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Thesis (PhD (Biochemistry))--University of Stellenbosch, 2011. / ENGLISH ABSTRACT: Metabolic Control Analysis (MCA) provides a powerful quantitative framework for understanding and explaining the control and regulation within a cellular system. MCA allows the global control of a steady-state system to be quantified in terms of control coeficients, which we can express in terms of the local properties referred to as elasticity coeficients. MCA relates elasticities to control coeficients through a matrix inversion, thus allowing scientists to predict and quantify how the kinetics of the individual enzymes affect the systemic behaviour of cellular systems. Traditionally we solved this problem numerically, while we used algebraic and symbolic control analysis techniques less frequently. By using symbolic algebraic computation we present a general implementation of the symbolic matrix inversion of MCA, known as SymCA, which requires only the description of any allosteric modifier interactions and the stoichiometry of a cellular system. The algebraic expressions generated allow an in-depth analysis of the distribution of the control within a system and also of the parameters which exhibit the greatest effect on this control distribution. This also applies when the exact values for the elasticities or control coeficients are unknown. We have demonstrated that by quantifying the control patterns, referred to as `routes of regulation', inherent in all control coeficient expressions, we can gain insight into how perturbations are propagated through a cellular system and which regulatory pathways are favoured under changing conditions. / AFRIKAANSE OPSOMMING: Metaboliese Kontrole-Analise (MKA) bied 'n kragtige kwantitatiewe raamwerk om die beheer en regulering binne sellulere sisteme te verstaan en te verduidelik. 'n Sleutelaspek van MKA is dat die globale beheer van 'n sisteem met 'n bestendige toestand gekwantifiseer kan word in terme van kontrole-koefisente en dat hierdie koefisente uitgedruk kan word in terme van die sisteem se lokale eienskappe, genaamd elastisiteitskoefisente. Deur van matriksinversie gebruik te maak kan MKA die verband tussen elastisiteitskoefisente en kontrole-koefisente aflei wat mens in staat stel om te sien hoe die kinetika van die individuele ensiemreaksies die sisteemgedrag op sellulere vlak beinvloed. Die probleem word tradisioneel hoofsaaklik op numeriese wyse bereken terwyl die gebruik van algebraiese en simboliese kontrole-analise minder gereeld gebruik word. In hierdie proefskrif verskaf ons, deur van simboliese algebraiese metodes gebruik te maak, 'n generiese implementasie van die simboliese matriksinversie van MKA, genaamd SymCA, wat slegs 'n beskrywing van 'n sellulere sisteem se allosetriese interaksies en die stoichiometrie benodig. Die algebraiese uitdrukkings sodanig gegenereer stel mens in staat om 'n in-diepte analise te doen om vas te stel waar die beheer binne 'n sisteem le, asook watter parameters die grootste effek op die kontrole-verspreiding het. Dit geld selfs in die geval waar die presiese waardes van die elastisiteitskoefisente of kontrole-koefisente onbekend is. Hierdie proefskrif demonstreer hoe die kwantifisering van kontrole-patrone, ook gesien as 'roetes van regulering', wat inherent is aan kontrole-koefisent vergelykings, mens in staat stel om te sien hoe perturbasies in 'n sellulere sisteem voortplant en watter regulatoriese paaie bevoordeel word onder veranderde kondisies.

The current study was designed to evaluate the utility of progressing sequentially from multiple-respondent anecdotal assessments through test-control treatment analysis as an effective and efficient method of identifying the environmental determinants of problem behavior. the goal of the study was to evaluate overall agreement among multiple respondents on the primary function of aberrant behavior using the Motivation Assessment Scale (MAS) and Questions About Behavioral Function (QABF) and, if agreement was obtained, conduct a test-control evaluation to confirm anecdotal assessment findings while simultaneously evaluating the effects of function-based treatment. for 4 individuals, at least 4 of 5 respondents to the anecdotal assessments agreed (both within and across assessments) on the probable maintaining consequence for their problem behaviors. Test-control multielement evaluations were then conducted in which baseline sessions, corresponding to the suspected operant function of each individual’s problem behavior, were alternated with sessions in which the identified contingency was arranged for alternative behavior. Each evaluation showed substantial decreases in problem behavior and maintenance of alternative responses.

Thesis (MSc (Biochemistry))--University of Stellenbosch, 2010. / ENGLISH ABSTRACT: The Hodgkin-Huxley model, created in 1952, was one of the first models in computational neuroscience and remains the best studied neuronal model to date. Although many other models have a more detailed system description than the Hodgkin-Huxley model, it nonetheless gives an accurate account of various high-level neuronal behaviours. The fields of computational neuroscience and Systems Biology have developed as separate disciplines for a long time and only fairly recently has the neurosciences started to incorporate methods from Systems Biology. Metabolic Control Analysis (MCA), a Systems Biology tool, has not been used in the neurosciences. This study aims to further bring these two fields together, by testing the feasibility of an MCA approach to analyse the Hodgkin-Huxley model. In MCA it is not the parameters of the system that are perturbed, as in the more traditional sensitivity analysis, but the system processes, allowing the formulation of summation and connectivity theorems. In order to determine if MCA can be performed on the Hodgkin-Huxley model, we identified all the discernable model processes of the neuronal system. We performed MCA and quantified the control of the model processes on various high-level time invariant system observables, e.g. the action potential (AP) peak, firing threshold, propagation speed and firing frequency. From this analysis we identified patterns in process control, e.g. the processes that would cause an increase in sodium current, would also cause the AP threshold to lower (decrease its negative value) and the AP peak, propagation speed and firing frequency to increase. Using experimental inhibitor titrations from literature we calculated the control of the sodium channel on AP characteristics and compared it with control coefficients derived from our model simulation. Additionally, we performed MCA on the model’s time-dependent state variables during an AP. This revealed an intricate linking of the system variables via the membrane potential. We developed a method to quantify the contribution of the individual feedback loops in the system. We could thus calculate the percentage contribution of the sodium, potassium and leak currents leading to the observed global change after a system perturbation. Lastly, we compared ion channel mutations to our model simulations and showed how MCA can be useful in identifying targets to counter the effect of these mutations. In this thesis we extended the framework of MCA to neuronal systems and have successfully applied the analysis framework to quantify the contribution of the system processes to the model behaviour. / AFRIKAANSE OPSOMMINMG: Die Hodgkin-Huxley-model, wat in 1952 ontwikkel is, was een van die eerste modelle in rekenaarmagtige neurowetenskap en is vandag steeds een van die bes-bestudeerde neuronmodelle. Hoewel daar vele modelle bestaan met ’n meer uitvoerige sisteembeskrywing as die Hodgkin-Huxley-model gee dié model nietemin ’n akkurate beskrywing van verskeie hoëvlak-sisteemverskynsels. Die twee velde van sisteembiologie en neurowetenskap het lank as onafhanklike dissiplines ontwikkel en slegs betreklik onlangs het die veld van neurowetenskap begin om metodes van sisteembiologie te benut. ’n Sisteembiologiemetode genaamd metaboliese kontrole-analise (MKA) is tot dusver nog nie in die neurowetenskap gebruik nie. Hierdie studie het gepoog om die twee velde nader aan mekaar te bring deurdat die toepasbaarheid van die MKA-raamwerk op die Hodgkin-Huxley-model getoets word. In MKA is dit nie die parameters van die sisteem wat geperturbeer word soos in die meer tradisionele sensitiwiteitsanalise nie, maar die sisteemprosesse. Dit laat die formulering van sommasie- en konnektiwiteitsteoremas toe. Om die toepasbaarheid van die MKA-raamwerk op die Hodgkin-Huxleymodel te toets, is al die onderskeibare modelprosesse van die neurale sisteem geïdentifiseer. Ons het MKA toegepas en die kontrole van die model-prosesse op verskeie hoëvlak, tydsonafhanklike waarneembare sisteemvlak-eienskappe, soos die aksiepotensiaal-kruin, aksiepotensiaal-drempel, voortplantingspoed en aksiepotensiaal-frekwensie, gekwantifiseer. Vanuit hierdie analise kon daar patrone in die proseskontrole geïdentifiseer word, naamlik dat die prosesse wat ’n toename in die natriumstroom veroorsaak, ook sal lei tot ’n afname in die aksiepotensiaal-drempel (die negatiewe waarde verminder) en tot ’n toename in die aksiepotensiaal-kruin, voortplantingspoed en aksiepotensiaalfrekwensie. Deur gebruik te maak van eksperimentele stremmer-titrasies vanuit die literatuur kon die kontrole van die natriumkanaal op die aksiepotensiaaleienskappe bereken en vergelyk word met die kontrole-koëffisiënte vanuit die modelsimulasie. Ons het ook MKA op die model se tydsafhanklike veranderlikes deur die verloop van die aksiepotensiaal uitgevoer. Die analise het getoon dat die sisteemveranderlikes ingewikkeld verbind is via die membraanpotensiaal. Ons het ’n metode ontwikkel om die bydrae van die individuele terugvoerlusse in die sisteem te kwantifiseer. Die persentasie-bydrae van die natrium-, kalium- en lekstrome wat tot die waarneembare globale verandering ná ’n sisteemperturbasie lei, kon dus bepaal word. Laastens het ons ioonkanaalmutasies met ons modelsimulasies vergelyk en getoon hoe MKA nuttig kan wees in die identifisering van teikens om die effek van hierdie mutasies teen te werk. In hierdie tesis het ons die raamwerk van MKA uitgebrei na neurale sisteme en die analise-raamwerk suksesvol toegepas om die bydrae van die sisteemprosesse tot die modelgedrag te kwantifiseer.

Thesis (PhD (Biochemistry))--University of Stellenbosch, 2010. / ENGLISH ABSTRACT: In the last decade a need arose to find a theoretical framework capable of gaining a quantitative understanding of ecosystems. Control analysis was proposed as a suitable candidate for the analysis of ecosystems with various theoretical applications being developed, i.e. trophic control analysis (TCA) and ecological control analysis (ECA). We set out to test the latter approach through experimental means by applying techniques akin to enzyme kinetics of biochemistry on a simple ecosystem between Saccharomyces cerevisiae and Gluconobacter oxydans. However, this exercise was far more complex than we originally expected due to the extra metabolic activities presented by both organisms. Nevertheless, we derived suitable kinetic equations to describe the metabolic behaviour of both organisms, with regards to the activities of interest to us, from pure culture experiments. We developed new techniques to determine ethanol and oxygen sensitivity of G. oxydans based on its obligately aerobic nature. These parameters were then used to build a simple kinetic model and a more complex model incorporating oxygen limited metabolism we observed at higher cell densities of G. oxydans. Our models could predict both situations satisfactorily for pure cultures and especially the more complex model could describe the lack of linearity observed between metabolic activity and cell density at higher cell densities of G. oxydans. Mixed populations of S. cerevisiae and G. oxydans reached quasi-steady states in terms of ethanol concentration and acetate flux, which was a positive indication for the application of control analysis on the ecosystem. However, the theoretical models based on parameters derived from pure culture experiments did not predict mixed culture steady states accurately. Careful analysis showed that these parameters were mostly under-estimated for G. oxydans and overestimated for S. cerevisiae. Hence, we calculated the kinetic parameters for mixed population assays directly from the experimental data obtained from mixed cultures. We could calculate the control coefficients directly from the experimental data of mixed population studies and compare it with those from theoretical models based on 3 different parameter sets. Our analysis showed that the yeast had all the control over the acetate flux while control over the steady-state ethanol was shared. The strength of our approach lies in designing our experiments with a control analysis approach in mind, but we have also shown that even for simple ecosystems this approach is non-trivial. Despite the various experimental challenges, this approach was very rewarding due to the extra information obtained especially regarding control structure with regards to the steady-state ethanol concentration. / AFRIKAANSE OPSOMMING: In die afgelope dekade het daar ’n behoefte ontstaan na ‘n teoretiese raamwerk om tot ‘n kwantitatiewe begrip van ekosisteme te kom. As kandidaat vir so tipe raamwerk is kontrole analise voorgestel gepaardgaande met die ontwikkeling van verskeie teoretiese toepassings, i.e. trofiese kontrole analise en ekologiese kontrole analise. In hierdie tesis het ons laasgenoemde aanslag eksperimenteel ondersoek op ‘n eenvoudige ekosisteem, tussen Saccharomyces cerevisiae en Gluconobacter oxydans, deur gebruik te maak van tegnieke vanuit ensiemkinetika van biochemie. Hierdie strategie was egter baie meer kompleks as wat oorspronklik verwag is as gevolg van verdere metabolise aktiwiteite aanwesig in beide organismes. Ons het egter steeds daarin geslaag om kinetiese vergelykings af te lei, vanuit suiwer kulture, wat die metaboliese gedrag van beide organismes beskryf vir die aktiwiteite van belang vir ons studie. Ons het nuwe tegnieke, gebaseer op die aerobiese natuur van G. oxydans, ontwikkel om die sensitiwiteit van G. oxydans vir etanol en suurstof te bepaal. Hierdie parameters is gebruik om eers ’n eenvoudige model en toe ‘n meer gevorderde model, wat die suurstof-beperkte metabolisme van G. oxydans by hoër biomassa te beskryf, op te stel. Beide modelle was baie effektief in die voorspelling van die situasies waarvoor hulle ontwikkel is vir die suiwer kulture waar veral die meer gevorderde model die gebrek aan ‘n linieêre verband tussen die metabolisme van G. oxydans en biomassa by hoër biomassa kon beskryf. ’n Bemoedigende aanduiding dat kontrole analise toegepas kon word op die ekosisteem was dat mengkulture van S. cerevisiae en G. oxydans het quasi-bestendige toestande bereik het in terme van etanol konsentrasies en asetaat-fluksie. Die teoretiese modelle gebaseer op die parameters afgelei vanaf suiwer kulture kon egter nie die bestendige toestande in mengkulture akkuraat voorspel nie. Nadere ondersoek het aangedui dat die parameters meesal onderskat is vir G. oxydans en oorskat is vir S. cerevisiae. Gevolglik het ons die kinetiese parameters vir mengkulture direk van eksperimentele data van die mengkulture bereken. Verder kon ons die kontrole koeffisiente ook direk vanaf die eksperimentele data van mengkulture bereken en vergelyk met dié bereken vanuit die teoretiese modelle gebaseer op drie verskillende paremeter-stelle. Ons analise het gewys dat die gis alle beheer op die asetaat-fluksie uitoefen en dat die beheer oor die etanol-konsnetrasie gedeel is tussen die twee organismes. Die krag van ons aanslag lê daarin dat die eksperimente ontwerp is met ‘n kontrole analise in gedagte, maar ons het ook bewys dat hierdie aanslag selfs vir eenvoudige ekosisteme nie triviaal is nie. Ten spyte van die eksperimentele uitdagings, was die aanslag baie waardevol as gevolg van die ekstra inligting verkry met spesifieke klem op die kontrole-struktuur met betrekking tot die etanol konsentrasie by bestendige toestand.

The development of human society, which is highly dependent on fossil fuels, is now facing a range of global issues, such as rising energy prices, energy security and climate changes. To successfully tackle the resultant issues, the energy transition from fossil fuels to renewable energy sources, such as solar energy, tide energy, hydroelectric power, geothermal heat and biofuels, is under way. Biodiesel, as an important type of biofuels, has been increasingly produced from vegetable oil or used cooking oil, especially in Europe. Nevertheless, considering the high production cost of biodiesel, there is still much to be done to improve the economics of biodiesel industry. Utilisation of crude glycerol, the main by-product of the biodiesel industry, to produce value-added products appears to be a promising solution. Poly(3-hydroxybutyric acid) (PHB), a biodegradable plastic, can be converted from glycerol by Cupriavidus necator DSM 545 under unbalanced growth conditions, such as nitrogen limitation. One way to enhance the batch production of PHB is to genetically engineer the strain of C. necator, which requires insights of the dynamic impact of extracellular environment on cell phenotypes. Hence in this thesis, we aim to perform metabolic modelling based on experimental measurements to gain a better understanding of the behaviour of the metabolic network of Cupriavidus necator DSM 545 and identify potential bottlenecks of the process. Initially, C. necator DSM 545 is a strain that hardly grows on glycerol, so in a preliminary study, we investigate the process by which the strain was adapted to consume glycerol through serial subcultivation. It is found that the adaptation can be achieved within 15 cell generations over three passages in basal mineral medium, and the acquired phenotype is sufficiently stable upon further passage. The study of metabolism started with the reconstruction of the cell's metabolic network, followed by a thermodynamic analysis to check the feasibility and reversibility of all the biochemical reactions included. Then the static flux balance analysis was extended and applied to analyse the shift of metabolic states during the microbial fermentation in different batch conditions. The resulting patterns of flux distribution reveal the TCA cycle to be the major competitor for PHB synthesis at the ACCoA node. Cells have the potential to enter an efficient PHB-production phase that features minimal TCA/PHB flux split ratio, and the length of the phase can be manipulated by aeration. Although low aeration rate favours optimal flux split ratio, such condition that limits respiration also limits nutrient uptake, leading to low PHB productivity overall. To identify the actual limiting factors of PHB synthesis in the system, we further performed metabolic control analysis based on the calculated flux distributions. The analysis demonstrated how the distribution of the metabolic control can vary widely, depending on the aeration conditions used and the flux split ratios. Glycerolipid pathway, glycolysis, PHB metabolism, as well as the electron transport chain are revealed to be potential engineering targets as they contribute to the great majority of the positive control of PHB flux.

In this study, firstly, bioprocess characteristics for Serine Alkaline Protease (SAP) production, using recombinant Bacillus subtilis carrying pHV1431::subC, were examined. The cell concentration, substrate concentration, SAP activity and SAP synthesis rate profiles demonstrated that the system reaches to a steady state in terms of cell growth and SAP synthesis between t=15-25 h, therefore, this time interval is appropriate to employ both metabolic flux analysis and metabolic control analysis, which apply strictly to steady state systems. After that, three separate perturbations were introduced by addition of aspartate to the production medium at a certain time of the bioprocess. The response of the cells were observed and / by comparing the changes in intracellular reactions of aspartate pathway, Asn, Thr and Ile productions were determined to be the bottlenecks in aspartate pathway and the branchpoints splitting from Asp and AspSa were identified to be weakly rigid branchpoints. Lastly, metabolic control analysis principles were applied to determine the elasticity and flux control coefficients of the simplified aspartate pathway. Aspartate formation reaction and Lys, Thr, Ile, Met producing group share the control of asparagine synthesis. The results revealed that lysine producing branch flux dominates the other branch fluxes, therefore to eliminate bottlenecks and increase SAP production, the activity of the branches leading to the formation of Asn, Thr and Ile should be increased while decreasing the activity of lysine synthesizing branch. This could be achieved either by genetic manipulation or by addition of specific inhibitors or activators to the system.

Space missions increasingly require sophisticated guidance, navigation and control algorithms, the development of which is reliant on verification and validation (V&V) techniques to ensure mission safety and success. A crucial element of V&V is the assessment of control system robust performance in the presence of uncertainty. In addition to estimating average performance under uncertainty, it is critical to determine the worst case performance. Industrial V&V approaches typically employ mu-analysis in the early control design stages, and Monte Carlo simulations on high-fidelity full engineering simulators at advanced stages of the design cycle. While highly capable, such techniques present a critical gap between pessimistic worst case estimates found using analytical methods, and the optimistic outlook often presented by Monte Carlo runs. Conservative worst case estimates are problematic because they can demand a controller redesign procedure, which is not justified if the poor performance is unlikely to occur. Gaining insight into the probability associated with the worst case performance is valuable in bridging this gap. It should be noted that due to the complexity of industrial-scale systems, V&V techniques are required to be capable of efficiently analysing non-linear models in the presence of significant uncertainty. As well, they must be computationally tractable. It is desirable that such techniques demand little engineering effort before each analysis, to be applied widely in industrial systems. Motivated by these factors, this thesis proposes and develops an efficient algorithm, based on the cross entropy simulation method. The proposed algorithm efficiently estimates the probabilities associated with various performance levels, from nominal performance up to degraded performance values, resulting in a curve of probabilities associated with various performance values. Such a curve is termed the probability profile of performance (PPoP), and is introduced as a tool that offers insight into a control system's performance, principally the probability associated with the worst case performance. The cross entropy-based robust performance analysis is implemented here on various industrial systems in European Space Agency-funded research projects. The implementation on autonomous rendezvous and docking models for the Mars Sample Return mission constitutes the core of the thesis. The proposed technique is implemented on high-fidelity models of the Vega launcher, as well as on a generic long coasting launcher upper stage. In summary, this thesis (a) develops an algorithm based on the cross entropy simulation method to estimate the probability associated with the worst case, (b) proposes the cross entropy-based PPoP tool to gain insight into system performance, (c) presents results of the robust performance analysis of three space industry systems using the proposed technique in conjunction with existing methods, and (d) proposes an integrated template for conducting robust performance analysis of linearised aerospace systems.

The environment in South Africa has changed dramatically with regard to health services during the past five years especially for state-funded hospitals in the public sector. At the Johannesburg Hospital the admittance of chronic patients has increased considerably over the past five years, thus increasing the workload for the physiotherapists. In spite of the increased workload the staff complement of the Physiotherapy Department has decreased from forty-one to eighteen staff members due to the severe budget constraints. This investigation was initiated to determine whether the department was operating optimally under present conditions, and what the major problem areas were. This document describes the methods used and results obtained during the investigation. Several known techniques such as the brainstorming and nominal group technique were used during the facilitation of workshops. Timesheets were completed over a six-month period and interviews were held with the personnel in the department. The approach followed with the statistical analysis of the timesheets was to use confidence intervals to compare the standard treatment times with the actual treatment times. Hypotheses testing were used to determine whether it would be possible to standardise on similar treatments in different treatment areas. The required capacity was calculated based on the amount of time spent on direct patient care by the physiotherapists during the six-month period of the investigation. Several major issues were identified during the workshops that need to be addressed. Important conclusions drawn were that there was indeed a shortage of staff in the physiotherapy department. It also became clear that standardisation of treatments in different treatment areas is not possible. There is a need for a recognition system and teambuilding exercises, which should have a favourable impact on the motivation of employees. A maintenance plan for equipment needs to be implemented and interdepartmental communication needs to improve. / Dissertation (MEng (Industrial Engineering))--University of Pretoria, 2006. / Industrial and Systems Engineering / unrestricted

Thesis (MSc (Biochemistry))--Stellenbosch University, 2008. / The aim of this study is the theoretical investigation of carbon fixation in sugarcane leaves. Sugarcane has a well known reputation for accumulating sucrose in the stalk to levels as high as 650 mM, almost a fifth of the plant’s fresh weight. Although this is an efficient accumulating mechanism, there is an even more efficient ‘carbon pump’ found in C4 plants. This is a well documented carbon concentrating mechanism and one of the first to be studied. However scientists are still trying to understand the carboxylating mechanism and the regulation thereof. It has been speculated that this mechanism is at its saturation level and elevating carbon dioxide will have little or no effect on further carbon fixation. Futher, studies suggest that the sucrose accumulating sink is able to regulate photosynthesis. Therefore a regulatory mechanism should exist from the sink to carbon fixation in order for such regulation to occur. Thework in this thesis therefore lays the foundation for investigating regulation of photosynthesis. The field of systems biology is the study of cellular networks by assemblingmodels. Pathways are considered as systems and notmerely collections of single components. This allows the interaction of pathway metabolites and the regulation that they have on one another to be studied. The questions asked pertaining to a pathway, will determine the types of model analysis. Structural analysis is useful for studying stoichiometric models, determining characteristics like energy consumption, futile cycles and valid pathways through a system at steady-state. Kinetic analysis on the other hand, gives insight into system dynamics and the control exerted by the system components, predicting time-course and steady states. In this thesis we begin to investigate photosynthesis in sugarcane leaves and the role it has in accumulating sucrose in the plant. Firstly, a structural model was developed incorporating carbon fixation, sucrose production in the leaf and subsequent transport of sucrose to the storage parenchyma and accumulation. The model was analysed using elementary mode analysis, showing that there are twelve routes for producing sucrose with no pathway beingmore energy efficient than any other. Further, it highlighted a futile cycle transporting triose phosphates and phosphoglycerate between the two photosynthetic compartments in the leaf. In the storage parenchyma, manymore futile cycleswere revealed,many of them energetically wasteful. Three other sets of elementary modes describe sucrose’s destination in either the vacuole or use in glycolysis or fibre formation, each with a different amount of required energy equivalents. The fourth set describes how sucrose cannot be converted to fibre precursors without also being used for glycolyis building blocks. Secondly, a kinetic model of carbon fixation in the leaf was assembled with the primary goal of characterising thismoiety-conserved cycle. This included the collation of kinetic data, incorporating volumes of the compartments and the areas of the location of the transporters into the model. This model was then analysed using metabolic control analysis. The model was able to predict metabolite concentration in the pathway at steady-state which were compared to those found experimentally. However, modifications need to be made to the model before further analysis is done so that the model predicted values match the experimental values more accurately. Time course analysis and response coefficients were also calculated for the carbon fixation cycle. Thework in this thesis therefore paves the way for understanding photosynthesis and its regulation in sugarcane leaves. Such work has the potential to pinpoint genetic engineering target points, allowing for better hybrid selection and propagation.