| Code | Faculty | Department |
|---|---|---|
| 02133173 | Faculty of Natural and Agricultural Sciences | Department: Chemistry |
| Credits | Duration | NQF level |
|---|---|---|
| Minimum duration of study: 3 years | Total credits: 430 | NQF level: 07 |
Those students registered for the BSc (Chemistry) programme and who have opted to select any of the dual major fields of study offered within this programme must take note of the following:
Bachelor of Science
Chemistry
Important information for all prospective students for 2023
The admission requirements below apply to all who apply for admission to the University of Pretoria with a National Senior Certificate (NSC) and Independent Examination Board (IEB) qualifications. Click here for this Faculty Brochure.
Minimum requirements | |||
Achievement level | |||
English Home Language or English First Additional Language | Mathematics | Physical Sciences | APS |
NSC/IEB | NSC/IEB | NSC/IEB | |
5 | 5 | 5 | 34 |
Life Orientation is excluded when calculating the APS.
You will be considered for final admission to degree studies if space allows, and if you have a National Senior Certificate (NSC) or equivalent qualification with admission to bachelor’s degree studies, and comply with the minimum subject requirements as well as the APS requirements of your chosen programme.
Applicants with qualifications other than the abovementioned should refer to the Brochure: Undergraduate Programme Information 2023: Qualifications other than the NSC and IEB, available at click here.
International students: Click here.
Transferring students
A transferring student is a student who, at the time of applying at the University of Pretoria (UP) is/was a registered student at another tertiary institution. A transferring student will be considered for admission based on NSC or equivalent qualification and previous academic performance. Students who have been dismissed from other institutions due to poor academic performance will not be considered for admission to UP.
Closing dates: Same as above.
Returning students
A returning student is a student who, at the time of application for a degree programme is/was a registered student at UP, and wants to transfer to another degree at UP. A returning student will be considered for admission based on NSC or equivalent qualification and previous academic performance.
Note:
Closing date for applications from returning students
Unless capacity allows for an extension of the closing date, applications from returning students must be submitted before the end of August via your UP Student Centre.
Candidates who do not comply with the minimum admission requirements for BSc (Chemistry), may be considered for admission to the BSc – Extended programme – Physical Sciences, which requires an additional year of study.
BSc – Extended Programme – Physical Sciences Minimum requirements | |||
Achievement level | |||
English Home Language or English First Additional Language | Mathematics | Physical Sciences | APS |
NSC/IEB | NSC/IEB | NSC/IEB | |
4 | 4 | 4 | 28 |
Note:
*The BSc – Extended programmes are not available for students who meet all the requirements for the corresponding mainstream programme.
*Please note that only students who apply in their final NSC or equivalent qualification year will be considered for admission into any of the BSc – Extended programmes. Students who are upgrading or taking a gap year will not be considered.
1.1 Requirements for specific modules
A candidate who:
or
or
1.2 Fundamental modules
A student will be promoted to the following year of study if he or she passed 100 credits of the prescribed credits for a year of study, unless the Dean on the recommendation of the relevant head of department decides otherwise. A student who does not comply with the requirements for promotion to the following year of study, retains the credit for the modules already passed and may be admitted by the Dean, on recommendation of the relevant head of department, to modules of the following year of study to a maximum of 48 credits, provided that it will fit in with both the lecture and examination timetable.
General promotion requirements in the faculty
All students whose academic progress is not acceptable can be suspended from further studies.
University of Pretoria Programme Qualification Mix (PQM) verification project
The higher education sector has undergone an extensive alignment to the Higher Education Qualification Sub-Framework (HEQF) across all institutions in South Africa. In order to comply with the HEQSF, all institutions are legally required to participate in a national initiative led by regulatory bodies such as the Department of Higher Education and Training (DHET), the Council on Higher Education (CHE), and the South African Qualifications Authority (SAQA). The University of Pretoria is presently engaged in an ongoing effort to align its qualifications and programmes with the HEQSF criteria. Current and prospective students should take note that changes to UP qualification and programme names, may occur as a result of the HEQSF initiative. Students are advised to contact their faculties if they have any questions.
Minimum credits: 142
Fundamental = 14
Core = 96
Elective = 32
Elective Modules
Students must select elective modules with a total number of at least 32 credits.
Depending on a student’s second major and other interests, the following combinations of modules are recommended (deviations allowed with permission from the head of department):
Additional Information:
Module content:
Find, evaluate, process, manage and present information resources for academic purposes using appropriate technology.
Module content:
Apply effective search strategies in different technological environments. Demonstrate the ethical and fair use of information resources. Integrate 21st-century communications into the management of academic information.
Module content:
The module aims to equip students with the ability to cope with the reading and writing demands of scientific disciplines.
Module content:
General introduction to inorganic, analytical and physical chemistry. Atomic structure and periodicity. Molecular structure and chemical bonding using the VSEOR model. Nomenclature of inorganic ions and compounds. Classification of reactions: precipitation, acid-base, redox reactions and gas-forming reactions. Mole concept and stoichiometric calculations concerning chemical formulas and chemical reactions. Principles of reactivity: energy and chemical reactions. Physical behaviour gases, liquids, solids and solutions and the role of intermolecular forces. Rate of reactions: Introduction to chemical kinetics.
Module content:
Theory: General physical-analytical chemistry: Chemical equilibrium, acids and bases, buffers, solubility equilibrium, entropy and free energy, electrochemistry. Organic chemistry: Structure (bonding), nomenclature, isomerism, introductory stereochemistry, introduction to chemical reactions and chemical properties of organic compounds and biological compounds, i.e. carbohydrates and aminoacids. Practical: Molecular structure (model building), synthesis and properties of simple organic compounds.
Module content:
SI-units. Significant figures. Waves: intensity, superposition, interference, standing waves, resonance, beats, Doppler. Geometrical optics: Reflection, refraction, mirrors, thin lenses, instruments. Physical optics: Young-interference, coherence, diffraction, polarisation. Hydrostatics and dynamics: density, pressure, Archimedes’ principle, continuity, Bernoulli. Heat: temperature, specific heat, expansion, heat transfer. Vectors. Kinematics of a point: Relative, projectile, and circular motion. Dynamics: Newton’s laws, friction. Work: point masses, gasses (ideal gas law), gravitation, spring, power. Kinetic energy: Conservative forces, gravitation, spring. Conservation of energy. Conservation of momentum. Impulse and collisions. System of particles: Centre of mass, Newton’s laws. Rotation: torque, conservation of angular momentum, equilibrium, centre of gravity.
Module content:
Simple harmonic motion and pendulums. Coulomb’s law. Electric field: dipoles, Gauss’ law.Electric potential. Capacitance. Electric currents: resistance, resistivity, Ohm’s law, energy, power, emf, RC-circuits. Magnetic Field: Hall-effect, Bio-Savart. Faraday’s and Lenz’s laws. Oscillations: LR-circuits. Alternating current: RLC-circuits, power, transformers. Introductory concepts to modern physics. Nuclear physics: Radioactivity.
Module content:
*This module serves as preparation for students majoring in Mathematics (including all students who intend to enrol for WTW 218 and WTW 220). Students will not be credited for more than one of the following modules for their degree: WTW 114, WTW 158, WTW 134, WTW 165.
Functions, limits and continuity. Differential calculus of single variable functions, rate of change, graph sketching, applications. The mean value theorem, the rule of L'Hospital. Definite and indefinite integrals, evaluating definite integrals using anti-derivatives, the substitution rule.
Module content:
*Students will not be credited for more than one of the following modules for their degree:
WTW 124, WTW 146, WTW 148 and WTW 164. This module serves as preparation for students majoring in Mathematics (including all students who intend to enrol for WTW 218, WTW 211 and WTW 220).
The vector space Rn, vector algebra with applications to lines and planes, matrix algebra, systems of linear equations, determinants. Complex numbers and factorisation of polynomials. Integration techniques and applications of integration. The formal definition of a limit. The fundamental theorem of Calculus and applications. Vector functions and quadratic curves.
Module content:
*Students will not be credited for more than one of the following modules for their degree:
WTW 124, WTW 146 and WTW 164. The module WTW 146 is designed for students who require Mathematics at 100 level only and does not lead to admission to Mathematics at 200 level.
Vector algebra, lines and planes, matrix algebra, solution of systems of equations, determinants. Complex numbers and polynomial equations. All topics are studied in the context of applications.
Module content:
*Students will not be credited for more than one of the following modules for their degree:
WTW 124, WTW 148 and WTW 164. The module WTW 148 is designed for students who require Mathematics at 100 level only and does not lead to admission to Mathematics at 200 level.
Integration techniques. Modelling with differential equations. Functions of several variables, partial derivatives, optimisation. Numerical techniques. All topics are studied in the context of applications.
Module content:
Simple statistical analysis: Data collection and analysis: Samples, tabulation, graphical representation, describing location, spread and skewness. Introductory probability and distribution theory. Sampling distributions and the central limit theorem. Statistical inference: Basic principles, estimation and testing in the one- and two-sample cases (parametric and non-parametric). Introduction to experimental design. One- and twoway designs, randomised blocks. Multiple statistical analysis: Bivariate data sets: Curve fitting (linear and non-linear), growth curves. Statistical inference in the simple regression case. Categorical analysis: Testing goodness of fit and contingency tables. Multiple regression and correlation: Fitting and testing of models. Residual analysis. Computer literacy: Use of computer packages in data analysis and report writing.
Module content:
Botanical principles of structure and function; diversity of plants; introductory plant systematics and evolution; role of plants in agriculture and food security; principles and applications of plant biotechnology; economical and valuable medicinal products derived from plants; basic principles of plant ecology and their application in conservation and biodiversity management.
This content aligns with the United Nation's Sustainable Debelopment Goals of No Poverty, Good Health and Well-being, Climate Action, Responsible Consumption and Production, and Life on Land.
Module content:
Introducing the basic concepts and interrelationships required to understand the complexity of natural environmental problems, covering an introduction to environmental science and biogeography; including a first introduction to SDGs and Aichi targets.
Module content:
This module begins by fostering an understanding of human geography. Then follows with the political ordering of space; cultural diversity as well as ethnic geography globally and locally; population geography of the world and South Africa: and four economic levels of development. The purpose is to place South Africa in a world setting and to understand the future of the country.
Module content:
Note: Students cannot register for both GGY 166 and GGY 168.
Investigating southern African landscapes and placing them in a theoretical and global context. The geomorphological evolution of southern Africa. Introduction to the concepts of Geomorphology and its relationships with other physical sciences (e.g. meteorology, climatology, geology, hydrology and biology). The processes and controls of landform and landscape evolution. Tutorial exercises cover basic techniques of geomorphological analysis, and topical issues in Geomorphology.
Module content:
Solar system; structure of solid matter; minerals and rocks; introduction to symmetry and crystallography; important minerals and solid solutions; rock cycle; classification of rocks. External geological processes (gravity, water, wind, sea, ice) and their products (including geomorphology). Internal structure of the earth. The dynamic earth – volcanism, earthquakes, mountain building – the theory of plate tectonics. Geological processes (magmatism, metamorphism, sedimentology, structural geology) in a plate tectonic context. Geological maps and mineral and rock specimens. Interaction between man and the environment, and nature of anthropogenic climate change.
Module content:
This module will give an overview of earth history, from the Archaean to the present. Important concepts such as the principles of stratigraphy and stratigraphic nomenclature, geological dating and international and South African time scales will be introduced. A brief introduction to the principles of palaeontology will be given, along with short descriptions of major fossil groups, fossil forms, ecology and geological meaning. In the South African context, the major stratigraphic units, intrusions and tectonic/metamorphic events will be detailed, along with related rock types, fossil contents, genesis and economic commodities. Anthropogenic effects on the environment and their mitigation. Practical work will focus on the interpretation of geological maps and profiles.
Module content:
History, present and future of cartography. Introductory geodesy: shape of the earth, graticule and grids, datum definition, elementary map projection theory, spherical calculations. Representation of geographical data on maps: Cartographic design, cartographic abstraction, levels of measurement and visual variables. Semiotics for cartography: signs, sign systems, map semantics and syntactics, explicit and implicit meaning of maps (map pragmatics). Critique maps of indicators to measure United Nations Sustainable Development Goals in South Africa.
Module content:
Chromosomes and cell division. Principles of Mendelian inheritance: locus and alleles, dominance interactions, extensions and modifications of basic principles.. Probability studies. Sex determination and sex linked traits. Pedigree analysis. Genetic linkage and chromosome mapping. Chromosome variation.
Module content:
The module will introduce the student to the field of Microbiology. Basic Microbiological aspects that will be covered include introduction into the diversity of the microbial world (bacteria, archaea, eukaryotic microorganisms and viruses), basic principles of cell structure and function, microbial nutrition and microbial growth and growth control. Applications in Microbiology will be illustrated by specific examples i.e. bioremediation, animal-microbial symbiosis, plant-microbial symbiosis and the use of microorganisms in industrial microbiology. Wastewater treatment, microbial diseases and food will be introduced using specific examples.
Module content:
Introduction to the molecular structure and function of the cell. Basic chemistry of the cell. Structure and composition of prokaryotic and eukaryotic cells. Ultrastructure and function of cellular organelles, membranes and the cytoskeleton. General principles of energy, enzymes and cell metabolism. Selected processes, e.g. glycolysis, respiration and/or photosynthesis. Introduction to molecular genetics: DNA structure and replication, transcription, translation. Cell growth and cell division.
Module content:
Introduction to weather and climate. Climate of South Africa. Urban and rural climate. Meteorological instruments. Motion of the earth. Atmospheric mass and pressure. Energy and heat budget. Moisture in the atmosphere. Cloud development. Climate change. ENSO. Electromagnetic spectrum and remote sensing in meteorology. Synoptic weather systems of South Africa.
Module content:
Characterisation of a set of measurements: Graphical and numerical methods. Random sampling. Probability theory. Discrete and continuous random variables. Probability distributions. Generating functions and moments.
Module content:
Sampling distributions and the central limit theorem. Statistical inference: Point and interval estimation. Hypothesis testing with applications in one and two-sample cases. Introductory methods for: Linear regression and correlation, analysis of variance, categorical data analysis and non-parametric statistics. Identification, use, evaluation and interpretation of statistical computer packages and statistical techniques.
Module content:
Propositional logic: truth tables, logical equivalence, implication, arguments. Mathematical induction and well-ordering principle. Introduction to set theory. Counting techniques: elementary probability, multiplication and addition rules, permutations and combinations, binomial theorem, inclusion-exclusion rule.
Module content:
Non-linear equations, numerical integration, initial value problems for differential equations, systems of linear equations. Algorithms for elementary numerical techniques are derived and implemented in computer programmes. Error estimates and convergence results are treated.
Module content:
The module serves as an introduction to computer programming as used in science. Modelling of dynamical processes using difference equations; curve fitting and linear programming are studied. Applications are drawn from real-life situations in, among others, finance, economics and ecology.
Module content:
*Students will not be credited for more than one of the following modules for their degree: WTW 162 and WTW 264.
Introduction to the modelling of dynamical processes using elementary differential equations. Solution methods for first order differential equations and analysis of properties of solutions (graphs). Applications to real life situations.
Module content:
Animal classification, phylogeny organisation and terminology. Evolution of the various animal phyla, morphological characteristics and life cycles of parasitic and non-parasitic animals. Structure and function of reproductive,
respiratory, excretory, circulatory and digestive systems in various animal phyla. In-class discussion will address the sustainable development goals #3, 12, 13, 14 and 15 (Good Health and Well-being. Responsible Consumption and Production, Climate Action, Life Below Water, Life on Land).
Minimum credits: 144
Core = 48
Elective = 96
Additional information:
Elective Modules (Credits = 96)
Students who do not intend to continue with Mathematics on third year level may replace WTW 220 with WTW 224
Students must select elective modules with a total number of at least 96 credits.
Depending on a student’s second major and other interests, the following modules are recommended (deviations allowed with permission from the head of department):
Module content:
Theory: Classical chemical thermodynamics, gases, first and second law and applications, physical changes of pure materials and simple compounds. Phase rule: Chemical reactions, chemical kinetics, rates of reactions.
Module content:
Statistical evaluation of data in line with ethical practice, gravimetric analysis, aqueous solution chemistry, chemical equilibrium, precipitation-, neutralisation- and complex formation titrations, redox titrations, potentiometric methods, introduction to electrochemistry. Examples throughout the course demonstrate the relevance of the theory to meeting the sustainable development goals of clean water and clean, affordable energy.
Module content:
Resonance, conjugation and aromaticity. Acidity and basicity. Introduction to 13C NMR spectroscopy. Electrophilic addition: alkenes. Nucleophilic substitution, elimination, addition: alkyl halides, alcohols, ethers, epoxides, carbonyl compounds: ketones, aldehydes, carboxylic acids and their derivatives Training in an ethical approach to safety that protects self, others and the environment is integral to the practical component of the course.
Module content:
Atomic structure, structure of solids (ionic model). Coordination chemistry of transition metals: Oxidation states of transition metals, ligands, stereochemistry, crystal field theory, consequences of d-orbital splitting, chemistry of the main group elements, electrochemical properties of transition metals in aqueous solution, industrial applications of transition metals. Fundamentals of spectroscopy and introduction to IR spectroscopy. During practical training students learn to acquire and report data ethically. Practical training also deals with the misuse of chemicals and appropriate waste disposal to protect the environment and meet the UN sustainable development goals.
Module content:
Structural and ionic properties of amino acids. Peptides, the peptide bond, primary, secondary, tertiary and quaternary structure of proteins. Interactions that stabilise protein structure, denaturation and renaturation of proteins. Introduction to methods for the purification of proteins, amino acid composition, and sequence determinations. Enzyme kinetics and enzyme inhibition. Allosteric enzymes, regulation of enzyme activity, active centres and mechanisms of enzyme catalysis. Examples of industrial applications of enzymes and in clinical pathology as biomarkers of diseases. Online activities include introduction to practical laboratory techniques and Good Laboratory Practice; techniques for the quantitative and qualitative analysis of biological molecules; enzyme activity measurements; processing and presentation of scientific data.
Module content:
Carbohydrate structure and function. Blood glucose measurement in the diagnosis and treatment of diabetes. Bioenergetics and biochemical reaction types. Glycolysis, gluconeogenesis, glycogen metabolism, pentose phosphate pathway, citric acid cycle and electron transport. Total ATP yield from the complete oxidation of glucose. A comparison of cellular respiration and photosynthesis. Online activities include techniques for the study and analysis of metabolic pathways and enzymes; PO ratio of mitochondria, electrophoresis, extraction, solubility and gel permeation techniques; scientific method and design.
Module content:
Chemical foundations. Weak interactions in aqueous systems. Ionisation of water, weak acids and weak bases. Buffering against pH changes in biological systems. Water as a reactant and function of water. Carbohydrate structure and function. Biochemistry of lipids and membrane structure. Nucleotides and nucleic acids. Other functions of nucleotides: energy carriers, components of enzyme cofactors and chemical messengers. Introduction to metabolism. Bioenergetics and biochemical reaction types. Online activities include introduction to laboratory safety and Good Laboratory Practice; basic biochemical calculations; experimental method design and scientific controls, processing and presentation of scientific data.
Module content:
Biochemistry of lipids, membrane structure, anabolism and catabolism of lipids. Total ATP yield from the complete catabolism of lipids. Electron transport chain and energy production through oxidative phosphorylation. Nitrogen metabolism, amino acid biosynthesis and catabolism. Biosynthesis of neurotransmitters, pigments, hormones and nucleotides from amino acids. Catabolism of purines and pyrimidines. Therapeutic agents directed against nucleotide metabolism. Examples of inborn errors of metabolism of nitrogen containing compounds. The urea cycle, nitrogen excretion. Online activities include training in scientific reading skills; evaluation of a scientific report; techniques for separation analysis and visualisation of biological molecules; hypothesis design and testing, method design and scientific controls.
Module content:
Origin and affinity of South African flora and vegetation types; principles of plant geography; plant diversity in southern Africa; characteristics, environments and vegetation of South African biomes and associated key ecological processes; centra of plant endemism; rare and threatened plant species; biodiversity conservation and ecosystem management; invasion biology; conservation status of South African vegetation types.
Module content:
Nitrogen metabolism in plants; nitrogen fixation in Agriculture; plant secondary metabolism and natural products; photosynthesis and carbohydrate metabolism in plants; applications in solar energy; plant growth regulation and the Green Revolution; plant responses to the environment; developing abiotic stress tolerant and disease resistant plants. Practicals: Basic laboratory skills in plant physiology; techniques used to investigate nitrogen metabolism, carbohydrate metabolism, pigment analysis, water transport in plant tissue and response of plants to hormone treatments.
Module content:
Introduces basic concepts and interrelationships required to understand our atmosphere, with a strong focus on an introduction to weather and climate. A key component of the course is an introduction to climate change, including the science of climate change, introducing climate change projections, and climate change impacts. A key focus of the second part of the course will be climate change implications for the attainment of SDGs and Aichi targets on the African continent, under a range of plausible scenarios.
Module content:
The module introduces students to urban settlement patterns, processes and structures. Using a series of case studies, it aims to develop an understanding of the challenges facing urban areas both in South Africa and globally.
Module content:
Physical processes that influence the earth’s surface and management. Specific processes and their interaction in themes such as weathering; soil erosion; slope, mass movement and periglacial processes. Practical laboratory exercises and assignments are based on the themes covered in the module theory component.
Module content:
Introduction to Geographic Information Systems (GIS), theoretical concepts and applications of GIS. The focus will be on the GIS process of data input, data analysis, data output and associated technologies. This module provides the foundations for more advanced GIS and Geoinformatics topics. Practical assessments and a mini-project make use of South African and African examples and foster learning and application of concepts aligned to the UN Sustainable Development Goals.
Module content:
The nature of geographical data and measurement.Application of statistics in the geographical domain. Probability, probability distributions and densities, expected values and variances, Central Limit theorem. Sampling techniques. Exploratory data analysis, descriptive statistics, statistical estimation, hypothesis testing, correlation analysis and regression analysis. Examples used throughout the course are drawn from South African and African case studies and taught within the framework of the UN Sustainable Development Goals.
Module content:
Note: Enrolment is limited. Preference will be given based on choice of majors. Students should enquire at the department if they wish to register for the module, but are unable to do so.
*GIS 221 does not lead to admission to any module at 300 level.
Introduction to Geographic Information Systems (GIS), theoretical concepts and applications of GIS. The focus will be on the GIS process of data input, data analysis, data output and associated technologies.This module teaches students to use GIS as a tool. Examples used throughout the course are drawn from South African case studies.
Module content:
Soil is a finite resource and with the global challenges we are facing, it is more important than ever to understand and sustainably manage soil. Our daily lives are impacted by soil in several ways, including the food we eat, the water we drink, and the environment we live in. In this Introductory Soils module, we will look at how basic and more advanced abiotic and biotic soil properties impact us and the larger environment. We will also examine the fundamental principles behind sustainable soil use management.
Module content:
Introduction to sedimentology; grain studies; composition and textures of sedimentary rocks; flow dynamics and behaviour of sediment particles in transport systems; description and genesis of sedimentary structures; diagenesis; depositional environments and their deposits, modern and ancient; chemical sedimentary rocks; economic sedimentology; field data acquisition from sedimentary rocks and writing of reports; sieve analysis; Markov analysis; analysis of palaeocurrent trends; interpretation of sedimentary profiles.
Module content:
Fundamental concepts in mineralogy, and practical applications of mineralogy, including: the basics of crystal structure; the crystallographic groups; the rules of atomic substitution; phase transitions and phase diagrams; the structure and uses of olivine, pyroxene, feldspar, amphibole, mica, aluminosilicates, garnet, cordierite, and more uncommon mineral groups such as oxides, sulphides and carbonates; the calculation of mineral formulae from chemical analyses using various methods. Practical sessions: the basics of optical mineralogy and the use of transmitted light microscopy for thin section examination of minerals and rocks; the practicals will develop mineral identification skills for the minerals covered in the lectures, and cover basic textural identification.
Module content:
Classification and nomenclature of igneous rocks. The nature of silicate melts; physical and chemical factors influencing crystallisation and textures of igneous rocks. Phase diagrams, fractional crystallisation and partial melting. Trace elements and isotopes, and their use in petrogenetic studies. Global distribution of magmatism and its origin. Mid-oceanic ridges, active continental margins, intraplate magmatism. Classification of metamorphic rocks. Anatexis, migmatite and granite; eclogite. Metamorphic textures. PT-time loops. Metamorphism in various plate tectonic environments.
Module content:
The chemical nature of DNA. The processes of DNA replication, transcription, RNA processing, translation. Control of gene expression in prokaryotes and eukaryotes. Recombinant DNA technology and its applications in gene analysis and manipulation.
Module content:
Chromosome structure and transposable elements. Mutation and DNA repair. Genomics and proteomics. Organelle genomes. Introduction to genetic analysis of populations: allele and genotypic frequencies, Hardy Weinberg Law, its extensions and implications for different mating systems. Introduction to quantitative and evolutionary genetics.
Module content:
Growth, replication and survival of bacteria, Energy sources, harvesting from light versus oxidation, regulation of catabolic pathways, chemotaxis. Nitrogen metabolism, iron-scavenging. Alternative electron acceptors: denitrification, sulphate reduction, methanogenesis. Bacterial evolution, systematic and genomics. Biodiversity; bacteria occurring in the natural environment (soil, water and air), associated with humans, animals, plants, and those of importance in foods and in the water industry.
Module content:
Organisation and molecular architecture of fungal thalli, chemistry of the fungal cell. Chemical and physiological requirements for growth and nutrient acquisition. Mating and meiosis; spore development; spore dormancy, dispersal and germination. Fungi as saprobes in soil, air, plant, aquatic and marine ecosystems; role of fungi as decomposers and in the deterioration of materials; fungi as predators and parasites; mycoses, mycetisms and mycotoxicoses; fungi as symbionts of plants, insects and animals. Applications of fungi in biotechnology.
Module content:
Vibrating systems and waves (14 lectures)
Simple harmonic motion (SHM). Superposition (different frequencies, equal frequencies). Perpendicular vibrations (Lissajous figures). Damped SHM. Forced oscillations. Resonance. Q-value. Transverse wave motion. Plane wave solution using method of separation of variables. Reflection and transmission at a boundary. Normal and eigenmodes. Wave packets. Group velocity.
Modern physics (30 lectures)
Special relativity: Galilean and Lorentz transformations. Postulates. Momentum and energy. 4 vectors and tensors. General relativity. Quantum physics. Failure of classical physics. Bohr model. Particle-wave duality. Schrödinger equation. Piece-wise constant potentials. Tunneling. X-rays. Laser. Nuclear physics: Fission. Fusion. Radioactivity.
Heat and thermodynamics (12 lectures)
Heat. First Law. Kinetic theory of gases. Mean free path. Ideal, Clausius, Van der Waals and virial gases. Entropy. Second Law. Engines and refrigerators. Third Law. Thermodynamic potentials: Enthalpy Helmholtz and Gibbs free energies, Chemical potential. Legendre transformations (Maxwell relations). Phase equilibrium. Gibbs phase rule.
Modelling and simulation (7 practical sessions)
Introduction to programming in a high level system: Concept of an algorithm and the basic logic of a computer programme. Symbolic manipulations, graphics, numerical computations. Applications: Selected illustrative examples.
Error Analysis (7 practical sessions)
Experimental uncertainties. Propagation of uncertainties. Statistical analysis of random uncertainties. Normal distribution. Rejection of data. Least-squares fitting. Covariance and correlation.
Module content:
Classical mechanics (28 lectures)
Fundamental concepts, energy and angular momentum, calculus of variations and Lagrangian mechanics, conservative central forces and two body problems, scattering, mechanics in rotating reference frames, many body systems.
Physical Optics (14 lectures)
Maxwell’s equations, wave equation and plane wave solution, coherence, interference,
diffraction, polarisation.
Physics of Materials (14 lectures)
Classification of materials. Atomic bonding. Crystallography. Defects. Material strength.
Phase diagram's, Ceramics. Polymers. Composites. Fracture. Electrical and
magnetic properties. Semiconductors. Smart materials Nanotechnology.
Experiments (14 sessions)
Module content:
Set theory. Probability measure functions. Random variables. Distribution functions. Probability mass functions. Density functions. Expected values. Moments. Moment generating functions. Special probability distributions: Bernoulli, binomial, hypergeometric, geometric, negative binomial, Poisson, Poisson process, discrete uniform, uniform, gamma,exponential, Weibull, Pareto, normal. Joint distributions: Multinomial, extended hypergeometric, joint continuous distributions. Marginal distributions. Independent random variables. Conditional distributions. Covariance, correlation. Conditional expected values. Transformation of random variables: Convolution formula. Order statistics. Stochastic convergence: Convergence in distribution. Central limit theorem. Practical applications. Practical statistical modelling and analysis using statistical computer packages and the interpretation of the output.
Module content:
Stochastic convergence: Asymptotic normal distributions, convergence in probability. Statistics and sampling distributions: Chi-squared distribution. Distribution of the sample mean and sample variance for random samples from a normal population. T-distribution. F-distribution. Beta distribution. Point estimation: Method of moments. Maximum likelihood estimation. Unbiased estimators. Uniform minimum variance unbiased estimators. Cramer-Rao inequality. Efficiency. Consistency. Asymptotic relative efficiency.
Bayes estimators. Sufficient statistics. Completeness. The exponential class. Confidence intervals. Test of statistical hypotheses. Reliability and survival distributions. Practical applications. Practical statistical modelling and analysis using statistical computer packages and the interpretation of the output.
Module content:
This is an introduction to linear algebra on Rn. Matrices and linear equations, linear combinations and spans, linear independence, subspaces, basis and dimension, eigenvalues, eigenvectors, similarity and diagonalisation of matrices, linear transformations.
Module content:
Calculus of multivariable functions, directional derivatives. Extrema and Lagrange multipliers. Multiple integrals, polar, cylindrical and spherical coordinates.
Module content:
*This module is recommended as an elective only for students who intend to enrol for WTW 310 and/or WTW 320. Students will not be credited for more than one of the following modules for their degree: WTW 220 and WTW 224.
Properties of real numbers. Analysis of sequences and series of real numbers. Power series and theorems of convergence. The Bolzano-Weierstrass theorem. The intermediate value theorem and analysis of real-valued functions on an interval. The Riemann integral: Existence and properties of the interval.
Module content:
Abstract vector spaces, change of basis, matrix representation of linear transformations, orthogonality, diagonalisability of symmetric matrices, some applications.
Module content:
*This module does not lead to admission to WTW 310 or WTW 320. Students will not be credited for more than one of the following modules for their degree: WTW 220 and WTW 224.
Sequences of real numbers: convergence and monotone sequences. Series of real numbers: convergence, integral test, comparison tests, alternating series, absolute convergence, ratio and root tests. Power series: representation of functions as power series, Taylor and Maclaurin series. Application to series solutions of differential equations.
Module content:
Vectors and geometry. Calculus of vector functions with applications to differential geometry, kinematics and dynamics. Vector analysis, including vector fields, line integrals of scalar and vector fields, conservative vector fields, surfaces and surface integrals, the Theorems of Green, Gauss and Stokes with applications.
Module content:
Setting up and solving recurrence relations. Equivalence and partial order relations. Graphs: paths, cycles, trees, isomorphism. Graph algorithms: Kruskal, Prim, Fleury. Finite state automata.
Module content:
*Students will not be credited for more than one of the modules for their degree: WTW 264, WTW 286
Theory and solution methods for ordinary differential equations and initial value problems: separable and linear first-order equations, linear equations of higher order, systems of linear equations. Application to mathematical models. Numerical methods applied to nonlinear systems.Qualitative analysis of linear systems.
Minimum credits: 144
Core = 72
Elective = 72
Students must select elective modules with a total number of at least 72 credits.
Depending on a student’s second major and other interests, the following modules are recommended (deviations allowed with permission from the head of department):
Module content:
Theory: Molecular quantum mechanics. Introduction: Shortcomings of classical physics, dynamics of microscopic systems, quantum mechanical principles, translational, vibrational and rotational movement. Atomic structure and spectra: Atomic hydrogen, multiple electron systems, spectra of complex atoms, molecular structure, the hydrogen molecule ion, diatomic and polyatomic molecules, structure and properties of molecules. Molecules in motion: Viscosity, diffusion, mobility. Surface chemistry: Physisorption and chemisorption, adsorption isotherms, surface tension, heterogeneous catalytic rate reactions, capillarity.
Module content:
Separation methods: Extraction, multiple extraction, chromatographic systems. Spectroscopy: Construction of instruments, atomic absorption and atomic emission spectrometry, surface analysis techniques. Mass spectrometry. These techniques are discussed in terms of their use in environmental analysis and the value they contribute to meeting the UN sustainable development goals (#3,6 & 11). Instrumental electrochemistry. The relevance of electrochemistry to providing affordable and clean energy (UN SDG#7) is addressed.
Module content:
Theory: NMR spectroscopy: applications. Aromatic chemistry, Synthetic methodology in organic chemistry. Carbon-carbon bond formation: alkylation at nucleophilic carbon sites, aldol and related condensations, Wittig and related reactions, acylation of carbanions (Claisen condensation). Practical: Laboratory sessions are designed to develop the rational thinking behind the design of organic chemistry experiments. An industrial project specifically prepares students for work in SA industry context and honours projects. As part of this practical programme the UN sustainable development goals must be considered in evaluating the best industrial process.
Module content:
Theory: Structure and bonding in inorganic chemistry. Molecular orbital approach, diatomic and polyatomic molecules, three-centre bonds, metal-metal bonds, transition metal complexes, magnetic properties, electronic spectra, reactivity and reaction mechanisms, reaction types, acid-base concepts, non-aqueous solvents, special topics.
Module content:
Structure, function, bioinformatics and biochemical analysis of (oligo)nucleotides, amino acids, proteins and ligands – and their organisation into hierarchical, higher order, interdependent structures. Principles of structure-function relationships, protein folding, sequence motifs and domains, higher order and supramolecular structure, self-assembly, conjugated proteins, post-translational modifications. Molecular recognition between proteins, ligands, DNA and RNA or any combinations. The RNA structural world, RNAi, miRNA and ribosomes. Cellular functions of coding and non-coding nucleic acids. Basic principles of mass spectrometry, nuclear magnetic resonance spectroscopy, X-ray crystallography and proteomics. Protein purification and characterisation including, pI, molecular mass, amino acid composition and sequence. Mechanistic aspects and regulation of information flow from DNA via RNA to proteins and back. Practical training includes hands-on nucleic acid purification and sequencing, protein production and purification, analysis by SDS-PAGE or mass spectrometry, protein structure analysis and 3D protein modelling.
Module content:
Regulation of metabolic pathways. Analysis of metabolic control. Elucidation of metabolic pathways with isotopes. Metabolomics. Coordinated regulation of glycolysis/gluconeogenesis and glycogen breakdown/synthesis. Overview of homone action. Metabolism of xenobiotics. Hormonal regulation of feul metabolism. Metabolic adaptions during diabetes. Obesity and the regulation of body mass. Obesity, metabolic syndrome and Type 2 diabetes (T2D). Management of T2D with diet, exercise and medication. Practical sessions cover tutorials on case studies and biochemical calculations, and hands-on isolation of an enzyme, determination of pH and temperature optima, determination of Km and Vmax, enzyme activation and enzyme inhibition.
Module content:
Visualising cell structure and localisation of proteins within cells. Cell ultrastructure. Purification of subcellular organelles. Culturing of cells. Biomembrane structure. Transmembrane transport of ions and small molecules and the role of these processes in disease. Moving proteins into membranes and organelles. Vesicular traffic, secretion, exocytosis and endocytosis. Cell organisation and movement motility based on the three types of cytoskeletal structures including microfilaments, microtubules and intermediate filaments as well as their associated motor proteins. Cell-cell and cell-matrix adhesion through corresponding proteins and morphological structures. Practical training includes tutorials on cytometry and microscopy, mini-research projects where students are introduced and guided through aspects of research methodology, experimental planning techniques associated with cellular assays, buffer preparation, active transport studies in yeast cells, structure-function analyses of actin and binding partners.
Module content:
Molecular mechanisms behind exogenous and endogenous diseases. Foundational knowledge of the immune system, with innate-, adaptive- and auto-immunity (molecular mechanisms of the maintenance and failure of the recognition of foreign in the context of self in the mammalian body) being some of the key concepts. Molecular pathology and immunobiochemistry of exogenous diseases against viral, bacterial and parasitic pathogens with a focus on the human immunodeficiency virus (HIV), tuberculosis (TB) and malaria. Endogenous disease will describe the biochemistry of normal cell cycle proliferation, quiescence, senescence, differentiation and apoptosis, and abnormal events as illustrated by cancer. Tutorials will focus on immunoassays, vaccines, diagnostic tests for diseases and drug discovery towards therapeuticals.
Module content:
Introduction to plant ecophysiology and plants response to environmental stress. Understanding how various biotic and abiotic factors affect plant metabolic processes, including photosynthesis and respiration. Emphasis is placed on the efficiency of the mechanisms whereby C3-, C4 and CAM-plants bind CO2 and how they are impacted by the environment. To understand the functioning of plants in diverse environments, the relevant structural properties of plants, the impact of soil composition, water flow in the soil-plant air continuum and long distance transport of assimilates will be discussed. Students will research a topic relevant to plant ecophysiology and present this in the form of an oral presentation. Students will conduct a practical project to study the effects of environmental factors on C3 and C4 plant growth and physiology. Students will present the report in a written format according to the guidelines of a relevant scientific journal. Relevant readings will be used to highlight the alignment of the module with the Sustainable Development Goals, with emphasis placed on climate action.
Module content:
Theory of plant community concepts, floristic and structural composition, plant diversity, ecological succession, landscape ecology. Data processing techniques. Species interactions and an evaluation of their effects on interacting species. Fundamentals of plant population biology: life tables; plant breeding systems and pollination; population dynamics; life history strategies; intraspecific competition; interspecific competition and co-existence. There is a compulsory field-based practical run over a weekend in the first month of the first semester.
Module content:
The module will include a review on the discovery and use of plant medicines and phyto-therapeutically important molecules obtained from plants. Certain aspects of natural product chemistry i.e. the biosynthesis, ecological role and toxicity of the three main classes of secondary compounds; terpenoids, phenolics, and alkaloids are discussed. An introduction to the principles and applications of metabolomics is presented. The role of these natural products in defense against microorganisms and herbivores is reviewed during the module. The importance of ethnobotany and phylogenetics in modern drug discovery from biodiversity will presented along with legal and ethical considerations surrounding bioprospecting. This will follow on with modern theories and practices regarding sustainable utilisation and conservation of medicinal plants. The basics of alternative medicines, with an emphasis on traditional African and Chinese medicines, are also discussed as well as current evidence-based research and product development derived from these. Biotechnological approaches to medicinal natural product production, ‘farmer to pharma’, will be covered, including plant cell culture and bioreactors. Practical sessions on drug discovery approaches using chromatographic techniques for phytochemical analysis of secondary metabolites such as tannins, alkaloids, and saponins are conducted. Bioassays on micro-organisms are also done during the practical sessions in order to develop the skills for the potential discovery of new antibiotics.
Module content:
Basic principles and methods of plant classification. Sources of plant variation. Modern methods to ascertain evolutionary relationships among plants. The extent and significance of vascular plant diversity. General structural and biological characteristics of evolutionary and ecologically important plant groups. Botanical nomenclature. Plant identification in practice; identification methods, keys, herbaria and botanical gardens. Diagnostic characters for the field identification of trees, wild flowers and grasses. Family recognition of southern African plants. Available literature for plant identification. Methods to conduct floristic surveys. Nature and significance of voucher specimens.
Module content:
The module serves as an introduction to human-environment relations, on contemporary environmental issues in Africa.
The module begins with different theories and schools of thought in human-environment relations, followed by recent and future impacts of human pressures on natural resources, the state of the environment in South Africa, management of critical resources, population trends, biodiversity loss, pollution, water scarcity, desertification, climate change, waste accumulation and management, environmental management tools, environmental education and environmental management legislation. A key focus here is future scenarios for the African continent in terms of SDGs and Aichi targets; given current and projected driving forces.
Module content:
Classic economic development theories and frameworks. Spatial development history and legacy in South Africa. Rural and agricultural reconstruction. Land reform. Urban development and strategy. Urban spatial reconstruction. National spatial development frameworks. Integration of environmental, economic, and social components of sustainable development, including challenges, actors and actions in sustainable development.
Module content:
*Note: The module is available for BSc (Geography) and BSc (Environmental Sciences) students only. The theory content of this module is the same as GGY 363 and students are not allowed to earn credits for both GGY 361 and GGY 363.
Interactions of geomorphic processes within the physical and built environments; themes such as geomorphology and environmental change, slope processes and the environment, geomorphic risks and hazards, soil erosion and conservation, geomorphology in environmental management, applied weathering. Practicals involve fieldwork including sampling and mapping and subsequent laboratory analysis.
Module content:
Advanced theory and practice of Geographic Information Systems; GIS applications; design and implementation of GIS applications. A project or assignments of at least 64 notional hours. Diverse South African examples will be used to expose the students to various data sources, geospatial analyses, and data representation to support the UN Sustainable Development Goals.
Module content:
Construction of Raster Geovisualisations, spatial model construction and use, multi-criteria decision analysis. Factor analysis: Principle component analysis. Geostatistics: Spatial dependence modelling, ordinary kriging. Markov chains and cellular Automata, combined models. Examples using data from South Africa are implemented. A project or assignment of at least 64 notional hours.
Module content:
Integrated theoretical and practical course dealing with the principles of rock deformation and analysis of deformed rocks. Stress, strain and rheology, joints, experimental rock deformation, fault systems and Anderson's theory of faulting. Folds and interference folding, tectonic fabrics, shear zone, progressive deformation. Stereographic projection and structural analysis.
Module content:
The hydrological cycle, water resources and water usage; porosity and permeability, heterogeneity and isotropy; the occurrence of groundwater, vadose and phreatic zones; aquifer types, relations and groundwater flow; hydrostratigraphy, surface water and groundwater interaction, springs; water balance, water flow, recharge and baseflow; Darcy’s Law, hydraulic conductivity and subsurface flow; capillarity, hydraulics, Bernoulli’s equation and the continuity principle; hydraulic parameters and their derivation from aquifer pumping tests, including Theis, Cooper-Jacob and other modifications; water quality, solubility, natural waters, ionic balance and plotting water chemistry data; groundwater mining, aquifer compaction and subsidence; saline intrusion, dryland salinity, pollution, NAPLs; site remediation and toxicology.
Module content:
This module details the genesis and exploitation of major ore deposits, with an emphasis on South African examples. The processes through which ore deposits are formed and modified will be discussed, highlighting the relevance of sedimentary, metamorphic and igneous processes in the genesis of world-class ore bodies. The module will also address the methods of mining commonly used, and the international commodity market, including a brief introduction to ore reserve estimation and the evaluation of potential ore deposits. The section of the module involving mineral exploration and mining will emphasize the need of pursuing a sustainable mineral resources development mindset, by addressing and sharing ideas on the impact that mining has on environmental, social and economic issues including community welfare, impact of mining on land use, and rehabilitation post mining.
Module content:
Electronics (14 lectures)
Thévenin and Norton equivalent circuits, superposition principle, RC, LC and LRC circuits. Semiconductor diode. Bipolar transistor. Operational amplifiers. Computer controlled instrumentation.
Electromagnetism (21 lectures)
Electrostatics: Coulomb’s law, divergence and curl of E, Gauss’ law, Laplace’s equation, image charge problems, multipole expansion.
Magnetostatics: Lorenz force, Biot-Savart law, divergence and curl of magnetic field strength, Ampère’s law, magnetic vector potential, multipole expansion, boundary conditions.
Electrodynamics: Electromotive force, electromagnetic induction, Maxwell’s equations, wave equation.
Electric and magnetic fields in matter: Polarisation, electric displacement and Gauss’s law in dielectrics, linear dielectrics. Magnetisation (diamagnets, paramagnets, ferromagnets), auxiliary field H and Ampère’s law in magnetised materials, linear and nonlinear media.
Quantum mechanics (28 lectures)
The Schrödinger equation, the statistical interpretation of the wave function, momentum, the uncertainty principle, the time-independent Schrödinger equation, stationary states, the infinite square well potential, the harmonic oscillator, the free particle, the Delta-Function potential, the finite square well potential, Hilbert spaces, observables, eigen functions of a Hermitian operator, Dirac notation, the Schrödinger equation in spherical coordinates, the hydrogen atom, angular momentum spin.
Module content:
Statistical mechanics (28 lectures)
Isolated systems in thermodynamical equilibrium. Systems in equilibrium with a heat bath: the canonical ensemble, Gibbs' entropic formula, classical statistical mechanics, energy equipartition theorem, thermodynamic potentials, paramagnetism.
The classical limit of perfect gases: non-distinguishable character of quantum particles, the equation of state of the classical ideal gas. Quantum perfect gases: Black body radiation, the grand canonical ensemble, Fermi-Dirac distribution, the free electron gas in metals, the Bose-Einstein distribution, Bose-Einstein condensation.
Solid state physics (28 lectures)
Crystal structures, the reciprocal lattice, x-ray diffraction, lattice vibration, the Debye model, characteristics of solids, the free electron model, Pauli paramagnetism, electronic heat capacity, the relaxation time, electrical conduction, the classical Hall effect, thermal conduction in metals, failures of the free electron model, the independent electron model, band theory of solids.
Computational Physics and modelling. Assessment will be done through a portfolio of project reports. The topics for the projects will be selected from various sub-disciplines of Physics.
Module content:
Data exploration. Data wrangling. Statistical coding. Algorithmic thinking. Sampling: basic techniques in probability, non-probability, and resampling methods. Text mining and analytics. Machine learning: classification and clustering. Statistical concepts are demonstrated and interpreted through practical coding and simulation within a data science framework.
Module content:
Multivariate statistical distributions: Moments of a distribution, moment generating functions, independence. Multivariate normal distribution: Conditional distributions, partial and multiple correlations. Distribution of quadratic forms in normal variables. Multivariate normal samples: Estimation of the mean vector and covariance matrix, estimation of correlation coefficients, distribution of the sample mean, sample covariance matrix. Principal component analysis.The linear model: Models of full rank, least squares estimators, test of hypotheses.The generalised linear model: Exponential family mean and variance, link functions, deviance and residual analysis, test statistics, log- linear and logit models. Practical applications: Practical statistical modelling and analysis using statistical computer packages and interpretation of the output.
Module content:
Definition of a stochastic process. Stationarity. Covariance stationary. Markov property. Random walk. Brownian motion. Markov chains. Chapman-Kolmogorov equations. Recurrent and transient states. First passage time. Occupation times. Markov jump processes. Poisson process. Birth and death processes. Structures of processes. Structure of the time-homogeneous Markov jump process. Applications in insurance. Practical statistical modelling, analysis and simulation using statistical computer packages and the interpretation of the output.
Module content:
Note: Only one of the modules WST 321 or STK 320 may be included in any study programme.
Stationary and non-stationary univariate time-series. Properties of autoregressive moving average (ARMA) and autoregressive integrated moving average (ARIMA) processes. Identification, estimation and diagnostic testing of a time-series model. Forecasting. Multivariate time-series. Practical statistical modelling and analysis using statistical computer packages, including that of social responsibility phenomena.
Module content:
Topology of finite dimensional spaces: Open and closed sets, compactness, connectedness and completeness. Theorems of Bolzano-Weierstrass and Heine-Borel. Properties of continuous functions and applications. Integration theory for functions of one real variable. Sequences of functions.
Module content:
Series of functions, power series and Taylor series. Complex functions, Cauchy- Riemann equations, Cauchy's theorem and integral formulas. Laurent series, residue theorem and calculation of real integrals using residues.
Module content:
Group theory: Definition, examples, elementary properties, subgroups, permutation groups, isomorphism, order, cyclic groups, homomorphisms, factor groups. Ring theory: Definition, examples, elementary properties, ideals, homomorphisms, factor rings, polynomial rings, factorisation of polynomials. Field extensions, applications to straight-edge and compass constructions.
Module content:
Matrix exponential function: homogeneous and non-homogeneous linear systems of differential equations. Qualitative analysis of systems: phase portraits, stability, linearisation, energy method and Liapunov's method. Introduction to chaotic systems. Application to real life problems.
Module content:
Direct methods for the numerical solution of systems of linear equations, pivoting strategies. Iterative methods for solving systems of linear equations and eigenvalue problems. Iterative methods for solving systems of nonlinear equations. Introduction to optimization. Algorithms for the considered numerical methods are derived and implemented in computer programmes. Complexity of computation is investigated. Error estimates and convergence results are proved.
Module content:
Conservation laws and modelling. Fourier analysis. Heat equation, wave equation and Laplace's equation. Solution methods including Fourier series. Energy and other qualitative methods.
Module content:
Kinematics of a continuum: Configurations, spatial and material description of motion. Conservation laws. Analysis of stress, strain and rate of deformation. Linear constitutive equations. Applications: Vibration of beams, equilibrium problems in elasticity and special cases of fluid motion.
Module content:
Axiomatic development of neutral, Euclidean and hyperbolic geometry. Using models of geometries to show that the parallel postulate is independent of the other postulates of Euclid.
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