Methods for construction and analysis of computational models in systems biology : applications to the modelling of the heat shock response and the self-assembly of intermediate filaments

Systems biology is a new, emerging and rapidly developing, multidisciplinary research field that aims to study biochemical and biological systems from a holistic perspective, with the goal of providing a comprehensive, system- level understanding of cellular behaviour. In this way, it addresses one of the greatest challenges faced by contemporary biology, which is to compre- hend the function of complex biological systems. Systems biology combines various methods that originate from scientific disciplines such as molecu- lar biology, chemistry, engineering sciences, mathematics, computer science and systems theory. Systems biology, unlike “traditional” biology, focuses on high-level concepts such as: network, component, robustness, efficiency, control, regulation, hierarchical design, synchronization, concurrency, and many others. The very terminology of systems biology is “foreign” to “tra- ditional” biology, marks its drastic shift in the research paradigm and it indicates close linkage of systems biology to computer science. One of the basic tools utilized in systems biology is the mathematical modelling of life processes tightly linked to experimental practice. The stud- ies contained in this thesis revolve around a number of challenges commonly encountered in the computational modelling in systems biology. The re- search comprises of the development and application of a broad range of methods originating in the fields of computer science and mathematics for construction and analysis of computational models in systems biology. In particular, the performed research is setup in the context of two biolog- ical phenomena chosen as modelling case studies: 1) the eukaryotic heat shock response and 2) the in vitro self-assembly of intermediate filaments, one of the main constituents of the cytoskeleton. The range of presented approaches spans from heuristic, through numerical and statistical to ana- lytical methods applied in the effort to formally describe and analyse the two biological processes. We notice however, that although applied to cer- tain case studies, the presented methods are not limited to them and can be utilized in the analysis of other biological mechanisms as well as com- plex systems in general. The full range of developed and applied modelling techniques as well as model analysis methodologies constitutes a rich mod- elling framework. Moreover, the presentation of the developed methods, their application to the two case studies and the discussions concerning their potentials and limitations point to the difficulties and challenges one encounters in computational modelling of biological systems. The problems of model identifiability, model comparison, model refinement, model inte- gration and extension, choice of the proper modelling framework and level of abstraction, or the choice of the proper scope of the model run through this thesis.

Broadband excitation in the system identification of active magnetic bearing rotor systems

One of the targets of the climate and energy package of the European Union is to increase the energy efficiency in order to achieve a 20 percent reduction in primary energy use compared with the projected level by 2020. The energy efficiency can be improved for example by increasing the rotational speed of large electrical drives, because this enables the elimination of gearboxes leading to a compact design with lower losses. The rotational speeds of traditional bearings, such as roller bearings, are limited by mechanical friction. Active magnetic bearings (AMBs), on the other hand, allow very high rotational speeds. Consequently, their use in large medium- and high-speed machines has rapidly increased. An active magnetic bearing rotor system is an inherently unstable, nonlinear multiple-input, multiple-output system. Model-based controller design of AMBs requires an accurate system model. Finite element modeling (FEM) together with the experimental modal analysis provides a very accurate model for the rotor, and a linearized model of the magneticactuators has proven to work well in normal conditions. However, the overall system may suffer from unmodeled dynamics, such as dynamics of foundation or shrink fits. This dynamics can be modeled by system identification. System identification can also be used for on-line diagnostics. In this study, broadband excitation signals are adopted to the identification of an active magnetic bearing rotor system. The broadband excitation enables faster frequency response function measurements when compared with the widely used stepped sine and swept sine excitations. Different broadband excitations are reviewed, and the random phase multisine excitation is chosen for further study. The measurement times using the multisine excitation and the stepped sine excitation are compared. An excitation signal design with an analysis of the harmonics produced by the nonlinear system is presented. The suitability of different frequency response function estimators for an AMB rotor system are also compared. Additionally, analytical modeling of an AMB rotor system, obtaining a parametric model from the nonparametric frequency response functions, and model updating are discussed in brief, as they are key elements in the modeling for a control design. Theoretical methods are tested with a laboratory test rig. The results conclude that an appropriately designed random phase multisine excitation is suitable for the identification of AMB rotor systems.

Energy Efficiency of Pumping Medium Consistency Pulp with Centrifugal Pump

Approximately a quarter of electrical power consumption in pulp and paper industry is used in different pumping systems. Therefore, improving pumping system efficiency is a considerable way to reduce energy consumption in different processes. Pumping of wood pulp in different consistencies is common in pulp and paper industry. Earlier, centrifugal pumps were used to pump pulp only at low consistencies, but development of MC technology has made it possible to pump medium consistency pulp. Pulp is a non-Newtonian fluid, which flow characteristics are significantly different than what of water. In this thesis is examined the energy efficiency of pumping medium consistency pulp with centrifugal pump. The factors effecting the pumping of MC pulp are presented and through case study is examined the energy efficiency of pumping in practice. With data obtained from the case study are evaluated the effects of pump rotational speed and pulp consistency on energy efficiency. Additionally, losses caused by control valve and validity of affinity laws in pulp pumping are evaluated. The results of this study can be used for demonstrating the energy consumption of MC pumping processes and finding ways to improve energy efficiency in these processes.

Configuring Health Care Services - Service Control Improvement

The costs of health care are increasing, and at the same time, population is aging. This leads health care organizations to focus more on home based care services. This thesis focuses on the home care organization of the South Karelian District of Social and Health Services (Eksote), which was established in 2010; how its operation is organized and managed, and which problem types are faced in the daily operation of home care. This thesis examines home care services through an extensive interview study, process mapping and statistical data analysis. To be able to understand the nature of services and special environment theory models, such as service management and performance measurement, service processes and service design are introduced. This study is conducted from an external researcher‟s point of view and should be used as a discussion opener. The outcome of this thesis is an upper level development path for Eksote home care. The organization should evaluate and build a service offering, then productize home care services and modularize the products and identify similarities. Service processes should be mapped to generate efficiency for repeating tasks. Units should be reasonably sized and geographically located to facilitate management and operation. All this can be done by recognizing the different types of service products: runners repeaters and strangers. Furthermore, the organization should not hide behind medical issues and should understand the legislative, medical and operational frameworks in health care.

Material embodiment and energy flows as efficiency indicators of soybean (Glycine max) production in Brazil

As the requirement for agriculture to be environmentally suitable there is a necessity to adopt indicators and methodologies approaching sustainability. In Brazil, biodiesel addition into diesel is mandatory and soybean oil is its main source. The material embodiment determines the convergence of inputs into the crop. Moreover, the material flows are necessary for any environmental analysis. This study evaluated distinct production scenarios, and also conventional versus GMO crops, through the material embodiment and energy analysis. GMO crops demanded less indirectly applied inputs. The energy balance showed linearity with yield, whereas for EROI, the increases in input and yield were not affected.

Setting efficiency indicators for center pivots

In this study, it was discussed the efficiency criteria in each of the elements that compose a central pivot, and this analysis was applied to two sets of systems located in regions of Cruz Alta and Santo Augusto, state of Rio Grande do Sul, Brazil. The methodology used combines water and energy assessment through an indicator called Normalized Specific Consumption in Irrigation (C ENI), allowing thus a comparison between equipment and projects. The C ENI in Cruz Alta region showed 72% of the equipment above the standard (8.68 kWh mm-1 ha-1 100m-1), and in Santo Augusto region 64.28% with consumption above the standard. The mean irrigation efficiency for Cruz Alta region was 29.85%, with standard deviation of 5.41%, and for Santo Augusto region, it was 29.02%, with standard deviation of 5.15%.

Technical evaluation of artificial ligthing systems for broiler houses

The spatial distribution of illuminance and the electric consumption of artificial lighting system is one of the main problems related to broiler production. Therefore, the aim of this study was to evaluate the spatial distribution of luminance level and energy efficiency of different lighting systems for broiler houses. Six types of lamps were tested in two different configurations to find the minimum illuminance of 20 and 5 lux. The tested lamps were incandescent (IL) 100 W, compact fluorescent (CFL) 34 W, mixed (ML) 160 W, sodium vapor (SVL) 70 W, T8 fluorescent tube (T8 FTL) 40 W and T5 fluorescent tube (T5 FTL) 28 W. The first four were evaluated with and without reflective light fixture and the latter two without light fixture. It was observed that the tested system with light fixtures negatively affected the spatial distribution of illuminance inside the house. The systems composed by IL and ML without light fixture led to better results in meeting the minimum illuminance of 20 lux and 5 lux, respectively. T5 FTL presented the lowest energy demand.

Influence of different systems of minimum ventilation on air quality in broiler houses

To maintain a competitive development of the Brazilian aviculture, some measures must be taken to enable the identification and reduction of risks to the health of birds, as well as for the physical environment. Therefore, the aim of this study was to evaluate the effectiveness of three different systems of minimum ventilation (positive pressure - SVMP, negative pressure - SVMN and natural ventilation - SVMNat) in the air quality during the first 21 days of life of broiler chicks, during winter. Three points were selected along the length to verify ammonia, carbon monoxide and oxygen concentrations at 3a.m., 9a.m., 3p.m. and 9p.m., by the respiration level of birds and workers. The averages of pollutant gases did not exceed the tolerance levels for the three minimum ventilation systems evaluated, which is 20 and 10ppm for the birds level and 20 and 39ppm for the workers level, for ammonia and carbon monoxide, respectively. It was evident that the minimum ventilation systems were appropriately sized for the required minimum ambient air renovation, in respect to ventilation rates applied for the SVMN and SVMP systems, and with air velocity at levels that do not stress the chicks, including for the SVMNat. The three studied systems of minimum ventilation allowed the birds to externalize their productive performance, with values close to the ones considered satisfactory for all evaluated parameters, in accordance with the Brazilian aviculture standards.

Energetic sustainability of three arabica coffee growing systems used by family farming units in Espírito Santo state

Three growing systems of Arabica coffee were evaluated under the energy perspective, in the state of Espírito Santo in Brazil. The systems are conventional cultivation (CC), cultivation with good agricultural practices (CGP) and organic farming (OF). It was made a comparison of the energy flows within these three systems to show sustainable levels of each one based on production average data of several family-farming units. Therefore, we analyzed crop yield, total energy efficiency reverse (TEER), energy efficiency of ripe coffee (EERC) and non-renewable energy efficiency (NREE). OF system had values for TEER, EERC and NREE of 3.3 4.7 and 7.9 respectively. Yet CC showed values of 1.8, 1.9 and 1.6 for TEER, EERC and NREE respectively. Furthermore, CGP presented values for TEER, EERC and NREE of 0.7, 1.3 and 1.4 respectively. The highest yield was observed in CGP, reaching an amount of 1794 kg ha-1(17,455 MJ); however, this system expends more energy than it converts. Thus, over those points, OF is the most sustainable system.

Technical-economic analysis of different lighting systems for broiler poultry

ABSTRACT Broiler poultry is highly dependent on artificial lightening. Power consumption costs of artificial lighting systems is the second largest expense related to broiler industry, second only to feed expenses. Therefore, the current study focused to analyze technical and economic feasibility of replacing incandescent lamps already used in aviaries with other lamp types. Costs related to power consumption, implementation and maintenance of the lighting systems were evaluated with the aid of financial mathematics using net present value, return over investment and payback. Systems composed of six lamp types were analyzed in two different configurations to meet the minimum illuminance of 5 and 20 lux and for use in conventional sheds and dark house. The lamps tested were incandescent (LI) of 100 W, compact fluorescent (CFL) of 34 W, mixed (ML) 160 W sodium vapor (SVL) of 70 W, tubular fluorescent T8 (TFL T8) of 40 W and tubular fluorescent T5 (TFL T5) of 28 W. For the systems tested, it was found that the tubular fluorescent lamps T8 and T5 showed the best results of technical and economic feasibility.

Information integration and its impacts on logistics performance - Using information technology and systems to facilitate information integration

Fast changing environment sets pressure on firms to share large amount of information with their customers and suppliers. The terms information integration and information sharing are essential for facilitating a smooth flow of information throughout the supply chain, and the terms are used interchangeably in research literature. By integrating and sharing information, firms want to improve their logistics performance. Firms share information with their suppliers and customers by using traditional communication methods (telephone, fax, Email, written and face-to-face contacts) and by using advanced or modern communication methods such as electronic data interchange (EDI), enterprise resource planning (ERP), web-based procurement systems, electronic trading systems and web portals. Adopting new ways of using IT is one important resource for staying competitive on the rapidly changing market (Saeed et al. 2005, 387), and an information system that provides people the information they need for performing their work, will support company performance (Boddy et al. 2005, 26). The purpose of this research has been to test and understand the relationship between information integration with key suppliers and/or customers and a firm’s logistics performance, especially when information technology (IT) and information systems (IS) are used for integrating information. Quantitative and qualitative research methods have been used to perform the research. Special attention has been paid to the scope, level and direction of information integration (Van Donk & van der Vaart 2005a). In addition, the four elements of integration (Jahre & Fabbe-Costes 2008) are closely tied to the frame of reference. The elements are integration of flows, integration of processes and activities, integration of information technologies and systems and integration of actors. The study found that information integration has a low positive relationship to operational performance and a medium positive relationship to strategic performance. The potential performance improvements found in this study vary from efficiency, delivery and quality improvements (operational) to profit, profitability or customer satisfaction improvements (strategic). The results indicate that although information integration has an impact on a firm’s logistics performance, all performance improvements have not been achieved. This study also found that the use of IT and IS have a mediocre positive relationship to information integration. Almost all case companies agreed on that the use of IT and IS could facilitate information integration and improve their logistics performance. The case companies felt that an implementation of a web portal or a data bank would benefit them - enhance their performance and increase information integration.

Theoretical Analysis and Numerical Simulation of Spectral Radiative Properties of Combustion Gases in Oxy/Air-Fired Combustion Systems

Energy efficiency is one of the major objectives which should be achieved in order to implement the limited energy resources of the world in a sustainable way. Since radiative heat transfer is the dominant heat transfer mechanism in most of fossil fuel combustion systems, more accurate insight and models may cause improvement in the energy efficiency of the new designed combustion systems. The radiative properties of combustion gases are highly wavelength dependent. Better models for calculating the radiative properties of combustion gases are highly required in the modeling of large scale industrial combustion systems. With detailed knowledge of spectral radiative properties of gases, the modeling of combustion processes in the different applications can be more accurate. In order to propose a new method for effective non gray modeling of radiative heat transfer in combustion systems, different models for the spectral properties of gases including SNBM, EWBM, and WSGGM have been studied in this research. Using this detailed analysis of different approaches, the thesis presents new methods for gray and non gray radiative heat transfer modeling in homogeneous and inhomogeneous H2O–CO2 mixtures at atmospheric pressure. The proposed method is able to support the modeling of a wide range of combustion systems including the oxy-fired combustion scenario. The new methods are based on implementing some pre-obtained correlations for the total emissivity and band absorption coefficient of H2O–CO2 mixtures in different temperatures, gas compositions, and optical path lengths. They can be easily used within any commercial CFD software for radiative heat transfer modeling resulting in more accurate, simple, and fast calculations. The new methods were successfully used in CFD modeling by applying them to industrial scale backpass channel under oxy-fired conditions. The developed approaches are more accurate compared with other methods; moreover, they can provide complete explanation and detailed analysis of the radiation heat transfer in different systems under different combustion conditions. The methods were verified by applying them to some benchmarks, and they showed a good level of accuracy and computational speed compared to other methods. Furthermore, the implementation of the suggested banded approach in CFD software is very easy and straightforward.

Energy Efficiency of a Diesel-Electric MobileWorking Machine

The power demand of many mobile working machines such as mine loaders, straddle carriers and harvesters varies significantly during operation, and typically, the average power demand of a working machine is considerably lower than the demand for maximum power. Consequently, for most of the time, the diesel engine of a working machine operates at a poor efficiency far from its optimum efficiency range. However, the energy efficiency of dieseldriven working machines can be improved by electric hybridization. This way, the diesel engine can be dimensioned to operate within its optimum efficiency range, and the electric drive with its energy storages responds to changes in machine loading. A hybrid working machine can be implemented in many ways either as a parallel hybrid, a series hybrid or a combination of these two. The energy efficiency of hybrid working machines can be further enhanced by energy recovery and reuse. This doctoral thesis introduces the component models required in the simulation model of a working machine. Component efficiency maps are applied to the modelling; the efficiency maps for electrical machines are determined analytically in the whole torque–rotational speed plane based on the electricalmachine parameters. Furthermore, the thesis provides simulation models for parallel, series and parallel-series hybrid working machines. With these simulation models, the energy consumption of the working machine can be analysed. In addition, the hybridization process is introduced and described. The thesis provides a case example of the hybridization and dimensioning process of a working machine, starting from the work cycle of the machine. The selection and dimensioning of the hybrid system have a significant impact on the energy consumption of a hybrid working machine. The thesis compares the energy consumption of a working machine implemented by three different hybrid systems (parallel, series and parallel-series) and with different component dimensions. The payback time of a hybrid working machine and the energy storage lifetime are also estimated in the study.

Reusable formal architectures for networked systems

Today's networked systems are becoming increasingly complex and diverse. The current simulation and runtime verification techniques do not provide support for developing such systems efficiently; moreover, the reliability of the simulated/verified systems is not thoroughly ensured. To address these challenges, the use of formal techniques to reason about network system development is growing, while at the same time, the mathematical background necessary for using formal techniques is a barrier for network designers to efficiently employ them. Thus, these techniques are not vastly used for developing networked systems. The objective of this thesis is to propose formal approaches for the development of reliable networked systems, by taking efficiency into account. With respect to reliability, we propose the architectural development of correct-by-construction networked system models. With respect to efficiency, we propose reusable network architectures as well as network development. At the core of our development methodology, we employ the abstraction and refinement techniques for the development and analysis of networked systems. We evaluate our proposal by employing the proposed architectures to a pervasive class of dynamic networks, i.e., wireless sensor network architectures as well as to a pervasive class of static networks, i.e., network-on-chip architectures. The ultimate goal of our research is to put forward the idea of building libraries of pre-proved rules for the efficient modelling, development, and analysis of networked systems. We take into account both qualitative and quantitative analysis of networks via varied formal tool support, using a theorem prover the Rodin platform and a statistical model checker the SMC-Uppaal.

On the Efficiency of Alternatives in Process Plans

Process planning is a very important industrial activity, since it determines how a part or a product is manufactured. Process planning decisions include machine selection, tool selection, and cutting conditions determination, and thus it is a complex activity. In the presence of unstable demand, flexibility has become a very important characteristic of today's successful industries, for which Flexible Manufacturing Systems (FMSs) have been proposed as a solution. However, we believe that FMS control software is not flexible enough to adapt to different manufacturing system conditions aiming at increasing the system's efficiency. One means to overcome this limitation is to include pre-planned alternatives in the process plan; then planning decisions are made by the control system in real time to select the most appropriate alternative according to the conditions of the shop floor. Some of the advantages of this approach reported in the literature are the reduction of the number of tool setups, and the selection of a replacement machine for executing an operation. To verify whether the presence of alternatives in process plans actually increases the efficiency of the manufacturing system, an investigation was carried out using simulation and design of experiments techniques for alternative plans on a single machine. The proposed methodology and the results are discussed within this paper.