Enhanced conformational sampling in Monte Carlo simulations of proteins: application to a constrained peptide.

A Monte Carlo simulation method for globular proteins, called extended-scaled-collective-variable (ESCV) Monte Carlo, is proposed. This method combines two Monte Carlo algorithms known as entropy-sampling and scaled-collective-variable algorithms. Entropy-sampling Monte Carlo is able to sample a large configurational space even in a disordered system that has a large number of potential barriers. In contrast, scaled-collective-variable Monte Carlo provides an efficient sampling for a system whose dynamics is highly cooperative. Because a globular protein is a disordered system whose dynamics is characterized by collective motions, a combination of these two algorithms could provide an optimal Monte Carlo simulation for a globular protein. As a test case, we have carried out an ESCV Monte Carlo simulation for a cell adhesive Arg-Gly-Asp-containing peptide, Lys-Arg-Cys-Arg-Gly-Asp-Cys-Met-Asp, and determined the conformational distribution at 300 K. The peptide contains a disulfide bridge between the two cysteine residues. This bond mimics the strong geometrical constraints that result from a protein's globular nature and give rise to highly cooperative dynamics. Computation results show that the ESCV Monte Carlo was not trapped at any local minimum and that the canonical distribution was correctly determined.

O impacto conjunto do empreendedorismo e das redes interorganizacionais sobre o desenvolvimento de inovações globais: evidências das subsidiárias estrangeiras operando no país

As subsidiárias de corporações multinacionais sofrem pressões do ambiente interno e externo. Internamente competem por recursos e reconhecimento da matriz, externamente precisam se preocupar com os concorrentes e demais forças do mercado, de maneira que para desenvolver-se a subsidiária deve explorar as oportunidades de mercado e mostrar o potencial empreendedor que possui. Essas oportunidades podem estar num produto ou processo novo ou substancialmente aprimorado no qual a subsidiária teve o auxílio de um parceiro da rede em que está inserida. Particularmente, essa pesquisa analisa as inovações desenvolvidas localmente (dentro do país hospedeiro) através das subsidiárias instaladas no país, essas inovações são passíveis de serem transferidas para as suas matrizes e então utilizadas pelas demais subsidiárias espalhadas pelo mundo, tornando-se inovações globais. O foco principal deste estudo está em compreender a influência do empreendedorismo e das redes de empresas sobre o desenvolvimento e transferência dessas inovações. Para tanto, o presente estudo analisa uma amostra de 172 subsidiárias estrangeiras que operam no Brasil, a qual foi modelada utilizando-se a técnica de equações estruturais para o teste das hipóteses, mensuração do efeito mediador e comparação multigrupos visando avaliar o efeito moderador referente ao porte das subsidiárias. Os resultados sugerem que o empreendedorismo da subsidiária exerce influência significativa sobre o desenvolvimento das parcerias e consequente enraizamento da subsidiária na rede de empresas do mercado emergente, esse enraizamento na rede é um fator determinante para o desenvolvimento de inovações na subsidiária as quais podem ser transferidas para a matriz e então tornarem-se inovações globais. A partir desses resultados, a pesquisa contribui para um maior entendimento dos direcionadores de inovação nas subsidiárias e aprofunda a discussão sobre o desenvolvimento de inovações globais, particularmente àquelas provenientes de mercados emergentes.

Extração de casos de teste utilizando Redes de Petri hierárquicas e validação de resultados utilizando OWL.

Este trabalho propõe dois métodos para teste de sistemas de software: o primeiro extrai ideias de teste de um modelo desenvolvido em rede de Petri hierárquica e o segundo valida os resultados após a realização dos testes utilizando um modelo em OWL-S. Estes processos aumentam a qualidade do sistema desenvolvido ao reduzir o risco de uma cobertura insuficiente ou teste incompleto de uma funcionalidade. A primeira técnica apresentada consiste de cinco etapas: i) avaliação do sistema e identificação dos módulos e entidades separáveis, ii) levantamento dos estados e transições, iii) modelagem do sistema (bottom-up), iv) validação do modelo criado avaliando o fluxo de cada funcionalidade e v) extração dos casos de teste usando uma das três coberturas de teste apresentada. O segundo método deve ser aplicado após a realização dos testes e possui cinco passos: i) primeiro constrói-se um modelo em OWL (Web Ontology Language) do sistema contendo todas as informações significativas sobre as regras de negócio da aplicação, identificando as classes, propriedades e axiomas que o regem; ii) em seguida o status inicial antes da execução é representado no modelo através da inserção das instâncias (indivíduos) presentes; iii) após a execução dos casos de testes, a situação do modelo deve ser atualizada inserindo (sem apagar as instâncias já existentes) as instâncias que representam a nova situação da aplicação; iv) próximo passo consiste em utilizar um reasoner para fazer as inferências do modelo OWL verificando se o modelo mantém a consistência, ou seja, se não existem erros na aplicação; v) finalmente, as instâncias do status inicial são comparadas com as instâncias do status final, verificando se os elementos foram alterados, criados ou apagados corretamente. O processo proposto é indicado principalmente para testes funcionais de caixa-preta, mas pode ser facilmente adaptado para testes em caixa branca. Obtiveram-se casos de testes semelhantes aos que seriam obtidos em uma análise manual mantendo a mesma cobertura do sistema. A validação provou-se condizente com os resultados esperados, bem como o modelo ontológico mostrouse bem fácil e intuitivo para aplicar manutenções.

Aplicação de modelos de defeitos na geração de conjuntos de teste completos a partir de Sistemas de Transição com Entrada/Saída

O Teste Baseado em Modelos (TBM) emergiu como uma estratégia promissora para minimizar problemas relacionados à falta de tempo e recursos em teste de software e visa verificar se a implementação sob teste está em conformidade com sua especificação. Casos de teste são gerados automaticamente a partir de modelos comportamentais produzidos durante o ciclo de desenvolvimento de software. Entre as técnicas de modelagem existentes, Sistemas de Transição com Entrada/Saída (do inglês, Input/Output Transition Systems - IOTSs), são modelos amplamente utilizados no TBM por serem mais expressivos do que Máquinas de Estado Finito (MEFs). Apesar dos métodos existentes para geração de testes a partir de IOTSs, o problema da seleção de casos de testes é um tópico difícil e importante. Os métodos existentes para IOTS são não-determinísticos, ao contrário da teoria existente para MEFs, que fornece garantia de cobertura completa com base em um modelo de defeitos. Esta tese investiga a aplicação de modelos de defeitos em métodos determinísticos de geração de testes a partir de IOTSs. Foi proposto um método para geração de conjuntos de teste com base no método W para MEFs. O método gera conjuntos de teste de forma determinística além de satisfazer condições de suficiência de cobertura da especificação e de todos os defeitos do domínio de defeitos definido. Estudos empíricos avaliaram a aplicabilidade e eficácia do método proposto: resultados experimentais para analisar o custo de geração de conjuntos de teste utilizando IOTSs gerados aleatoriamente e um estudo de caso com especificações da indústria mostram a efetividade dos conjuntos gerados em relação ao método tradicional de Tretmans.

European Corporate Governance Reform and the German Party Paradox. CES Germany & Europe Working Papers, No. 03.1, 2003

This paper addresses the current discussion on links between party politics and production regimes. Why do German Social Democrats opt for more corporate governance liberalization than the CDU although, in terms of the distributional outcomes of such reforms, one would expect the situation to be reversed? I divide my analysis into three stages. First, I use the European Parliament’s crucial vote on the European takeover directive in July 2001 as a test case to show that the left-right dimension does indeed matter in corporate governance reform, beside cross-class and cross-party nation-based interests. In a second step, by analyzing the party positions in the main German corporate governance reforms in the 1990s, I show that the SPD and the CDU behave “paradoxically” in the sense that the SPD favored more corporate governance liberalization than the CDU, which protected the institutions of “Rhenish,” “organized” capitalism. This constellation occurred in the discussions on company disclosure, management accountability, the power of banks, network dissolution, and takeover regulation. Third, I offer two explanations for this paradoxical party behavior. The first explanation concerns the historical conversion of ideas. I show that trade unions and Social Democrats favored a high degree of capital organization in the Weimar Republic, but this ideological position was driven in new directions at two watersheds: one in the late 1940s, the other in the late 1950s. My second explanation lies in the importance of conflicts over managerial control, in which both employees and minority shareholders oppose managers, and in which increased shareholder power strengthens the position of works councils.

Nord Stream II - yes or no? - Political decision of a political Commission. EPC Commentary, 14 June 2016

When the new European Commission started work in autumn 2014, the president of the Commission took great pride in calling it a ‘political Commission’, which will be big on big things and small on small. Whilst the EU is currently dealing with many crises, reality is that things do not come much bigger than Nord Stream II. Will this be a political Commission that stands by its principles, including respect for liberty, democracy, the rule of law and human rights? Will this Commission have the backbone to politically assess a project that threatens EU unity and its core values, undermines the Union’s commonly agreed commitment to building an Energy Union and facilitates Russia’s aggression against Ukraine? President Juncker’s controversial visit to Russia and meeting with President Putin on 16-17 June is a test-case: will this Commission be ready to defend its commitments and principles when discussing ‘economic issues’?

A numerical model for predicting shoreline changes /

A mathematical model for long-term, three-dimensional shoreline evolution is developed. The combined effects of variations of sea level; wave refraction and diffraction; loss of sand by density currents during storms, by rip currents, and by wind; bluff erosion and berm accretion; effects of manmade structures such as long groin or navigational structures; and beach nourishment are all taken into account. A computer program is developed with various subroutines which permit modification as the state-of-the-art progresses. The program is applied to a test case at Holland Harbor, Michigan. (Author).

A Kinetic Vlasov Model for Plasma Simulation Using Discontinuous Galerkin Method on Many-Core Architectures

Thesis (Ph.D.)--University of Washington, 2016-03

Evaluating Neural Futures: Good Technoscience and the Challenge of Co-Production

Thesis (Ph.D.)--University of Washington, 2016-06

Dealing with non-determinism in testing concurrent java components

The testing of concurrent software components can be difficult due to the inherent non-determinism present in these components. For example, if the same test case is run multiple times, it may produce different results. This non-determinism may lead to problems with determining expected outputs. In this paper, we present and discuss several possible solutions to this problem in the context of testing concurrent Java components using the ConAn testing tool. We then present a recent extension to the tool that provides a general solution to this problem that is sufficient to deal with the level of non-determinism that we have encountered in testing over 20 components with ConAn. © 2005 IEEE

Numerical modelling of unsteady mixed flows

This thesis concerns mixed flows (which are characterized by the simultaneous occurrence of free-surface and pressurized flow in sewers, tunnels, culverts or under bridges), and contributes to the improvement of the existing numerical tools for modelling these phenomena. The classic Preissmann slot approach is selected due to its simplicity and capability of predicting results comparable to those of a more recent and complex two-equation model, as shown here with reference to a laboratory test case. In order to enhance the computational efficiency, a local time stepping strategy is implemented in a shock-capturing Godunov-type finite volume numerical scheme for the integration of the de Saint-Venant equations. The results of different numerical tests show that local time stepping reduces run time significantly (between −29% and −85% CPU time for the test cases considered) compared to the conventional global time stepping, especially when only a small region of the flow field is surcharged, while solution accuracy and mass conservation are not impaired. The second part of this thesis is devoted to the modelling of the hydraulic effects of potentially pressurized structures, such as bridges and culverts, inserted in open channel domains. To this aim, a two-dimensional mixed flow model is developed first. The classic conservative formulation of the 2D shallow water equations for free-surface flow is adapted by assuming that two fictitious vertical slots, normally intersecting, are added on the ceiling of each integration element. Numerical results show that this schematization is suitable for the prediction of 2D flooding phenomena in which the pressurization of crossing structures can be expected. Given that the Preissmann model does not allow for the possibility of bridge overtopping, a one-dimensional model is also presented in this thesis to handle this particular condition. The flows below and above the deck are considered as parallel, and linked to the upstream and downstream reaches of the channel by introducing suitable internal boundary conditions. The comparison with experimental data and with the results of HEC-RAS simulations shows that the proposed model can be a useful and effective tool for predicting overtopping and backwater effects induced by the presence of bridges and culverts.

A multi-agent system using iterative bidding mechanism to enhance manufacturing agility

The global market has become increasingly dynamic, unpredictable and customer-driven. This has led to rising rates of new product introduction and turbulent demand patterns across product mixes. As a result, manufacturing enterprises were facing mounting challenges to be agile and responsive to cope with market changes, so as to achieve the competitiveness of producing and delivering products to the market timely and cost-effectively. This paper introduces a currency-based iterative agent bidding mechanism to effectively and cost-efficiently integrate the activities associated with production planning and control, so as to achieve an optimised process plan and schedule. The aim is to enhance the agility of manufacturing systems to accommodate dynamic changes in the market and production. The iterative bidding mechanism is executed based on currency-like metrics; each operation to be performed is assigned with a virtual currency value and agents bid for the operation if they make a virtual profit based on this value. These currency values are optimised iteratively and so does the bidding process based on new sets of values. This is aimed at obtaining better and better production plans, leading to near-optimality. A genetic algorithm is proposed to optimise the currency values at each iteration. In this paper, the implementation of the mechanism and the test case simulation results are also discussed. © 2012 Elsevier Ltd. All rights reserved.

An iterative agent bidding mechanism for responsive manufacturing

In today's market, the global competition has put manufacturing businesses in great pressures to respond rapidly to dynamic variations in demand patterns across products and changing product mixes. To achieve substantial responsiveness, the manufacturing activities associated with production planning and control must be integrated dynamically, efficiently and cost-effectively. This paper presents an iterative agent bidding mechanism, which performs dynamic integration of process planning and production scheduling to generate optimised process plans and schedules in response to dynamic changes in the market and production environment. The iterative bidding procedure is carried out based on currency-like metrics in which all operations (e.g. machining processes) to be performed are assigned with virtual currency values, and resource agents bid for the operations if the costs incurred for performing them are lower than the currency values. The currency values are adjusted iteratively and resource agents re-bid for the operations based on the new set of currency values until the total production cost is minimised. A simulated annealing optimisation technique is employed to optimise the currency values iteratively. The feasibility of the proposed methodology has been validated using a test case and results obtained have proven the method outperforming non-agent-based methods.

Handling varying amounts of missing data when classifying mental-health risk levels

One of the main challenges of classifying clinical data is determining how to handle missing features. Most research favours imputing of missing values or neglecting records that include missing data, both of which can degrade accuracy when missing values exceed a certain level. In this research we propose a methodology to handle data sets with a large percentage of missing values and with high variability in which particular data are missing. Feature selection is effected by picking variables sequentially in order of maximum correlation with the dependent variable and minimum correlation with variables already selected. Classification models are generated individually for each test case based on its particular feature set and the matching data values available in the training population. The method was applied to real patients' anonymous mental-health data where the task was to predict the suicide risk judgement clinicians would give for each patient's data, with eleven possible outcome classes: zero to ten, representing no risk to maximum risk. The results compare favourably with alternative methods and have the advantage of ensuring explanations of risk are based only on the data given, not imputed data. This is important for clinical decision support systems using human expertise for modelling and explaining predictions.

Generation of Testing Source Code for Object-Oriented Programs

Красимир Манев, Антон Желязков, Станимир Бойчев - В статията е представена имплементацията на последната фаза на автоматичен генератор на тестови данни за структурно тестване на софтуер, написан на обектно-ориентиран език за програмиране – генерирането на изходен код на тестващия модул. Някои детайли от имплементацията на останалите фази, които са важни за имплементацията на последната фаза, са представени първо. След това е описан и алгоритъмът за генериране на кода на тестващия модул.