulted in three overarching themes – the defining characteristics of network governance, the political landscape, and intersectoral linkages – that interconnect multifariously based the nature of the Canadian federal government and its relationship with the voluntary sector for physical activity. Despite progress in driving Active Canada 20/20 forward, entrenched dynamics of power need to be navigated within the political landscape surrounding network governance.

Dynamics in large scale networks

In this thesis we study the properties of two large dynamic networks, the competition network of advertisers on the Google and Bing search engines and the dynamic network of friend relationships among avatars in the massively multiplayer online game (MMOG) Planetside 2. We are particularly interested in removal patterns in these networks. Our main finding is that in both of these networks the nodes which are most commonly removed are minor near isolated nodes. We also investigate the process of merging of two large networks using data captured during the merger of servers of Planetside 2. We found that the original network structures do not really merge but rather they get gradually replaced by newcomers not associated with the original structures. In the final part of the thesis we investigate the concept of motifs in the Barabási-Albert random graph. We establish some bounds on the number of motifs in this graph.

W3233 -- Networks and Complexity in Social Systems (Collective Dynamics Group ISERP -- Columbia University) Course Syllabus

The Networks and Complexity in Social Systems course commences with an overview of the nascent field of complex networks, dividing it into three related but distinct strands: Statistical description of large scale networks, viewed as static objects; the dynamic evolution of networks, where now the structure of the network is understood in terms of a growth process; and dynamical processes that take place on fixed networks; that is, "networked dynamical systems". (A fourth area of potential research ties all the previous three strands together under the rubric of co-evolution of networks and dynamics, but very little research has been done in this vein and so it is omitted.) The remainder of the course treats each of the three strands in greater detail, introducing technical knowledge as required, summarizing the research papers that have introduced the principal ideas, and pointing out directions for future development. With regard to networked dynamical systems, the course treats in detail the more specific topic of information propagation in networks, in part because this topic is of great relevance to social science, and in part because it has received the most attention in the literature to date.

Lethal Closeness: The Evolution of a Small-World Drug Trafficking Network

The evolution of the drug trafficking network –so-called– ‘Cartel del Norte del Valle’, is studied using network analysis methods. We found that the average length between any pair of its members was bounded by 4 –an attribute of smallworld networks. In this tightly connected network, informational shocks induce fear and the unleashing of searches of threatening nodes, using available paths. Lethal violence ensues in clusters of increasing sizes that fragment the network, without compromising, however, the survival of the largest component, which proved to be resilient to massive violence. In spite of a success from the point of view of head counting, the US’ socialization program for drug traffickers did not effectively change the cyclical dynamics of the drug dealing business: war survivors took over what was left from the old network initiating a new cycle of business and violence.

The dynamics of local hiv-1 epidemics: the colombian and belgian cohorts

We aimed to characterize the HIV-1 epidemic of the Belgian and Colombian cohorts using an integrated approach that includes socio-demographic information, clinical data, and viral sequences, analyzed with statistical and phylogenetic approaches.

Network externalities across financial institutions

We propose and estimate a financial distress model that explicitly accounts for the interactions or spill-over effects between financial institutions, through the use of a spatial continuity matrix that is build from financial network data of inter bank transactions. Such setup of the financial distress model allows for the empirical validation of the importance of network externalities in determining financial distress, in addition to institution specific and macroeconomic covariates. The relevance of such specification is that it incorporates simultaneously micro-prudential factors (Basel 2) as well as macro-prudential and systemic factors (Basel 3) as determinants of financial distress. Results indicate network externalities are an important determinant of financial health of a financial institutions. The parameter that measures the effect of network externalities is both economically and statistical significant and its inclusion as a risk factor reduces the importance of the firm specific variables such as the size or degree of leverage of the financial institution. In addition we analyze the policy implications of the network factor model for capital requirements and deposit insurance pricing.

Use of essential and molecular dynamics to study gamma B-crystallin unfolding after non-enzymic post-translational modifications

Essential and Molecular Dynamics (ED/MD) have been used to model the conformational changes of a protein implicated in a conformational disease-cataract, the largest cause of blindness in the world-after non-enzymic post-translational modification. Cyanate modification did not significantly alter flexibility, while the Schiff's base adduct produced a more flexible N-terminal domain, and intra-secondary structure regions, than either the cyanate adduct or the native structure. Glycation also increased linker flexibility and disrupted the charge network. A number of post-translational adducts showed structural disruption around Cys15 and increased linker flexibility; this may be important in subsequent protein aggregation. Our modelling results are in accord with experimental evidence, and show that ED/MD is a useful tool in modelling conformational changes in proteins implicated in disease processes. (C) 2003 Published by Elsevier Ltd.

Neural network enhanced generalised minimum variance self-tuning controller for nonlinear discrete-time systems

A neural network enhanced self-tuning controller is presented, which combines the attributes of neural network mapping with a generalised minimum variance self-tuning control (STC) strategy. In this way the controller can deal with nonlinear plants, which exhibit features such as uncertainties, nonminimum phase behaviour, coupling effects and may have unmodelled dynamics, and whose nonlinearities are assumed to be globally bounded. The unknown nonlinear plants to be controlled are approximated by an equivalent model composed of a simple linear submodel plus a nonlinear submodel. A generalised recursive least squares algorithm is used to identify the linear submodel and a layered neural network is used to detect the unknown nonlinear submodel in which the weights are updated based on the error between the plant output and the output from the linear submodel. The procedure for controller design is based on the equivalent model therefore the nonlinear submodel is naturally accommodated within the control law. Two simulation studies are provided to demonstrate the effectiveness of the control algorithm.

A neural network enhanced generalized minimum variance self-tuning proportional, integral and derivative control algorithm for complex dynamic systems

A neural network enhanced proportional, integral and derivative (PID) controller is presented that combines the attributes of neural network learning with a generalized minimum-variance self-tuning control (STC) strategy. The neuro PID controller is structured with plant model identification and PID parameter tuning. The plants to be controlled are approximated by an equivalent model composed of a simple linear submodel to approximate plant dynamics around operating points, plus an error agent to accommodate the errors induced by linear submodel inaccuracy due to non-linearities and other complexities. A generalized recursive least-squares algorithm is used to identify the linear submodel, and a layered neural network is used to detect the error agent in which the weights are updated on the basis of the error between the plant output and the output from the linear submodel. The procedure for controller design is based on the equivalent model, and therefore the error agent is naturally functioned within the control law. In this way the controller can deal not only with a wide range of linear dynamic plants but also with those complex plants characterized by severe non-linearity, uncertainties and non-minimum phase behaviours. Two simulation studies are provided to demonstrate the effectiveness of the controller design procedure.

Identification of nonlinear systems with a dynamic recurrent neural network

Two approaches are presented to calculate the weights for a Dynamic Recurrent Neural Network (DRNN) in order to identify the input-output dynamics of a class of nonlinear systems. The number of states of the identified network is constrained to be the same as the number of states of the plant.