BEGIN:VCALENDAR VERSION:2.0 PRODID:-//CERN//INDICO//EN BEGIN:VEVENT SUMMARY:Computational chemistry and its application in pharmacy and drug d evelopment DTSTART;VALUE=DATE-TIME:20211201T123000Z DTEND;VALUE=DATE-TIME:20211201T130000Z DTSTAMP;VALUE=DATE-TIME:20260608T121241Z UID:indico-contribution-538-1575@events.chpc.ac.za DESCRIPTION:Speakers: Ponnadurai Ramasami ()\n**Summary:** \nComputational chemistry involves the use of theoretical methods and computers to solve chemistry and interdisciplinary problems. It has progressed with the explo sive increase of computational power and availability of user-friendly sof tware. Computational chemistry is also benefiting from the boom of the ICT sector.\nThis presentation gives an overview of the fundamentals of compu tational chemistry methods and their applications in pharmacy and drug dev elopment.\n\n**Objectives:** \n1. Collaboration with Computational Chemist ry Group\, Department of Chemistry\, Faculty of Science\, University of Ma uritius.\n2. Increase awareness of faculty and students about the importan ce of the computational chemistry and its use in all fields of science\, e specially in pharmacy and health sciences.\n3. Possibility to do joint gra duation project with Prof Ramasami.\n\nhttps://events.chpc.ac.za/event/98/ contributions/1575/ LOCATION: URL:https://events.chpc.ac.za/event/98/contributions/1575/ END:VEVENT BEGIN:VEVENT SUMMARY:Infectious disease susceptibility in the context of African geneti c diversity DTSTART;VALUE=DATE-TIME:20211202T120000Z DTEND;VALUE=DATE-TIME:20211202T123000Z DTSTAMP;VALUE=DATE-TIME:20260608T121241Z UID:indico-contribution-538-1572@events.chpc.ac.za DESCRIPTION:Speakers: Marlo Möller (Stellenbosch University)\nDuring late 2019\, the world saw the emergence of the Coronavirus Disease 2019 (COVID -19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To date\, more than 242 million infections have been obser ved in 223 countries/territories across the globe\, with a staggering 4.9 million individuals losing their lives to COVID-19. South Africa has not r emained unscathed by the pandemic\, having more than 2.9 million COVID-19 cases and over 88 000 COVID-19 deaths. Significant inter-individual variab ility has been observed in host responses to COVID-19\, with host genetic factors being proposed as a contributor to SARS-CoV-2 susceptibility and d isease severity. This observation echoes that of the ancient disease of tu berculosis (TB)\, still a chief cause of death in many areas\, with Africa home to most high burden countries. To find the genetic underpinnings of TB in South Africa\, we have studied the complete susceptibility spectrum\ , from individuals with rare susceptibility mutations to common genetic va riants in the general population. We used association studies\, genome wid e linkage studies and genome-wide association studies and incorporated pop ulation genetics and computational analyses to identify genes and loci tha t inform the variation in disease outcome between individuals. We are esta blishing a large COVID-19 cohort representative of South African populatio ns\, including individuals that have tested both positive and negative for SARS-CoV-2 to elucidate the underlying genetic markers that are associate d with both infection and severe/critical COVID-19. This includes whole ge nome sequencing of younger individuals diagnosed with a rare Multisystem I nflammatory Syndrome in Children (MIS-C) that is directly related to a pre vious SARS-CoV-2 infection\, which is often very mild or asymptomatic in c hildren. Our findings could assist with the management of infectious disea ses in resource-poor African settings\, where an overburdened healthcare s ystem in the past has not been able to accommodate infection surges.\n\nht tps://events.chpc.ac.za/event/98/contributions/1572/ LOCATION: URL:https://events.chpc.ac.za/event/98/contributions/1572/ END:VEVENT BEGIN:VEVENT SUMMARY:BoF: South African Modelling and Simulation Roadmap DTSTART;VALUE=DATE-TIME:20211202T131500Z DTEND;VALUE=DATE-TIME:20211202T141500Z DTSTAMP;VALUE=DATE-TIME:20260608T121241Z UID:indico-contribution-538-1569@events.chpc.ac.za DESCRIPTION:Speakers: Regina Maphanga (CSIR)\n**Birds-of-a-Feather (BoF):* *\n\nResearch and developments in Modelling and Simulation (M&S) domain ar e taking place in disparate communities considering different models and p henomena across the various length scales\, with considerable advancements in multiscale approaches and multidisciplinary optimisation. This BoF ses sion seeks to bring together M&S community across disciplines to engage on the National Science and Innovation System: Modelling and Simulation Doma in. The discussions will guide and contribute to the development of Modell ing and Simulation roadmap. \n\n**Programme:**\n\nWelcome - Prof Regina Ma phanga (3 min)\nBackground and Objectives for the M&S Program - Dr Jeffer y Baloyi (15 min)\nProposed Business Plan - Prof Regina Maphanga (15 min )\nDiscussions - All (20 min)\nWay forward - Dr Jeffery Baloyi (5 min)\n Closure\n\nhttps://events.chpc.ac.za/event/98/contributions/1569/ LOCATION: URL:https://events.chpc.ac.za/event/98/contributions/1569/ END:VEVENT BEGIN:VEVENT SUMMARY:Using genome-resolved metagenomics to understand microbial contrib utions to ecosystem functioning DTSTART;VALUE=DATE-TIME:20211203T120000Z DTEND;VALUE=DATE-TIME:20211203T123000Z DTSTAMP;VALUE=DATE-TIME:20260608T121241Z UID:indico-contribution-538-1567@events.chpc.ac.za DESCRIPTION:Speakers: Thulani Makhalanyane (University of Pretoria)\nMicro biomes mediate crucial ecosystem processes in terrestrial and marine envir onments\, yet data regarding their precise responses to climate change rem ains limited. This knowledge deficit is especially true for extreme Antarc tic environments where the importance of microbial communities is thought to be more pronounced due to the depauperate and oligotrophic nature of su ch systems. Here\, I will discuss our work in understudied deserts (such a s the McMurdo Dry Valleys) and oceans (such as the Southern Ocean) ecosyst ems. I will discuss key insights regarding the diversity and functional tr aits of microbiomes in these regions. I will also highlight how the applic ation of mesocosms (such as ocean acidification experiments) has allowed u s to predict the response of microbiomes to anthropogenic change. I will c onclude by discussing key questions for future research in Antarctic envir onments.\n\nhttps://events.chpc.ac.za/event/98/contributions/1567/ LOCATION: URL:https://events.chpc.ac.za/event/98/contributions/1567/ END:VEVENT BEGIN:VEVENT SUMMARY:Rational design of Sn(IV) porphyrins for photodynamic therapy: fur ther progress and future perspectives DTSTART;VALUE=DATE-TIME:20211202T123000Z DTEND;VALUE=DATE-TIME:20211202T130000Z DTSTAMP;VALUE=DATE-TIME:20260608T121241Z UID:indico-contribution-538-1566@events.chpc.ac.za DESCRIPTION:Speakers: John Mack (Rhodes University)\nOver the last year\, considerable further progress has been made in using a rational design app roach [1] guided by calculations with the Gaussian 09 software package on the Lengau cluster and an application of Michl’s perimeter model [1\,2] to prepare novel Sn(IV) complexes of porphyrin dyes and porphyrin analogue s that are suitable for use as photosensitizer dyes in photodynamic therap y [3-8]. Axial ligation results in low levels of aggregation\, while the S n(IV) ion promotes intersystem crossing resulting in relatively high singl et oxygen quantum yields through a heavy atom effect. Relatively low IC50 values have been obtained during *in vitro* studies against MCF-7 breast c ancer cells [3-9]. Future directions on the use of the Gaussian 09 softwar e package in the context of this research will be described.\n**References **\n[1] J. Mack\, *Chem. Rev.* **2017**\, *117*\, 3444-3478.\n[2] J. Michl \, *Tetrahedron* **1984**\, *40*\, 3845-3934.\n[3] B. Babu\, J. Mack\, T. Nyokong\, *Dalton Trans.* **2020**\, *49*\, 9568-9573.\n[4] B. Babu\, E. P rinsloo\, J. Mack\, T. Nyokong\, *New J. Chem.*\, **2020**\, *44*\, 11006- 11012.\n[5] B. Babu\, J. Mack\, T. Nyokong\, *Dalton Trans.* **2020**\, *4 9*\, 15180-15183.\n[6] B. Babu\, J. Mack\, T. Nyokong\, *Dalton Trans.* ** 2021**\, *50*\, 2177-2182.\n[7] B. Babu\, J. Mack\, T. Nyokong\, *New J. C hem.*\, **2021**\, *45*\, 5654-5658.\n[8] R.C. Soy\, B. Babu\, J. Mack\, T . Nyokong\, *Dyes Pigments*\, **2021**\, *194*\, 109631.\n[9] B. Babu\, A. Sindelo\, J. Mack\, T. Nyokong\, Dyes Pigments\, **2021**\, 185A\, 108886 .\n\nhttps://events.chpc.ac.za/event/98/contributions/1566/ LOCATION: URL:https://events.chpc.ac.za/event/98/contributions/1566/ END:VEVENT BEGIN:VEVENT SUMMARY:Understanding metal losses during furnace tapping operations using HPC DTSTART;VALUE=DATE-TIME:20211203T134500Z DTEND;VALUE=DATE-TIME:20211203T141500Z DTSTAMP;VALUE=DATE-TIME:20260608T121241Z UID:indico-contribution-538-1519@events.chpc.ac.za DESCRIPTION:Speakers: Quinn Reynolds (Mintek)\nDuring the pyrometallurgica l production of industrial commodities such as ferromanganese and ferrochr omium in electric smelting furnaces\, immiscible molten slag and metal pha ses are tapped from the unit at regular intervals. This process involves o pening a dedicated channel in the furnace sidewall (the tap-hole) and allo wing the contents of the vessel to drain through it. After exiting the tap -hole\, the stream of molten material is directed along open launder chann els and empties into one or more storage ladles. During this process inter mixing of slag and metal phases often occurs\, and if not carefully manage d\, can result in significant metal being lost to the waste slag by entrai nment. \n\nIn this presentation we show the results of a computational flu id dynamics study of the multiphase free surface fluid flow in tapping lad les\, and examine how the application of high-performance computing has gr eatly expanded our ability to explore the unusual and challenging paramete r spaces of problems in pyrometallurgy. Access to facilities such as CHPC allows us to build deeper intuition and fundamental understanding of the c omplex fluid flow phenomena occurring during ladle tapping\, and is able t o guide us to practical engineering solutions for mitigating losses due to phase mixing.\n\nhttps://events.chpc.ac.za/event/98/contributions/1519/ LOCATION: URL:https://events.chpc.ac.za/event/98/contributions/1519/ END:VEVENT BEGIN:VEVENT SUMMARY:Improved COVID-19 classification of cough audio DTSTART;VALUE=DATE-TIME:20211203T131500Z DTEND;VALUE=DATE-TIME:20211203T134500Z DTSTAMP;VALUE=DATE-TIME:20260608T121241Z UID:indico-contribution-538-1517@events.chpc.ac.za DESCRIPTION:Speakers: Thomas Niesler (University of Stellenbosch)\nWe repo rt progress in our research aiming to detect COVID-19 from smartphone aud io recordings. In our previous work we reported that it is possible to d iscriminate between recordings of COVID-19 positive coughs and coughs by COVID-19 negative or healthy individuals using machine learning algorithm s. Since the available datasets of COVID-19 coughs are small\, the classi fiers exhibited a fairly high variance. In subsequent work we have invest igated the effectiveness of transfer learning and bottleneck feature extr action for audio COVID-19 classification\, in this case performing experi ments for three sound classes: cough\, breath and speech. For pre-trainin g\, we use datasets that contain recordings of coughing\, sneezing\, spee ch and other noises\, but do not contain COVID-19 labels. Convolutional neural network (CNN)\, long short term memory (LSTM) and Resnet50 archite ctures were considered. The pre-trained networks are subsequently either f ine-tuned using smaller datasets of coughing with COVID-19 labels in the p rocess of transfer learning\, or are used as bottleneck feature extractors . Results show that a Resnet50 classifier trained by this transfer learni ng process delivers optimal or near-optimal performance across all dataset s achieving areas under the \nreceiver operating characteristic (ROC AUC) of 0.98\, 0.94 and 0.92 respectively for the three sound classes (coughs\ , breaths and speech). This indicates that coughs carry the strongest COV ID-19 signature\, followed by breath and speech. Our results also show th at applying transfer learning to capitalise on the larger datasets withou t COVID-19 labels leads not only to improved performance\, but also stron gly reduces the standard deviation of the classifier AUCs measured on the test sets during cross-validation\, indicating better generalisation. We conclude that transfer learning and bottleneck feature extraction can im prove COVID-19 cough\, breath and speech audio classification\, yielding automatic classifiers with higher accuracy. Since audio classification is non-contact\, does not require specialist medical expertise or laboratory facilities and can be deployed on inexpensive consumer hardware\, it rep resents an attractive method of screening.\n\nhttps://events.chpc.ac.za/ev ent/98/contributions/1517/ LOCATION: URL:https://events.chpc.ac.za/event/98/contributions/1517/ END:VEVENT BEGIN:VEVENT SUMMARY:Computational chemistry methods in understanding the properties of porous materials DTSTART;VALUE=DATE-TIME:20211203T123000Z DTEND;VALUE=DATE-TIME:20211203T130000Z DTSTAMP;VALUE=DATE-TIME:20260608T121241Z UID:indico-contribution-538-1521@events.chpc.ac.za DESCRIPTION:Speakers: Catharine Esterhuysen (Department of Chemistry and P olymer Science\, Stellenbosch University)\nIntermolecular interactions pla y a fundamentally important role in the properties of solid materials. For instance\, molecules ("guests") are taken up into porous materials ("host s") as a result of the interactions between these species\, while the mann er in which they interact has an influence on the sorption ability of the porous material. Several examples from our work will be used to show that calculations performed using the CHPC's computational facility allow us to explain the role that intermolecular interactions play in the unusual sor ption properties of various porous compounds. For instance\, the interacti ons between carbon dioxide and a host porous metal-organic framework yield anomalous sorption isotherms that can be explained by the electrostatic i nteractions between host and guest.[1] This can be extended to study mixtu res of gases\, where CO2 and N2 interact differently with the frameworks\, leading to non-ideal sorption behaviour that influences the ability of a porous compound to separate CO2 from N2.[2] Molecular dynamics calculation s and in combination with simulation of sorption isotherms using the BioVi a MaterialsStudio suite available through the CHPC can hence be used to id entify materials that will yield superior gas separation compounds. \n \n [1] Bezuidenhout\, C. X.\; Smith\, V. J.\; Bhatt\, P. M.\; Esterhuysen\, C .\; Barbour\, L. J. Angew. Chem. Int. Ed. 2015\, 54\, 2079–2083.\n[2] Co standius\, A. J.\; Barbour\, L. J.\; Esterhuysen\, C. In preparation.\n\nh ttps://events.chpc.ac.za/event/98/contributions/1521/ LOCATION: URL:https://events.chpc.ac.za/event/98/contributions/1521/ END:VEVENT BEGIN:VEVENT SUMMARY:Bioinformatics for vegetable breeding at Starke Ayres DTSTART;VALUE=DATE-TIME:20211203T104500Z DTEND;VALUE=DATE-TIME:20211203T111500Z DTSTAMP;VALUE=DATE-TIME:20260608T121241Z UID:indico-contribution-538-1515@events.chpc.ac.za DESCRIPTION:Speakers: Godwin Mafireyi (Starke Ayres)\nStarke Ayres is one of Africa’s largest seed companies in Africa which specializes in the de velopment of superior vegetable seed varieties. Bioinformatics forms a cru cial part of plant breeding as it helps researchers gain a deeper understa nding of the genetics of their germplasm. To do this\, we employ bioinform atics tools and software to perform computationally demanding processes su ch as read alignment to reference genomes\, variant discovery\, genome ass embly and phylogenetics among other processes. As bioinformatics must deal with large amounts of sequence data\, computational resources often becom e a limiting factor. We have been able to use CHPC massive computational p ower to accelerate molecular marker discovery for several traits. These pr ojects would have otherwise been extremely slow or not possible if we reli ed on desktop computers with limited memory\, processing power and storge. The vast amount of core bioinformatics tools and software that is preinst alled and configured on CHPC\, save a lot of time that could have been use d to configure and install these software packages on our local machines. In addition\, parallelization capabilities of CHPC using MPI have made dat a processing quicker and more efficient.\n\nhttps://events.chpc.ac.za/even t/98/contributions/1515/ LOCATION: URL:https://events.chpc.ac.za/event/98/contributions/1515/ END:VEVENT BEGIN:VEVENT SUMMARY:Regional and coastal ocean modelling: toward an operational system for well-informed decision making DTSTART;VALUE=DATE-TIME:20211203T101500Z DTEND;VALUE=DATE-TIME:20211203T104500Z DTSTAMP;VALUE=DATE-TIME:20260608T121241Z UID:indico-contribution-538-1513@events.chpc.ac.za DESCRIPTION:Speakers: Jennifer Veitch (South African Environmental Observa tion Network (SAEON))\nNumerical modelling is an essential component of in tegrated ocean monitoring and\, together with in situ observations and rem ote sensing products\, is one of the critical tools informing stakeholders about highly variable regional and coastal environments. Operational ocea n modelling becomes particularly valuable in South Africa when one conside rs the dynamic nature of its surrounding oceans\, including but not limite d to its proximity to one of the most energetic current systems in the wor ld\, the Agulhas Current. The Agulhas Current exhibits intense mesoscale activity in the form of events such as eddy shedding events at the Agulhas Retroflection\, the interaction of eddies from the Mozambique Channel wit h the Agulhas Current proper\, and the meandering nature of the Agulhas Re turn Current. The unpredictability and intensity of the currents represent a direct risk to industrial\, commercial and leisure activities\, for exa mple\, accidental pollutants\, such as oil spills\, which may advect onsho re to the detriment of the coastal environment. Furthermore\, the Benguela Current system is known to be sensitive to climate change\, and climate v ariability such as the El Niño Southern Oscillation (ENSO). Understanding these dynamics and their function in the ecosystem\, such as associations to harmful algal blooms (HABs) is an important part of resource managemen t. Hence\, the development of regional operational modelling capacity is o f key interest. This program supports SOMISANA (Sustainable Ocean Modellin g Initiative: a South African Approach) whose vision is to facilitate the local development and sustainability of an operational ocean current forec ast system for the South African exclusive economic zone and to do so in a transformative fashion. To this end\, its two immediate goals are: (1) to develop local numerical ocean modelling capacity via student supervision and (2) to develop high resolution ‘hindcast’ numerical models\, optim ized for South Africa’s shelf region as well as bay-scale forecast model s\, downscaled from freely available global products that poorly resolve t he processes in these regions. These objectives will not only lay the foun dation for the development of South Africa’s operational ocean forecasti ng system\, they will also ensure our contribution to UN Decade of Ocean S cience endorsed projects: CoastPredict and ForeSea.\n\nhttps://events.chpc .ac.za/event/98/contributions/1513/ LOCATION: URL:https://events.chpc.ac.za/event/98/contributions/1513/ END:VEVENT BEGIN:VEVENT SUMMARY:Application of Computational Alchemy to screen alloys of alumina ( Al2O3) as a catalyst support DTSTART;VALUE=DATE-TIME:20211202T104500Z DTEND;VALUE=DATE-TIME:20211202T111500Z DTSTAMP;VALUE=DATE-TIME:20260608T121241Z UID:indico-contribution-538-1522@events.chpc.ac.za DESCRIPTION:Speakers: Cecil Ouma (HySA - Infrastracturte)\nDescriptors de rived from density functional theory (DFT) calculations have been the stan dard when it comes to screening any alloy configuration space. However\, d eriving descriptors using DFT comes with high computational costs since an y alloy configuration space is expansive. DFT derived descriptors have bee n used for scaling relationships (SR)\, quantitative structure property re lationships (QSPR) and of late artificial intelligence/machine learning (A I/ML) in screening for alloys and catalysts. However\, SR and QSPR still r equire lots of DFT calculations and AI/ML need lots of training data. Cata lyst support have not been intensively investigated. Much of the focus has been on the catalyst. However\, alumina (Al2O3) has been the most dominan t support in use. Computational alchemy can be used to approximate a desc riptor on a large number of random/hypothetical alloy configurations with low computational cost. This is because it only requires a single set of r eference DFT calculations. Transition metal doped Al2O3 has been reported to possess excellent attributes\, such as the ability to promote surface d iffusion and prevent clustering/sintering by suppressing grain growth. In this study\, using the binding energy as a descriptor\, we screen for rand om/hypothetical alloys of the catalyst support Al2O3 using computational a lchemy. We explore in this study\, some of the limitations of challenges o f this approach in screening for a broad range of alloys. Pt is introduced at different locations within the alloy matrix to make Al2O3 a conductor and suitable for computational alchemy. Like previous studies\, on metal a lloys\, computational alchemy predicts adsorbate BEs in close agreement wi th those obtained using DFT calculations. This study provides insights on how computational alchemy can be useful in materials’ predictions at low computational costs.\n\nhttps://events.chpc.ac.za/event/98/contributions/ 1522/ LOCATION: URL:https://events.chpc.ac.za/event/98/contributions/1522/ END:VEVENT BEGIN:VEVENT SUMMARY:The usefulness of high-performance computing in small scale hydrop ower technology: Investigating the hydrodynamic effects of hydrokinetic tu rbines through validated CFD models DTSTART;VALUE=DATE-TIME:20211202T101500Z DTEND;VALUE=DATE-TIME:20211202T104500Z DTSTAMP;VALUE=DATE-TIME:20260608T121241Z UID:indico-contribution-538-1516@events.chpc.ac.za DESCRIPTION:Speakers: Chantel Niebuhr (University of Pretoria)\nHydrokinet ic energy generation devices within water infrastructure are becoming an e ver-increasing alternative power source. In these applications the extent and characteristics of the downstream wake are of great importance. The vo rtex formation and diffusion of the wake has a complex formation and is de pendent on numerous factors. Validated Computational Fluid Dynamics (CFD) models provide a detailed insight into these formations. These models allo w analysis of the wake behaviour which are helpful in design and installat ion of these systems. Additionally\, the effects of submergence depth and blockage ratio are also possible. Previously costly laboratory testing and simplified inaccurate numerical modelling was utilized due to the large c omputational resources needed to accurately simulate these applications. T he presentation will discuss the simulations made possible through the CHP C resource\, the challenges\, success\, and relevance of the results.\n\nh ttps://events.chpc.ac.za/event/98/contributions/1516/ LOCATION: URL:https://events.chpc.ac.za/event/98/contributions/1516/ END:VEVENT BEGIN:VEVENT SUMMARY:Investigating the Pressure Effects on Structural Behaviour of Garn et-Type Li7La3Zr2O12 Solid Electrolyte Material: A Classical Molecular Dyn amics Study DTSTART;VALUE=DATE-TIME:20211202T093000Z DTEND;VALUE=DATE-TIME:20211202T100000Z DTSTAMP;VALUE=DATE-TIME:20260608T121241Z UID:indico-contribution-538-1520@events.chpc.ac.za DESCRIPTION:Speakers: Raesibe Sylvia Ledwaba (University of Limpopo)\nThe cubic garnet-type Li7La3Zr2O12 is an eminent candidate for next-generation solid state battery technology due to its thermal stability and high ioni c conductivity. As such\, its operation mechanisms need to be thoroughly u nderstood\, particularly focusing on the structural instability challenge reported to occur at lower temperatures. Herein\, the statistical sampling capability of molecular dynamics simulations is employed during the inves tigation of fundamental structural\, kinetic and thermodynamic properties emanating its subjection to pressure and temperature. Systematic induction of pressure yielded transition of the tetragonal phase to the cubic phase at 2 GPa pressure. The lattice parameters for the cubic and tetragonal ph ases\, acquired in the current study are within 0.38 % agreement with lite rature. Furthermore\, the XRD graphs confirm varying phases under differen t pressure conditions. The temperature phase diagram for 0 GPa structure a grees well with the literature trends and interestingly\, the 2 GPa struct ure retained the cubic phase at various temperatures and confirmed in the XRDs and temperature phase diagram. Interrogation of LaO8 dodecahedral and ZrO6 octahedra demonstrated no significant variations in bond lengths and bond angles giving a good indication for the regulation of Li+-transport channel size in the 2 GPa structure. Efforts in this study are a prelimin ary stage to fully understanding the thermodynamic impact as a structural modification avenue pending further investigations.\n\nhttps://events.chpc .ac.za/event/98/contributions/1520/ LOCATION: URL:https://events.chpc.ac.za/event/98/contributions/1520/ END:VEVENT BEGIN:VEVENT SUMMARY:Agriculture Empowered by SuperComputing DTSTART;VALUE=DATE-TIME:20211202T090000Z DTEND;VALUE=DATE-TIME:20211202T093000Z DTSTAMP;VALUE=DATE-TIME:20260608T121241Z UID:indico-contribution-538-1518@events.chpc.ac.za DESCRIPTION:Speakers: Nicolas Erdody (Open Parallel Ltd)\nToday data is ga thered at different scales and at different frequencies by different organ isations using different types of devices much more than any other time in history. \n\nMost of it is gathered using already outdated technologies a nd systems. This creates an integration challenge: digesting data at the l ocal scale\, using it to update regional and nationwide scale models\, and feeding thus learned models back to the local scale to inform local infer ence. \n\nIf every farm has thousands of affordable sensors embedded in th eir environment (soil\, waterways\, animals) constantly “tasting” soil chemistry\, flow rates\, and any kind of biological activity\, it will pr oduce a massive amount of data per day that has to be stored\, analysed\, curated and maintained.\n\nWe could seed all the information such as crop variations\, soil health\, and weather patterns combined with insurance op tions\, credit availability and market forecasts into a single database an d then analyse it through AI and data analytics. Then the goal is to devel op personalised services for a sector replete with challenges such as peak ing yields\, water stress\, degrading soil and comparative lack of infrast ructure.\n\nThis is supercomputing territory. Real-time advanced modelling and simulation for quick decision-making requires significant computing p ower. In this talk\, Open Parallel's Nicolás Erdödy outlines the powerfu l modern technology tools and models available\, but not often used\, for the agriculture sector and how a system of systems similar to a digital tw in shall be developed -from the edge to exascale computing\, to optimise p roduction while measuring climate change as it happens.\n\nhttps://events. chpc.ac.za/event/98/contributions/1518/ LOCATION: URL:https://events.chpc.ac.za/event/98/contributions/1518/ END:VEVENT BEGIN:VEVENT SUMMARY:Computational Chemistry within the Laboratory of Applied Molecular Modelling at NWU DTSTART;VALUE=DATE-TIME:20211201T134500Z DTEND;VALUE=DATE-TIME:20211201T141500Z DTSTAMP;VALUE=DATE-TIME:20260608T121241Z UID:indico-contribution-538-1514@events.chpc.ac.za DESCRIPTION:Speakers: Cornie van Sittert (North-West University)\nIn 2002 with support from the Research Focus Area (Separation Technology) at North -West University (NWU)\, the Laboratory for Applied Molecular Modelling (L AMM) was established. After the evaluation of the researchers' abilities and the research needs\, an investment was made in Accelrys Materials Stud io software. Additionally\, ten workstations and a 12 CPU cluster were ac quired. The focus of the research done at that time in the LAMM was homog eneous catalysis\, which was limited to reactions in the gas phase. Trans ition state calculations\, as well as reaction in solutions\, were a chall enge.\n\nAround the same time\, the CHPC was established. However\, only on 23 January 2016\, the application to register a program at the CHPC was approved. The title of this program is: "Computational Chemistry within the Laboratory of Applied Molecular Modelling at NWU".\n\nWithin this prog ram\, the LAMM supports and facilitates the use of computational chemistry in research at NWU. The projects that ran between January 2016 and March 2018 was: 1. Solvent extraction of Ta\, Nb\, Hf and Zr from various minera ls\; 2. Polymer Blends - a collaboration with UFS and Qatar University. 3. Identification of mechanisms in biochemistry\; 4. Homogeneous and Heterog eneous catalysis\; 5. Collaboration with a group in China on polyphosphaze nes\; and 6. Interfaces in crystals with mechanical engineering at NWU. I n this period (26 months)\, the program used 213896 CPU hours per month. Since then\, some projects ran to completion\, some were added\, some were completed\, and some expanded. The CPU hours have increased to 790636 CP U hours per month.\n\nThe project that expanded the most is "Homogeneous a nd Heterogeneous catalysis"\, specifically heterogeneous catalysis. The f ocus in heterogeneous catalysis is on developing new/alternative catalysts to apply in the generation of alternative renewable energy and pollution control.\n\nhttps://events.chpc.ac.za/event/98/contributions/1514/ LOCATION: URL:https://events.chpc.ac.za/event/98/contributions/1514/ END:VEVENT BEGIN:VEVENT SUMMARY:Surface Enhanced Raman spectroscopy substrates: towards sensitive bio-sensing of infectious diseases DTSTART;VALUE=DATE-TIME:20211201T131500Z DTEND;VALUE=DATE-TIME:20211201T134500Z DTSTAMP;VALUE=DATE-TIME:20260608T121241Z UID:indico-contribution-538-1539@events.chpc.ac.za DESCRIPTION:Speakers: Nikiwe Mhlanga (Dr)\nSurface-enhanced Raman spectros copy (SERS) is a phenomenon that amplifies conventional Raman signal with roughened metallic substrates. Gold and silver metallic nanoparticles are commonly used as SERS substrates. The application of SERS in diagnostics yields sensitivity\, multiplexing\, and quantification of disease causati ves. However\, the understanding of the SERS architecture and mechanism i s still elusive. Hence the use of density functional theory (DFT) to stud y its chemistry. DFT is used to study the interaction of the metallic sub strates with SERS tags and biological molecules. The simulation results in form experimental work towards the fabrication of reproducible\, sensitive \, qualitative SERS biosensors.\n\nhttps://events.chpc.ac.za/event/98/cont ributions/1539/ LOCATION: URL:https://events.chpc.ac.za/event/98/contributions/1539/ END:VEVENT BEGIN:VEVENT SUMMARY:The IPCC Assessment Report Six: modelling contributions from the C HPC DTSTART;VALUE=DATE-TIME:20211201T120000Z DTEND;VALUE=DATE-TIME:20211201T123000Z DTSTAMP;VALUE=DATE-TIME:20260608T121241Z UID:indico-contribution-538-1512@events.chpc.ac.za DESCRIPTION:Speakers: Francois Engelbrecht (Global Change Institute\, Univ ersity of the Witwatersrand)\nThe Intergovernmental Panel on Climate Chang e (IPCC) Assessment Report Six (AR6) Working Group I (WGI) report\, releas ed in August 2021\, is widely regarded as the most influential and compreh ensive report on climate change composed to date. The report was described as a 'code red' for humanity by the United Nations Secretary General\, an d served as a direct input to the 26th Conference of the Parties (COP26) i n November 2021. African climate science is well represented in the report \, including several modelling papers on the projected climate change futu res of the African continent. The CHPC and most recently its Lengau cluste r played a critical role and in fact made feasible the completion of sever al computationally expensive simulations that underpinned several papers r eferenced by the IPCC AR6. This talk will review those papers\, and their significance. Future directions in Earth System Modelling will also be dis cussed\, in the context of convection permitting models and exascale compu ting\, and the role of the CHPC in ensuring that South African climate mod elling remains internationally competitive will be emphasized.\n\nhttps:// events.chpc.ac.za/event/98/contributions/1512/ LOCATION: URL:https://events.chpc.ac.za/event/98/contributions/1512/ END:VEVENT END:VCALENDAR