Petrogenesis of the Bysteek and Koenap Formation Migmatites, Central Namaqualand
- Authors: Moodley, Jason Anthony
- Date: 2013
- Subjects: Petrogenesis -- South Africa -- Namaqualand Migmatite -- South Africa -- Namaqualand Granulite -- South Africa -- Namaqualand Thermodynamics Geology, Stratigraphic -- Proterozoic Geology, Stratigraphic -- Proterozoic -- South Africa -- Namaqualand
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4914 , http://hdl.handle.net/10962/d1001574
- Description: The Mesoproterozoic rocks of the Bysteek and Koenap Formations of the Arribees Group are exposed within a NW-SE striking antiformal structure comprised of mafic granulites and metapelitic diatexites, and a number of marble and calc-silicate rock layers. The mafic granulites of the Bysteek Formation show a typological variety of anatectic features, including nebulitic, stromatitic mesosomes, melanosomes, quartz syenitic leucocratic vein networks and syenitic pools. Melanosomes consist of hedenbergitic to diopside-rich clinopyroxene (XMg: 0.40), anorthitic plagioclase (An90), with some quartz, minor apatite and titanite. Anatexis was caused by biotite dehydration melting and formed a melt of probably granitic composition. The leucosome composition ranges from either alkali-feldspar-granitic to plagioclase rich or granitic. This variation is interpreted as a result of variable extraction of melt from the source to granitic pools. The diatexites of the Koenap Formation are most likely of metapelitic or meta-greywacke origin. They are texturally variable but always contain high modal contents of alkali feldspar and quartz which generally form magmatic textures. Almandine-rich garnet (XMg: 0.18-0.25), cordierite (XMg: 0.71) form secondary biotite, sillimanite and magnetite during retrograde breakdown. Thermodynamic modelling of mafic granulite compositions suggests peak P-T conditions of ~865 °C and 8.6 kbar. Occasionally, garnet rich in ferric iron (XAdr: 0.55) forms by plagioclase-clinopyroxene breakdown under oxidising conditions at ~6 kilobar and ~ 800 °C. At the same stage amphibole forms in some melanosomes. P-T estimations for the diatexites based on thermodynamic modelling suggest the equilibration of the assemblage garnet, cordierite, alkali feldspar and melt at ~860 °C and 5.5 kbar. Conditions comparable to the peak pressure in the mafic granulites could not be established. However, since the diatexites and the mafic granulites are closely related in the field and no evidence of juxtaposition after the thermal peak exists, the P-T record of the diatexites might be incomplete
- Full Text:
- Date Issued: 2013
- Authors: Moodley, Jason Anthony
- Date: 2013
- Subjects: Petrogenesis -- South Africa -- Namaqualand Migmatite -- South Africa -- Namaqualand Granulite -- South Africa -- Namaqualand Thermodynamics Geology, Stratigraphic -- Proterozoic Geology, Stratigraphic -- Proterozoic -- South Africa -- Namaqualand
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4914 , http://hdl.handle.net/10962/d1001574
- Description: The Mesoproterozoic rocks of the Bysteek and Koenap Formations of the Arribees Group are exposed within a NW-SE striking antiformal structure comprised of mafic granulites and metapelitic diatexites, and a number of marble and calc-silicate rock layers. The mafic granulites of the Bysteek Formation show a typological variety of anatectic features, including nebulitic, stromatitic mesosomes, melanosomes, quartz syenitic leucocratic vein networks and syenitic pools. Melanosomes consist of hedenbergitic to diopside-rich clinopyroxene (XMg: 0.40), anorthitic plagioclase (An90), with some quartz, minor apatite and titanite. Anatexis was caused by biotite dehydration melting and formed a melt of probably granitic composition. The leucosome composition ranges from either alkali-feldspar-granitic to plagioclase rich or granitic. This variation is interpreted as a result of variable extraction of melt from the source to granitic pools. The diatexites of the Koenap Formation are most likely of metapelitic or meta-greywacke origin. They are texturally variable but always contain high modal contents of alkali feldspar and quartz which generally form magmatic textures. Almandine-rich garnet (XMg: 0.18-0.25), cordierite (XMg: 0.71) form secondary biotite, sillimanite and magnetite during retrograde breakdown. Thermodynamic modelling of mafic granulite compositions suggests peak P-T conditions of ~865 °C and 8.6 kbar. Occasionally, garnet rich in ferric iron (XAdr: 0.55) forms by plagioclase-clinopyroxene breakdown under oxidising conditions at ~6 kilobar and ~ 800 °C. At the same stage amphibole forms in some melanosomes. P-T estimations for the diatexites based on thermodynamic modelling suggest the equilibration of the assemblage garnet, cordierite, alkali feldspar and melt at ~860 °C and 5.5 kbar. Conditions comparable to the peak pressure in the mafic granulites could not be established. However, since the diatexites and the mafic granulites are closely related in the field and no evidence of juxtaposition after the thermal peak exists, the P-T record of the diatexites might be incomplete
- Full Text:
- Date Issued: 2013
Protein secondary structure prediction using neural networks and support vector machines
- Authors: Tsilo, Lipontseng Cecilia
- Date: 2009
- Subjects: Neural networks (Computer science) , Support vector machines , Proteins -- Structure -- Mathematical models
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5569 , http://hdl.handle.net/10962/d1002809 , Neural networks (Computer science) , Support vector machines , Proteins -- Structure -- Mathematical models
- Description: Predicting the secondary structure of proteins is important in biochemistry because the 3D structure can be determined from the local folds that are found in secondary structures. Moreover, knowing the tertiary structure of proteins can assist in determining their functions. The objective of this thesis is to compare the performance of Neural Networks (NN) and Support Vector Machines (SVM) in predicting the secondary structure of 62 globular proteins from their primary sequence. For each NN and SVM, we created six binary classifiers to distinguish between the classes’ helices (H) strand (E), and coil (C). For NN we use Resilient Backpropagation training with and without early stopping. We use NN with either no hidden layer or with one hidden layer with 1,2,...,40 hidden neurons. For SVM we use a Gaussian kernel with parameter fixed at = 0.1 and varying cost parameters C in the range [0.1,5]. 10- fold cross-validation is used to obtain overall estimates for the probability of making a correct prediction. Our experiments indicate for NN and SVM that the different binary classifiers have varying accuracies: from 69% correct predictions for coils vs. non-coil up to 80% correct predictions for stand vs. non-strand. It is further demonstrated that NN with no hidden layer or not more than 2 hidden neurons in the hidden layer are sufficient for better predictions. For SVM we show that the estimated accuracies do not depend on the value of the cost parameter. As a major result, we will demonstrate that the accuracy estimates of NN and SVM binary classifiers cannot distinguish. This contradicts a modern belief in bioinformatics that SVM outperforms other predictors.
- Full Text:
- Date Issued: 2009
- Authors: Tsilo, Lipontseng Cecilia
- Date: 2009
- Subjects: Neural networks (Computer science) , Support vector machines , Proteins -- Structure -- Mathematical models
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5569 , http://hdl.handle.net/10962/d1002809 , Neural networks (Computer science) , Support vector machines , Proteins -- Structure -- Mathematical models
- Description: Predicting the secondary structure of proteins is important in biochemistry because the 3D structure can be determined from the local folds that are found in secondary structures. Moreover, knowing the tertiary structure of proteins can assist in determining their functions. The objective of this thesis is to compare the performance of Neural Networks (NN) and Support Vector Machines (SVM) in predicting the secondary structure of 62 globular proteins from their primary sequence. For each NN and SVM, we created six binary classifiers to distinguish between the classes’ helices (H) strand (E), and coil (C). For NN we use Resilient Backpropagation training with and without early stopping. We use NN with either no hidden layer or with one hidden layer with 1,2,...,40 hidden neurons. For SVM we use a Gaussian kernel with parameter fixed at = 0.1 and varying cost parameters C in the range [0.1,5]. 10- fold cross-validation is used to obtain overall estimates for the probability of making a correct prediction. Our experiments indicate for NN and SVM that the different binary classifiers have varying accuracies: from 69% correct predictions for coils vs. non-coil up to 80% correct predictions for stand vs. non-strand. It is further demonstrated that NN with no hidden layer or not more than 2 hidden neurons in the hidden layer are sufficient for better predictions. For SVM we show that the estimated accuracies do not depend on the value of the cost parameter. As a major result, we will demonstrate that the accuracy estimates of NN and SVM binary classifiers cannot distinguish. This contradicts a modern belief in bioinformatics that SVM outperforms other predictors.
- Full Text:
- Date Issued: 2009
Guidelines for assessing single borehole yields in secondary aquifers
- Authors: Murray, Eric Charles
- Date: 1997
- Subjects: Aquifers -- Measurement
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:6026 , http://hdl.handle.net/10962/d1005512
- Description: The motivation for this research project arose from the realisation that many South African rural water supply schemes fail due to the over abstraction of groundwater from single boreholes. The main reason for this mis-management of groundwater is a result of inappropriate borehole yield recommendation methods. This research project set out to review existing borehole yield assessment methods and establish new methods which take the shortcomings of existing methods into account. The study is concerned with borehole yield assessment methods applicable to secondary aquifers, since these aquifers are by far the most common in South Africa. The yield assessment methods have been grouped into those that are based on aquifer yield analyses, and on the analysis of single borehole test pump data. In order to assess which methods give suitable yield recommendations, it was necessary to compare the yields obtained using the various methods, with established yields from production boreholes. The focus of the aquifer yield component of the study, was to develop a method for estimating the proportion of recharge that can be abstracted from a single borehole located in a relatively small aquifer. The method was developed by computer simulations of aquifers with different hydraulic properties, and by establishing a formula which describes the relationship between recharge and the abstractable proportion of recharge. Under specific hydrogeological conditions, the recharge based method proved to be reliable in relation to established yields from production boreholes. Of the borehole yield assessment methods based on the analysis of test pump data, none of the existing methods proved to be reliable. However, the yields obtained using the two newly developed methods compared favourably to the established yield of existing production boreholes. Both of these methods are based on the application of the Cooper-Jacob approximation of the Theis equation. This study reviews existing methods and presents newly developed methods for recommending borehole abstraction rates in secondary aquifers. While existing borehole yield assessment methods were found to be unreliable, some of the newly developed methods, if correctly applied, give acceptable yield recommendations.
- Full Text:
- Date Issued: 1997
- Authors: Murray, Eric Charles
- Date: 1997
- Subjects: Aquifers -- Measurement
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:6026 , http://hdl.handle.net/10962/d1005512
- Description: The motivation for this research project arose from the realisation that many South African rural water supply schemes fail due to the over abstraction of groundwater from single boreholes. The main reason for this mis-management of groundwater is a result of inappropriate borehole yield recommendation methods. This research project set out to review existing borehole yield assessment methods and establish new methods which take the shortcomings of existing methods into account. The study is concerned with borehole yield assessment methods applicable to secondary aquifers, since these aquifers are by far the most common in South Africa. The yield assessment methods have been grouped into those that are based on aquifer yield analyses, and on the analysis of single borehole test pump data. In order to assess which methods give suitable yield recommendations, it was necessary to compare the yields obtained using the various methods, with established yields from production boreholes. The focus of the aquifer yield component of the study, was to develop a method for estimating the proportion of recharge that can be abstracted from a single borehole located in a relatively small aquifer. The method was developed by computer simulations of aquifers with different hydraulic properties, and by establishing a formula which describes the relationship between recharge and the abstractable proportion of recharge. Under specific hydrogeological conditions, the recharge based method proved to be reliable in relation to established yields from production boreholes. Of the borehole yield assessment methods based on the analysis of test pump data, none of the existing methods proved to be reliable. However, the yields obtained using the two newly developed methods compared favourably to the established yield of existing production boreholes. Both of these methods are based on the application of the Cooper-Jacob approximation of the Theis equation. This study reviews existing methods and presents newly developed methods for recommending borehole abstraction rates in secondary aquifers. While existing borehole yield assessment methods were found to be unreliable, some of the newly developed methods, if correctly applied, give acceptable yield recommendations.
- Full Text:
- Date Issued: 1997
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