Computational models for and from biology : simple gene assembly and reaction systems

The advancement of science and technology makes it clear that no single perspective is any longer sufficient to describe the true nature of any phenomenon. That is why the interdisciplinary research is gaining more attention overtime. An excellent example of this type of research is natural computing which stands on the borderline between biology and computer science. The contribution of research done in natural computing is twofold: on one hand, it sheds light into how nature works and how it processes information and, on the other hand, it provides some guidelines on how to design bio-inspired technologies. The first direction in this thesis focuses on a nature-inspired process called gene assembly in ciliates. The second one studies reaction systems, as a modeling framework with its rationale built upon the biochemical interactions happening within a cell. The process of gene assembly in ciliates has attracted a lot of attention as a research topic in the past 15 years. Two main modelling frameworks have been initially proposed in the end of 1990s to capture ciliates’ gene assembly process, namely the intermolecular model and the intramolecular model. They were followed by other model proposals such as templatebased assembly and DNA rearrangement pathways recombination models. In this thesis we are interested in a variation of the intramolecular model called simple gene assembly model, which focuses on the simplest possible folds in the assembly process. We propose a new framework called directed overlap-inclusion (DOI) graphs to overcome the limitations that previously introduced models faced in capturing all the combinatorial details of the simple gene assembly process. We investigate a number of combinatorial properties of these graphs, including a necessary property in terms of forbidden induced subgraphs. We also introduce DOI graph-based rewriting rules that capture all the operations of the simple gene assembly model and prove that they are equivalent to the string-based formalization of the model. Reaction systems (RS) is another nature-inspired modeling framework that is studied in this thesis. Reaction systems’ rationale is based upon two main regulation mechanisms, facilitation and inhibition, which control the interactions between biochemical reactions. Reaction systems is a complementary modeling framework to traditional quantitative frameworks, focusing on explicit cause-effect relationships between reactions. The explicit formulation of facilitation and inhibition mechanisms behind reactions, as well as the focus on interactions between reactions (rather than dynamics of concentrations) makes their applicability potentially wide and useful beyond biological case studies. In this thesis, we construct a reaction system model corresponding to the heat shock response mechanism based on a novel concept of dominance graph that captures the competition on resources in the ODE model. We also introduce for RS various concepts inspired by biology, e.g., mass conservation, steady state, periodicity, etc., to do model checking of the reaction systems based models. We prove that the complexity of the decision problems related to these properties varies from P to NP- and coNP-complete to PSPACE-complete. We further focus on the mass conservation relation in an RS and introduce the conservation dependency graph to capture the relation between the species and also propose an algorithm to list the conserved sets of a given reaction system.

Ion-exchange resins as stationary phase in reactive chromatography

Dynamic behavior of bothisothermal and non-isothermal single-column chromatographic reactors with an ion-exchange resin as the stationary phase was investigated. The reactor performance was interpreted by using results obtained when studying the effect of the resin properties on the equilibrium and kinetic phenomena occurring simultaneously in the reactor. Mathematical models were derived for each phenomenon and combined to simulate the chromatographic reactor. The phenomena studied includes phase equilibria in multicomponent liquid mixture¿ion-exchange resin systems, chemicalequilibrium in the presence of a resin catalyst, diffusion of liquids in gel-type and macroporous resins, and chemical reaction kinetics. Above all, attention was paid to the swelling behavior of the resins and how it affects the kinetic phenomena. Several poly(styrene-co-divinylbenzene) resins with different cross-link densities and internal porosities were used. Esterification of acetic acid with ethanol to produce ethyl acetate and water was used as a model reaction system. Choosing an ion-exchange resin with a low cross-link density is beneficial inthe case of the present reaction system: the amount of ethyl acetate as well the ethyl acetate to water mole ratio in the effluent stream increase with decreasing cross-link density. The enhanced performance of the reactor is mainly attributed to increasing reaction rate, which in turn originates from the phase equilibrium behavior of the system. Also mass transfer considerations favor the use ofresins with low cross-link density. The diffusion coefficients of liquids in the gel-type ion-exchange resins were found to fall rapidly when the extent of swelling became low. Glass transition of the polymer was not found to significantlyretard the diffusion in sulfonated PS¿DVB ion-exchange resins. It was also shown that non-isothermal operation of a chromatographic reactor could be used to significantly enhance the reactor performance. In the case of the exothermic modelreaction system and a near-adiabatic column, a positive thermal wave (higher temperature than in the initial state) was found to travel together with the reactive front. This further increased the conversion of the reactants. Diffusion-induced volume changes of the ion-exchange resins were studied in a flow-through cell. It was shown that describing the swelling and shrinking kinetics of the particles calls for a mass transfer model that explicitly includes the limited expansibility of the polymer network. A good description of the process was obtained by combining the generalized Maxwell-Stefan approach and an activity model that was derived from the thermodynamics of polymer solutions and gels. The swelling pressure in the resin phase was evaluated by using a non-Gaussian expression forthe polymer chain length distribution. Dimensional changes of the resin particles necessitate the use of non-standard mathematical tools for dynamic simulations. A transformed coordinate system, where the mass of the polymer was used as a spatial variable, was applied when simulating the chromatographic reactor columns as well as the swelling and shrinking kinetics of the resin particles. Shrinking of the particles in a column leads to formation of dead volume on top of the resin bed. In ordinary Eulerian coordinates, this results in a moving discontinuity that in turn causes numerical difficulties in the solution of the PDE system. The motion of the discontinuity was eliminated by spanning two calculation grids in the column that overlapped at the top of the resin bed. The reactive and non-reactive phase equilibrium data were correlated with a model derived from thethermodynamics of polymer solution and gels. The thermodynamic approach used inthis work is best suited at high degrees of swelling because the polymer matrixmay be in the glassy state when the extent of swelling is low.

Development of an environmentally friendly method of starch oxidation by hydrogen peroxide and a complex water-soluble Iron catalyst

Oxidized starch is a key component in the paper industry, where it is used as both surfacing sizer and filler. Large quantities are annually used for this purpose; however, the methods for the oxidation are not environmentally friendly. In our research, we have studied the possibility to replace the harmful oxidation agents, such as hypochlorite or iodates and transition metal catalysts, with a more environmentally friendly oxidant, hydrogen peroxide (H2O2), and a special metal complex catalyst (FePcS), of which only a small amount is needed. The work comprised batch and semi-batch studies by H2O2, ultrasound studies of starch particles, determination of low-molecular by-products and determination of the decomposition kinetics of H2O2 in the presence of starch and the catalyst. This resulted in a waste-free oxidation method, which only produces water and oxygen as side products. The starch oxidation was studied in both semi-batch and batch modes in respective to the oxidant (H2O2) addition. The semi-batch mode proved to yield a sufficient degree of substitution (COOH groups) for industrial purposes. Treatment of starch granules by ultrasound was found to improve the reactivity of starch. The kinetic results were found out to have a rather complex pattern – several oxidation phases were observed, apparently due to the fact that the oxidation reaction in the beginning only took place on the surface, whereas after a prolonged reaction time, partial degradation of the solid starch granules allowed further reaction in the interior parts. Batch-mode experiments enabled a more detailed study of the mechanisms of starch in the presence of H2O2 and the catalyst, but yielded less oxidized starch due to rapid decomposition of H2O2 due to its high concentrations. The effect of the solid-liquid (S/L) ratio in the reaction system was studied in batch experiments. These studies revealed that the presence of the catalyst and the starch enhance the H2O2 decomposition.

Wet Oxidation of Concentrated Wastewaters: Process Combination and Reaction Kinetic Modeling

The accumulation of aqueous pollutants is becoming a global problem. The search for suitable methods and/or combinations of water treatment processes is a task that can slow down and stop the process of water pollution. In this work, the method of wet oxidation was considered as an appropriate technique for the elimination of the impurities present in paper mill process waters. It has been shown that, when combined with traditional wastewater treatment processes, wet oxidation offers many advantages. The combination of coagulation and wet oxidation offers a new opportunity for the improvement of the quality of wastewater designated for discharge or recycling. First of all, the utilization of coagulated sludge via wet oxidation provides a conditioning process for the sludge, i.e. dewatering, which is rather difficult to carry out with untreated waste. Secondly, Fe2(SO4)3, which is employed earlier as a coagulant, transforms the conventional wet oxidation process into a catalytic one. The use of coagulation as the post-treatment for wet oxidation can offer the possibility of the brown hue that usually accompanies the partial oxidation to be reduced. As a result, the supernatant is less colored and also contains a rather low amount of Fe ions to beconsidered for recycling inside mills. The thickened part that consists of metal ions is then recycled back to the wet oxidation system. It was also observed that wet oxidation is favorable for the degradation of pitch substances (LWEs) and lignin that are present in the process waters of paper mills. Rather low operating temperatures are needed for wet oxidation in order to destruct LWEs. The oxidation in the alkaline media provides not only the faster elimination of pitch and lignin but also significantly improves the biodegradable characteristics of wastewater that contains lignin and pitch substances. During the course of the kinetic studies, a model, which can predict the enhancements of the biodegradability of wastewater, was elaborated. The model includes lumped concentrations suchas the chemical oxygen demand and biochemical oxygen demand and reflects a generalized reaction network of oxidative transformations. Later developments incorporated a new lump, the immediately available biochemical oxygen demand, which increased the fidelity of the predictions made by the model. Since changes in biodegradability occur simultaneously with the destruction of LWEs, an attempt was made to combine these two facts for modeling purposes.

Modeling reaction kinetics and mass transfer in ozonation in water solutions

This dissertation is based on four articles dealing with modeling of ozonation. The literature part of this considers some models for hydrodynamics in bubble column simulation. A literature review of methods for obtaining mass transfer coefficients is presented. The methods presented to obtain mass transfer are general models and can be applied to any gas-liquid system. Ozonation reaction models and methods for obtaining stoichiometric coefficients and reaction rate coefficients for ozonation reactions are discussed in the final section of the literature part. In the first article, ozone gas-liquid mass transfer into water in a bubble column was investigated for different pH values. A more general method for estimation of mass transfer and Henry’s coefficient was developed from the Beltrán method. The ozone volumetric mass transfer coefficient and the Henry’s coefficient were determined simultaneously by parameter estimation using a nonlinear optimization method. A minor dependence of the Henry’s law constant on pH was detected at the pH range 4 - 9. In the second article, a new method using the axial dispersion model for estimation of ozone self-decomposition kinetics in a semi-batch bubble column reactor was developed. The reaction rate coefficients for literature equations of ozone decomposition and the gas phase dispersion coefficient were estimated and compared with the literature data. The reaction order in the pH range 7-10 with respect to ozone 1.12 and 0.51 the hydroxyl ion were obtained, which is in good agreement with literature. The model parameters were determined by parameter estimation using a nonlinear optimization method. Sensitivity analysis was conducted using object function method to obtain information about the reliability and identifiability of the estimated parameters. In the third article, the reaction rate coefficients and the stoichiometric coefficients in the reaction of ozone with the model component p-nitrophenol were estimated at low pH of water using nonlinear optimization. A novel method for estimation of multireaction model parameters in ozonation was developed. In this method the concentration of unknown intermediate compounds is presented as a residual COD (chemical oxygen demand) calculated from the measured COD and the theoretical COD for the known species. The decomposition rate of p-nitrophenol on the pathway producing hydroquinone was found to be about two times faster than the p-nitrophenol decomposition rate on the pathway producing 4- nitrocatechol. In the fourth article, the reaction kinetics of p-nitrophenol ozonation was studied in a bubble column at pH 2. Using the new reaction kinetic model presented in the previous article, the reaction kinetic parameters, rate coefficients, and stoichiometric coefficients as well as the mass transfer coefficient were estimated with nonlinear estimation. The decomposition rate of pnitrophenol was found to be equal both on the pathway producing hydroquinone and on the path way producing 4-nitrocathecol. Comparison of the rate coefficients with the case at initial pH 5 indicates that the p-nitrophenol degradation producing 4- nitrocathecol is more selective towards molecular ozone than the reaction producing hydroquinone. The identifiability and reliability of the estimated parameters were analyzed with the Marcov chain Monte Carlo (MCMC) method. @All rights reserved. No part of the publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise, without the prior permission of the author.

Reaction Kinetics and Viscosity Modelling in the Fusion Syntheses of Ca- and Ca/Mg-resinates

Rosin is a natural product from pine forests and it is used as a raw material in resinate syntheses. Resinates are polyvalent metal salts of rosin acids and especially Ca- and Ca/Mg- resinates find wide application in the printing ink industry. In this thesis, analytical methods were applied to increase general knowledge of resinate chemistry and the reaction kinetics was studied in order to model the non linear solution viscosity increase during resinate syntheses by the fusion method. Solution viscosity in toluene is an important quality factor for resinates to be used in printing inks. The concept of critical resinate concentration, c crit, was introduced to define an abrupt change in viscosity dependence on resinate concentration in the solution. The concept was then used to explain the non-inear solution viscosity increase during resinate syntheses. A semi empirical model with two estimated parameters was derived for the viscosity increase on the basis of apparent reaction kinetics. The model was used to control the viscosity and to predict the total reaction time of the resinate process. The kinetic data from the complex reaction media was obtained by acid value titration and by FTIR spectroscopic analyses using a conventional calibration method to measure the resinate concentration and the concentration of free rosin acids. A multivariate calibration method was successfully applied to make partial least square (PLS) models for monitoring acid value and solution viscosity in both mid-infrared (MIR) and near infrared (NIR) regions during the syntheses. The calibration models can be used for on line resinate process monitoring. In kinetic studies, two main reaction steps were observed during the syntheses. First a fast irreversible resination reaction occurs at 235 °C and then a slow thermal decarboxylation of rosin acids starts to take place at 265 °C. Rosin oil is formed during the decarboxylation reaction step causing significant mass loss as the rosin oil evaporates from the system while the viscosity increases to the target level. The mass balance of the syntheses was determined based on the resinate concentration increase during the decarboxylation reaction step. A mechanistic study of the decarboxylation reaction was based on the observation that resinate molecules are partly solvated by rosin acids during the syntheses. Different decarboxylation mechanisms were proposed for the free and solvating rosin acids. The deduced kinetic model supported the analytical data of the syntheses in a wide resinate concentration region, over a wide range of viscosity values and at different reaction temperatures. In addition, the application of the kinetic model to the modified resinate syntheses gave a good fit. A novel synthesis method with the addition of decarboxylated rosin (i.e. rosin oil) to the reaction mixture was introduced. The conversion of rosin acid to resinate was increased to the level necessary to obtain the target viscosity for the product at 235 °C. Due to a lower reaction temperature than in traditional fusion synthesis at 265 °C, thermal decarboxylation is avoided. As a consequence, the mass yield of the resinate syntheses can be increased from ca. 70% to almost 100% by recycling the added rosin oil.

Evaluating End-User Training Effectiveness in ERP System Implementation

Today’s business world demands more and more internal and external integration and transparency among companies at all fields. Integrated ERP (enterprise resource planning) systems offer a possibility to improve business practices and procedures by providing a unified view on the business including all functions and departments. Due to the obvious benefits, the popularity of integrated ERP systems keeps growing. The implementation of ERP systems has however proven risky. The implementation projects tend to be long, extensive, and costly – and often they end up in a failure. Due to the significant task and role changes ERP implementation brings to almost everybody in the company, training has been identified as one of the most critical success factors of an ERP implementation. To ensure that the training is conducted in the most effective and successful manner, the training outcomes should be evaluated. So far, training evaluation has however gained only limited attention at most companies investing in different training programs. Uponor corporation has initiated a large ERP implementation and process harmonization program in 2004. Thousands of end-users have been trained during this project so far, and the work still continues until the project is completed in 2010. In this thesis, the evaluation of end-user training in Uponor’s ERP program is brought further from the current state of performing the basic participant satisfaction survey in the end of each class. The results show that in order to reach reliable training effectiveness evaluation results, not only the reaction towards training but also transfer of skills and attitudes and the final results of the training program should be evaluated.

A generalized 1D particle transport method for convection diffusion reaction model

This work is devoted to the development of numerical method to deal with convection diffusion dominated problem with reaction term, non - stiff chemical reaction and stiff chemical reaction. The technique is based on the unifying Eulerian - Lagrangian schemes (particle transport method) under the framework of operator splitting method. In the computational domain, the particle set is assigned to solve the convection reaction subproblem along the characteristic curves created by convective velocity. At each time step, convection, diffusion and reaction terms are solved separately by assuming that, each phenomenon occurs separately in a sequential fashion. Moreover, adaptivities and projection techniques are used to add particles in the regions of high gradients (steep fronts) and discontinuities and transfer a solution from particle set onto grid point respectively. The numerical results show that, the particle transport method has improved the solutions of CDR problems. Nevertheless, the method is time consumer when compared with other classical technique e.g., method of lines. Apart from this advantage, the particle transport method can be used to simulate problems that involve movingsteep/smooth fronts such as separation of two or more elements in the system.

Quantitative refinement of reaction-based biomodels

In the field of molecular biology, scientists adopted for decades a reductionist perspective in their inquiries, being predominantly concerned with the intricate mechanistic details of subcellular regulatory systems. However, integrative thinking was still applied at a smaller scale in molecular biology to understand the underlying processes of cellular behaviour for at least half a century. It was not until the genomic revolution at the end of the previous century that we required model building to account for systemic properties of cellular activity. Our system-level understanding of cellular function is to this day hindered by drastic limitations in our capability of predicting cellular behaviour to reflect system dynamics and system structures. To this end, systems biology aims for a system-level understanding of functional intraand inter-cellular activity. Modern biology brings about a high volume of data, whose comprehension we cannot even aim for in the absence of computational support. Computational modelling, hence, bridges modern biology to computer science, enabling a number of assets, which prove to be invaluable in the analysis of complex biological systems, such as: a rigorous characterization of the system structure, simulation techniques, perturbations analysis, etc. Computational biomodels augmented in size considerably in the past years, major contributions being made towards the simulation and analysis of large-scale models, starting with signalling pathways and culminating with whole-cell models, tissue-level models, organ models and full-scale patient models. The simulation and analysis of models of such complexity very often requires, in fact, the integration of various sub-models, entwined at different levels of resolution and whose organization spans over several levels of hierarchy. This thesis revolves around the concept of quantitative model refinement in relation to the process of model building in computational systems biology. The thesis proposes a sound computational framework for the stepwise augmentation of a biomodel. One starts with an abstract, high-level representation of a biological phenomenon, which is materialised into an initial model that is validated against a set of existing data. Consequently, the model is refined to include more details regarding its species and/or reactions. The framework is employed in the development of two models, one for the heat shock response in eukaryotes and the second for the ErbB signalling pathway. The thesis spans over several formalisms used in computational systems biology, inherently quantitative: reaction-network models, rule-based models and Petri net models, as well as a recent formalism intrinsically qualitative: reaction systems. The choice of modelling formalism is, however, determined by the nature of the question the modeler aims to answer. Quantitative model refinement turns out to be not only essential in the model development cycle, but also beneficial for the compilation of large-scale models, whose development requires the integration of several sub-models across various levels of resolution and underlying formal representations.

A reaction engineering approach to homogeneously catalyzed glycerol hydrochlorination

The production of biodiesel through transesterification has created a surplus of glycerol on the international market. In few years, glycerol has become an inexpensive and abundant raw material, subject to numerous plausible valorisation strategies. Glycerol hydrochlorination stands out as an economically attractive alternative to the production of biobased epichlorohydrin, an important raw material for the manufacturing of epoxy resins and plasticizers. Glycerol hydrochlorination using gaseous hydrogen chloride (HCl) was studied from a reaction engineering viewpoint. Firstly, a more general and rigorous kinetic model was derived based on a consistent reaction mechanism proposed in the literature. The model was validated with experimental data reported in the literature as well as with new data of our own. Semi-batch experiments were conducted in which the influence of the stirring speed, HCl partial pressure, catalyst concentration and temperature were thoroughly analysed and discussed. Acetic acid was used as a homogeneous catalyst for the experiments. For the first time, it was demonstrated that the liquid-phase volume undergoes a significant increase due to the accumulation of HCl in the liquid phase. Novel and relevant features concerning hydrochlorination kinetics, HCl solubility and mass transfer were investigated. An extended reaction mechanism was proposed and a new kinetic model was derived. The model was tested with the experimental data by means of regression analysis, in which kinetic and mass transfer parameters were successfully estimated. A dimensionless number, called Catalyst Modulus, was proposed as a tool for corroborating the kinetic model. Reactive flash distillation experiments were conducted to check the commonly accepted hypothesis that removal of water should enhance the glycerol hydrochlorination kinetics. The performance of the reactive flash distillation experiments were compared to the semi-batch data previously obtained. An unforeseen effect was observed once the water was let to be stripped out from the liquid phase, exposing a strong correlation between the HCl liquid uptake and the presence of water in the system. Water has revealed to play an important role also in the HCl dissociation: as water was removed, the dissociation of HCl was diminished, which had a retarding effect on the reaction kinetics. In order to obtain a further insight on the influence of water on the hydrochlorination reaction, extra semi-batch experiments were conducted in which initial amounts of water and the desired product were added. This study revealed the possibility to use the desired product as an ideal “solvent” for the glycerol hydrochlorination process. A co-current bubble column was used to investigate the glycerol hydrochlorination process under continuous operation. The influence of liquid flow rate, gas flow rate, temperature and catalyst concentration on the glycerol conversion and product distribution was studied. The fluid dynamics of the system showed a remarkable behaviour, which was carefully investigated and described. Highspeed camera images and residence time distribution experiments were conducted to collect relevant information about the flow conditions inside the tube. A model based on the axial dispersion concept was proposed and confronted with the experimental data. The kinetic and solubility parameters estimated from the semi-batch experiments were successfully used in the description of mass transfer and fluid dynamics of the bubble column reactor. In light of the results brought by the present work, the glycerol hydrochlorination reaction mechanism has been finally clarified. It has been demonstrated that the reactive distillation technology may cause drawbacks to the glycerol hydrochlorination reaction rate under certain conditions. Furthermore, continuous reactor technology showed a high selectivity towards monochlorohydrins, whilst semibatch technology was demonstrated to be more efficient towards the production of dichlorohydrins. Based on the novel and revealing discoveries brought by the present work, many insightful suggestions are made towards the improvement of the production of αγ-dichlorohydrin on an industrial scale.