The UCT HPC team has been cited in various papers or theses which have been published by UCT Reseachers.
The UCT HPC team has been cited in various papers or theses which have been published by UCT Reseachers.
 Govender S, Gambu T, van Heerden T, Steen E (2019 Feb). Mechanistic pathways for oxygen removal on Pt-doped Co(111) in the Fischer-Tropsch reaction. doi.org/10.1016/j.cattod.2019.02.001
 Kuttel M, Ravenscroft N. (2019 Feb). Conformation and Cross-Protection in Group B Streptococcus Serotype III and Streptococcus pneumoniae Serotype 14: A Molecular Modeling Study. doi.org/10.3390/ph12010028
 Illig S, Cadier E, Bachèlery M, Kersalé M. (2018). Subseasonal Coastal Trapped Wave Propagations in the Southeastern Pacific and Atlantic Oceans: 1. A New Approach to Estimate Wave Amplitude doi.org/10.1029/2017JC013539
 Illig S, Cadier E, Bachèlery M. (2018). Subseasonal Coastal Trapped Wave Propagations in the Southeastern Pacific and Atlantic Oceans: 2. Wave Characteristics and Connection With Equatorial Variability doi.org/10.1029/2017JC013540
 Hlozek J, Kuttel M, Ravenscroft N. (2018). Conformations of Neisseria meningitidis serogroup A and X polysaccharides: The effects of chain length and O-acetylation doi.org/10.1016/j.carres.2018.06.007
 Oladele T, Lawrence B, Weatehrley D. (2018). DEM simulations of crack propagation during single particle impact
 Nickless A, Rayner P, Engelbrecht F, Brunke E, Erni B, Scholes R . (2018). Estimates of CO2 fluxes over the city of Cape Town, South Africa, through Bayesian inverse modelling. doi.org/10.5194/acp-18-4765-2018
 van der Laan L, Garcia-Prats A, Schaaf H, Tikiso T, Wiesner L, de Kock M, Winckler J, Norman J, McIlleron H, Denti P, Hesseling A. Pharmacokinetics and Drug-Drug Interactions of Lopinavir-Ritonavir Administered with First- and Second-Line Antituberculosis Drugs in HIV-Infected Children Treated for Multidrug-Resistant Tuberculosis. doi.org/10.1128/AAC.00420-17
 Nyangahu D, Lennard K, Brown B, Darby M, Wendoh J, Havyarimana E, Smith P, Butcher J, Stintzi A, Mulder N, Horsnell W, Jaspan H. Disruption of maternal gut microbiota during gestation alters offspring microbiota and immunity. doi.org/10.1186/s40168-018-0511-7
 Hawthorne R, Grzybowski L. Benefits from competition in a high-inequality economy: The case of mobile telephony in South Africa.
 Flaviani F, Declan D, Lebret K, Balestreri C, Highfield A, Schroeder J, Thorpe S, Moore K, Pasckiewicz K, Pfaff M, Rybicki E. Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar Current. doi.org/10.1186/s40168-018-0511-7
 Ghoor I. The response of concave singly curved fibre reinforced moulded sandwich and laminated composite panels to blast loading. hdl.handle.net/11427/27811
 Kuttel M, Ravenscroft N. The Role of Molecular Modeling in Predicting Carbohydrate Antigen Conformation and Understanding Vaccine Immunogenicity in Carbohydrate-Based Vaccines: From Concept to Clinic. Chapter 7, 139-173 ACS Symposium Series, Vol. 1290. (2018). doi:10.1021/bk-2018-1290.ch007
 Baichoo S, Souilmi Y, Panji S, Botha G, Meintjes A, Hazelhurst S, Bendou H, de Beste E, Mpangase P, Souiai O, Alghali M, Yi L, O’Connor B, Crusoe M, Armstrong D, Aron S, Joubert F, Ahmed A, Mbiyavanga M, Heusden P, Magosi L, Zermeno J, Mainzer L, Fadlelmola F, Jongeneel C and Mulder N. Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics (2018 Oct). doi:10.1186/s12859-018-2446-1
 Ragoo Y, Mahmood T. Determining the Surface Energies of MAX Phase Surfaces Using DFT.
 Gabin M, Gandhi S. The promotional effect of water on O2-dissociation over Pt (111).
 Moodley M, Mutataguta T. Segregation behaviour in Binary and Ternary alloy systems.
 Okendo J. Analysis of within-host evolution of Plasmodium Falciparum during treatment (2018). hdl.handle.net/11427/29305
 Ahnert, T., & Georg, C. P. (2017). Information contagion and systemic risk. Journal of Financial Stability. doi.org/10.1016/j.jfs.2017.05.009
 Alexeeva, N. V., Barashenkov, I. V., & Kivshar, Y. S. (2017). Solitons in-symmetric ladders of optical waveguides. New Journal of Physics, 19(11), 113032. doi: 10.1088/1367-2630/aa8fdd
 Davids, S. A., Langdon, G. S., & Nurick, G. N. (2017). The influence of charge geometry on the response of partially confined right circular stainless steel cylinders subjected to blast loading. International Journal of Impact Engineering. doi.org/10.1016/j.ijimpeng.2017.02.015
 de Moor, C. L., Butterworth, D. S., & van der Lingen, C. (2017). The Quantitative Use of Parasite Data in Multi-Stock Modelling of South African Sardine (Sardinops sagax). Canadian Journal of Fisheries and Aquatic Sciences, 74(11): 1895-1903, doi.org/10.1139/cjfas-2016-0280
 Dheda, K., Limberis, J. D., Pietersen, E., Phelan, J., Esmail, A., Lesosky, M., … & Dolby, T. (2017). Outcomes, infectiousness, and transmission dynamics of patients with extensively drug-resistant tuberculosis and home-discharged patients with programmatically incurable tuberculosis: a prospective cohort study. The Lancet Respiratory Medicine, 5(4), 269-281. doi:10.1016/S2213-2600(16)30433-7
 Flaviani, F., Schroeder, D. C., Balestreri, C., Schroeder, J. L., Moore, K., Paszkiewicz, K., … & Rybicki, E. P. (2017). A Pelagic Microbiome (Viruses to Protists) from a Small Cup of Seawater. Viruses, 9(3), 47. doi:10.3390/v9030047
 Kuttel, M. M., Cescutti, P., Distefano, M., & Rizzo, R. (2017). Fluorescence and NMR spectroscopy together with molecular simulations reveal amphiphilic characteristics of a Burkholderia biofilm exopolysaccharide. Journal of Biological Chemistry, jbc-M117. doi.org/10.1074/jbc.M117.785048
 Kuttel, M., Timol, Z., Ravenscroft, N. (2017). Cross-protection in Neisseria meningitidis serogroups Y and W polysaccharides: A comparative conformational analysis, In Carbohydrate Research, 446-447. doi.org/10.1016/j.carres.2017.05.004
 Lennard, K., Dabee, S., Barnabas, S. L., Havyarimana, E., Blakney, A., Jaumdally, S. Z., … & Gray, G. (2018). Microbial Composition Predicts Genital Tract Inflammation and Persistent Bacterial Vaginosis in South African Adolescent Females. Infection and immunity, 86(1), e00410-17. doi: 10.1128/IAI.00410-17
 Malahe, M. (2017). A High-Performance Crystal Plasticity Solver for CPU-GPU Architectures. Conference paper. XIV International Conference on Computational Plasticity.
 Ngandu, N. K., Carlson, J. M., Chopera, D. R., Ndabambi, N., Abdool Karim, Q., Abdool Karim, S., & Williamson, C. (2017). Brief Report: Selection of HIV-1 Variants With Higher Transmission Potential by 1% Tenofovir Gel Microbicide. Journal of Acquired Immune Deficiency Syndromes (1999), 76(1), 43–47. doi.org/10.1097/QAI.0000000000001458
 Ramanathan V. (2017). Measuring cross-section data for prompt gammas emitted during proton-nucleus collisions. PHD thesis.
 Ravenscroft, N., Omar, A., Hlozek, J., Edmonds-Smith, C., Follador, R., Serventi, F., … & Faridmoayer, A. (2017). Genetic and structural elucidation of capsular polysaccharides from Streptococcus pneumoniae serotype 23A and 23B, and comparison to serotype 23F. Carbohydrate research, 450, 19-29. doi.org/10.1016/j.carres.2017.08.006
 Sewpersad, T. (2017). Efficient Large-Scale Vegetation Simulation. Research Paper.
 Smuts, E. M., Deglon, D. A., & Meyer, C. J. (2017). A coupled CFD-DEM model for simulating the rheology of particulate suspensions. Progress in Computational Fluid Dynamics, an International Journal, 17(5), 290-301. doi.org/10.1504/PCFD.2017.086340
 Blumenthal, M. The impact of EPHA2 polymorphism on KSHV infectivity and KS prevalence among HIV/AIDS patients in South Africa.MSC Thesis
 Timol, Z. (2017). Chemical and conformational studies of bacterial cell surface polysaccharide repeating units (Doctoral dissertation, University of Cape Town). hdl.handle.net/11427/25484
 van Rooyen, J. (2017). Computational fluid dynamic based optimization of an industrial axial fan for rapid prototyping. PhD thesis
 Gambu T, Petersen M, Steen E. (2017). Probing the edge effect on the ORR activity using platinum nanorods: A DFT study. doi.org/10.1016/j.cattod.2017.12.026
 Shorten D. (2017). Spectral analysis of neutral evolution. hdl.handle.net/11427/27420
 Mugo J, Geza E, Joel Defo, Elsheikh S, Mazandu G, Mulder N, Chimusa E. (2017). A multi-scenario genome-wide medical population genetics simulation framework. doi.org/10.1093/bioinformatics/btx369
 Amato M, Carreno J. (Nov 2017). DFT Study of Diatomic Oxygen Adsorption on Pt(100) and Pt(111). Hons project
 Lennard K, Dabee S , Barnabas S, Havyarimana E, Jaumdally S, Botha G, Mkhize N, Bekker L, Gray G, Mulder N, PassmoreJ, Jaspan H. (2017). High rates of bacterial vaginosis and Chlamydia in a low-income, high-population-density community in Cape Town. dx.doi.org/10.4102/satnt.v36i1.1484
 Bernardo, P *., Muhire, B., François, S., Deshoux, M., Hartnady, P., Farkas, K., Kraberger, S., Filloux, D., Fernandez, E. and Galzi, S. Molecular characterization and prevalence of two capulaviruses: Alfalfa leaf curl virus from France and Euphorbia caput-medusae latent virus from South Africa. Virology, 493 (2016), 142-153. doi: 10.1016/j.virol.2016.03.016
 Davids, S. The Influence of charge geometry on the structural response of right circular cylinders to internal air blasting. Masters’ thesis, University of Cape Town, 2016. http://hdl.handle.net/11427/20400
 Kuttel, M. M., Ståhle, J. and Widmalm, G. CarbBuilder: Software for building molecular models of complex oligo‐and polysaccharide structures. Journal of Computational Chemistry, 37, 22 (2016), 2098-2105. doi:10.1002/jcc.24428
 Potgieter, M. G., Nakedi, K. C., Ambler, J. M., Nel, A. J., Garnett, S., Soares, N. C., Mulder, N. and Blackburn, J. M. Proteogenomic analysis of Mycobacterium smegmatis using high resolution mass spectrometry. Frontiers in microbiology, 7 (2016). doi:10.3389/fmicb.2016.00427
 Ross-Gillespie, A., Butterworth, D. Modelling cannibalism and inter-species predation for the Cape hake species Merluccius capensis and M. paradoxus. Research paper, University of Cape Town, 2016. http://hdl.handle.net/11427/18916
 Ross-Gillespie, A. Modelling cannibalism and inter-species predation for the Cape hake species Merluccius capensis and M. paradoxus. Research paper, University of Cape Town, 2016. http://hdl.handle.net/11427/18916
 Schomaker, M., Davies, M.-A., Malateste, K., Renner, L., Sawry, S., N’Gbeche, S., Technau, K.-G., Eboua, F., Tanser, F. and Sygnaté-Sy, H. Growth and mortality outcomes for different antiretroviral therapy initiation criteria in children ages 1–5 Years: a causal modeling analysis. Epidemiology, 27, 2 (2016), 237-246. doi: 10.1097/EDE.0000000000000412
 Schomaker, M., Leroy, V., Wolfs, T., Technau, K.-G., Renner, L., Judd, A., Sawry, S., Amorissani-Folquet, M., Noguera-Julian, A. and Tanser, F. Optimal timing of antiretroviral treatment initiation in HIV-positive children and adolescents: a multiregional analysis from Southern Africa, West Africa and Europe. International Journal of Epidemiology (2016), doi: 10.1093/ije/dyw097
 van Rooyen, J., Malan, A., Raad, E. High performance industrial fan optimization. Conference paper. European Congress on Computational Methods in Applied Sciences and Engineering (ECCOMAS 2016). Institute of Structural Analysis and Antiseismic Research, School of Civil Engineering, National Technical University of Athens (NTUA), Athens, 2016. https://www.eccomas2016.org/proceedings/pdf/6442.pdf
 Viljoen, J.-A. Ecological influences in the biogeography of the Austral sedges. Masters’ thesis, University of Cape Town, 2016. http://hdl.handle.net/11427/20302
 Williams, T. C. The impact of increased grid resolution on the mixed layer depth variability in the South Atlantic Ocean and Southern Ocean. Masters’ thesis, University of Cape Town, 2016. http://hdl.handle.net/11427/20814
 van Heerden, T. Metal support interactions on cobalt based FT catalysts – a DFT study of model inverse catalysts, 2016. DOI: 10.1039/C6FD00201C
 Vasic, L., Mudley T, Direct CO dissociation on B5 and B6 sites of fcc cobalt Fischer-Tropsch catalyst nanocrystals, 2016. Report
 Matsutsu, M, Pt38 cluster on OH- and COOH-functionalised graphene as a model for Pt/C-catalysts, 2016. DOI: 10.1039/C6CP04111F
 Deeplal, R, Stochastic Differentials Mixed Effect Models, 2016. PDF
 Venter, G, Catalytic enantioselective acyl transfer: the case for 4-PPY with a C-3 carboxamide peptide auxiliary based on synthesis and modelling studies, 2016. DOI: 10.1039/C6OB01991A
 Ross-Gillespie, A. and Butterworth, D.S. (2015) Implementing the 2014 three-stock model for Southern Hemisphere Breeding Stocks E1, Oceania and G. International Whaling Commission document: SC/66a/SH/05: 17pp
 Ross-Gillespie, A. and Butterworth, D.S. (2015) Modelling cannibalism and inter-species predation for Cape hake Merluccius capensis and M. paradoxus: Model specifications and preliminary results. International Stock Assessment Review Workshop document. MARAM/IWS/DEC15/Hake/P1: 26pp.
 Evan Smuts. A Methodology for Coupled CFD-DEM Modelling of Particulate Suspension Rheology *
 Andrew van Rooyen. Determining the optimal protocols for transfer of large data files. Dec 2015.
 Emmanuel Omatuku Ngongo. Modelling of Residual Stresses of Blood Vessels. 23 Nov 2015.
 Simeon Solomons. Proper Orthogonal Decomposition – Based Material Parameter Identification. Nov 2015. *
 Dezire Mikael Ettienne. Computational Inverse Analysis of Prestressed Concrete Structures. Nov 2015. *
 Jamie Hewland, Geoff Nitschke. The Benefits of Adaptive Behavior and Morphology for Cooperation in Robot Teams. Nov 2015.
 Vinay Ramaswami Shekhar. The effect of bend radius on the impulse transfer characteristics of V-hulls. 2015 Nov.
 Chimusa ER, Mbiyavanga M, Mazandu GK, Mulder NJ. ancGWAS: a post genome-wide association study method for interaction, pathway and ancestry analysis in homogeneous and admixed populations. 27 Oct 2015.
 Robert Spencer. Tensor Networks and Emergent Geometry. 2015 Oct 17.
 Renata Briarjaj. Simulating Blast Disruptions. 6 Oct 2015.
 Alexander Antrobus. Achieving baseline states in sparsely connected spiking-neural networks. July 2015
 Lubbe, S., Dube, F., Nicol, M. and Zar, H. Functional Data Analysis for the Investigation of Longitudinal Response Patterns in Health Care. Presentation presented at the International Federation of Classification Societies Conference, Bologna, Italy. July 2015
 S.J. Perkins, P.C. Marais, J.T.L. Zwart, I. Natarajan, C. Tasse, O. Smirnov. GPU accelerated radio interferometer measurement equations in support of Bayesian inference for radio observations. 19 June 2015.
 J. Gain, B. Merry, P. Marais. Parallel, Realistic and Controllable Terrain Synthesis. May 2015.
 Bevan W.S. Jones. Mesh Adaptation through r-refinement using a Truss Network Analogy. 4 May 2015
 Nathan Geffen. Optimising partner matching for microsimulations of the HIV epidemic. 24 March 2015.
 CL de Moor, DS Butterworth. Assessing the South African Sardine Resource. 16 March 2015.
 Shareefa Dalvie. Genetic Analysis of Bipolar Disorder and Alcohol Use Disorder. March 2015.
 Mayuresh Kulkarni. Simulation of x-rays using slot scanning technique. 2015.
 Bevan W.S. Jones, Arnaud G. Malan, Jacobus A. van Rooyen. A Ball-Vertex Approach to r-Refinement for Accuracy Enhancements in CFD Calculations. 2 May 2015.
 Michelle Lochner, Iniyan Natarajan, Jonathan T. L. Zwart, Oleg Smirnov, Bruce A. Bassett, Nadeem Oozeer and Martin Kunz. Bayesian inference for radio observations. 25 March 2015.
 Michelle M. Kuttel, Graham E. Jackson, Mpho Mafata, Neil Ravenscroft. Capsular polysaccharide conformations in pneumococcal serotypes 19F and 19A. 14 January 2015.
 Bierman A. Mapping and survey sequencing of Dn resistance genes in Triticum aestivum L. December 2014. hdl.handle.net/10019.1/96912
 Muhire B. Molecular diversity of Chickpea chlorotic dwarf virus in Sudan: High rates of intra-species recombination – a driving force in the emergence of new strains. 2014 Nov doi:10.1016/j.meegid.2014.11.024 *
 Combrink J. A Sensitivity Analysis of Model Structure in Stochastic Differential Equation and Agent-Based Epidemiological Models. 2014 Nov hdl.handle.net/11427/21645
 Mandikumba W. New nonreversible nucleotide substitution models to describe evolution of viral and cellular genome. 26 October 2014. Hons thesis
 Bantom M. An assessment of the contribution of a satellite laser ranging station at Matjiesfontein. 15 October 2014.BSc thesis
 Mongwane B. Problems in Cosmology and Numerical Relativity. October 2014. PhD thesis
 Hunt N. Development of an equivalent mechanical model for fuel slosh in the wing of an aircraft. October 2014. *
 Hussen J. Industrial Research. October 2014. *
 Le Clezio S. Rigid wing-mast design for a small sailing vessel. October 2014. *
 Lochner M. New Applications of Statistics in Astronomy and Cosmology. September 2014. PhD thesis
 Muhire B, Varsani A, Martin D. SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation. 26 September 2014. doi.org/10.1371/journal.pone.0108277
 Febraury S. Evolution of linear perturbations in spherically symmetric dust spacetimes. 19 August 2014. PhD thesis
 Muhire B. Revealing a Hidden Viral Infection with Deep Sequencing in a Plant Quarantine Context. 25 July 2014. doi.org/10.1371/journal.pone.0102945 *
 Govind R. Multi-technique Space Geodesy Analysis Centre at the University of Cape Town. 9 Jul 2014. Presentation
 Muhire B. Pigeon circoviruses display patterns of recombination, genomic secondary structure and selection similar to those of beak and feather disease viruses. 1 Jun 2014 dx.doi.org/10.1099/vir.0.063917-0 *
 Ross-Gillespie A. Report of the Sub-Committee on Other Southern Hemisphere Whale Stocks. 12 May 2014. Report
 Ross-Gillespie A. Assessment results for humpback breeding stocks. 10 May 2014. open.uct.ac.za/handle/11427/17837
 Golden M. Identification of evolutionarily conserved nucleic acid secondary structures within viral genomes. 2014. open.uct.ac.za/handle/11427/5972
 Kuttel M, Gordon M, Ravenscroft N. Comparative simulation of pneumococcal serogroup 19 polysaccharide repeating units with two carbohydrate force fields. 2014. doi-org.ezproxy.uct.ac.za/10.1016/j.carres.2014.02.026
 Olivier C, Alexeeva N. The direct scattering study of the parametrically driven nonliner Schroeding equation. 2013. arxiv.org/pdf/1312.7655.pdf
 Golden M. Identification of evolutionarily conserved nucleic acid secondary structures within viral genomes. 23 December 2013. hdl.handle.net/11427/5972
 Muasya A, Viljoen J, Dludlu M, Demissew S. Phylogenetic position of Cyperus clandestinus (Cypereae, Cyperaceae) clarified by morphological and molecular evidence. 12 December 2013. hdl.handle.net/11427/21206
 Viljoen J, Muasya A, Barrett R, Bruhl J, Gibbs A, Slingsby J, Wilson K, Verboom G. Radiation and Repeated Transoceanic Dispersal of Schoeneae (Cyperaceae) Through the Southern Hemisphere. Dec 2013. hdl.handle.net/11427/21215
 Robinson W. Modelling the impact of the South African small pelagic Fishery on African penguin dynamics. November 2013. hdl.handle.net/11427/18162
 Muhire B, Golden M, Murrell B, Lefeuvre P, Lett J, Gray A, Poon A, Ngandu N, Semegni Y, Tanov E, Monjane A, Harkins G, Varsani A, Shepherd D, Martin D. Evidence of pervasive biologically functional secondary-structures within the genomes of eukaryotic single-stranded DNA viruses. 27 November 2013. hdl.handle.net/11427/21202
 Kerry Kalweit. Prioritisation of candidate genes for psychiatric disorders. 25 October 2013. open.uct.ac.za/handle/11427/21223
 Hugo B. Fast online predictive compression of radio astronomy data. 25 October 2013. open.uct.ac.za/handle/11427/21225
 Bures P, Muasya A, Lipnerova I, Zedek F, Bauters K, Smarda P, Viljoen J, Elizondo M, Barrett R, Goetghebeur P, Bruhl J, Mwachala G, Prychid C, Hroudova Z, Thomas W, Wilson K. The evolution of genome size and base composition in Cyperid clade. July 2013. Conference paper
 Munyai R. A Systematic Study of South African Genus Prionium (Thurniaceae). May 2013. hdl.handle.net/11427/14030
 February S, Clarkson C, Maartens R. Galaxy correlations and the BAO in a void universe: structure formation as a test of the Copernican Principle. 19 March 2013. hdl.handle.net/11427/21222
 Muhire B, Martin D, Brown J, Navas-Castillo J , Moriones E, Zerbini F, Rivera-Bustamante R, Malathi V, Riddon R, Varsani A. A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae). 23 January 2013. hdl.handle.net/11427/21221
 Fadly Isaacs F. Spatial Transitions: Cape Town Case Study. January 2103. hdl.handle.net/11427/21224
 Bell L. High throughput proteomic analysis of Mycobacterium tuberculosis associated Immune Reconstitution Inflammatory Syndrome (TB-IRIS). December 2012. open.uct.ac.za/handle/11427/4397
 Tshiila A. Systematics of Ficinia clade December 2012 MSc dissertation. African Studies Collection – BUT 580 TSHI
 Dlodlo O. Rhizobia diversity and their effect on the distribution of indigenous legumes in the Cape Floristic Region. December 2012 MSc dissertation. African Studies Collection – BUT 580 DLOD
 Stephen Marquard. Improving Searchability of Automatically Transcribed Lectures Through Dynamic Language Modelling. December 2012. Thesis
 Alexeeva N, Barashenkov I, Sukhorukov A, Kivshar Y. Optical solitons in Parity Time symmetric nonlinear couplers with gain and loss. 28 June 2012. open.uct.ac.za/handle/11427/21216
[6.] Home-grown high-performance computing at ICTS. UCT Monday Paper – Volume 31.14 – 17 September 2012
 Lee-Thorp J. Spectral continuation study of the temporally periodic solitons of the damped-driven nonlinear Schodinger equations. 22 August 2012 hdl.handle.net/11427/11261
 Olivier C, Herbst B, Molchan M. A numerical study of the large-period limit of a Zakharov-Shabat eigenvalue problem with periodic potentials. 31 May 2012. hdl.handle.net/11427/21200