Our strategy at SCRU is to constantly benchmark our performance against research groups and centres at leading international institutions. Our primary vehicles for achieving this is through contact with these top ranking researchers and groups. A major activity is the Scientific Computing International Lecture Series (SCILS) annual event started in 2010 hosted by the Scientific Computing Research Unit. In this programme the our students, postdocs and staff are able to have weeklong discussions with major international leaders in the fields of computational chemistry, biology and biophysics and experimental chemical biology. In addition to the visitation of world leaders to SCRU we send students at least once a year to spend several months in major laboratories. Through this deep exposure of our students to international research practises and work ethics we aim to develop them into competitive leading researchers. SCILS has been suspended from 2020-2022 due to the global COVID pandemic and will resume in 2023.
The 2019 SCILS was the 10th annual Scientific Computing International Lecturer Series (SCILS) which was in the form of an interactive workshop entitled “The link between Machine Learning and Machines” including some applications of Deep Learning & AI conducted by industry leaders from IBM OpenPower, Mellanox and NVIDIA.
Ganesan Narayanasamy, is the Senior Technical Computing Solution and Client Care Manager, IBM, New York and the OpenPOWER leader for academia and research at the IBM Lab. Ganesan is best known for his contributions to High Performance Computing as a senior leader for nearly 15 years. He is also leading the WW Academia workgroup for OpenPOWER and putting together OpenPOWER ECO System development activities like setting up OpenPOWER centre of excellence, OpenPOWER lab.
Claudio Polla, is the Country Manager, Mellanox / Nvidia Technologies, South Africa an experienced Regional Manager with a demonstrated history of working in the information technology and services industry and skilled in Storage Infrastructure, Managed Services, Business Development.
The workshop was attended by some participants from the wider UCT community, students from the computational and modelling lab, as well as the informatics and visualisation lab and participants, had some hands-on exercises and live demonstrations.
Ganesan Narayanasamy and Claudio Polla presented the OpenPOWER and POWER9 features, Accelerated Inferencing and Large Model Support and Distributed Deep Learning as well as presented PowerAI Vision Demo.
Dr Niclas Karlsson, a Researcher in the Department of Medical Biochemistry and Cell biology at Institute of Biomedicine, University of Gothenberg, was invited for SCILS week from 15th - 19th October 2018. Dr Karlsson is the PI on the UniCarb-DB database that stores, integrates and processes data from manually annotated ms spectra glyco fragments.
The students from the computational and modelling lab as well as the informatics and visualisation lab had the opportunity to present their projects to Dr Karlsson and seek advice.
Dr Karlsson presented seminars to the unit entitled: "Glycomic mass spectrometry - Interpretation of data generated by glycomic workflows”, “Carbohydrates, the relevance of this dominating biomolecule class in life science” and Software and databases used in glycomics". He presented a departmental lecture “Osteoarthritis (OA) - A Life Science Glycoproblem”.
Professor Jonathan Essex, the Professor of Computational Systems Chemistry at the University of Southampton was invited for SCILS week from 9th - 13th October 2017.
The students from the computational and modelling lab as well as the informatics and visualisation lab had the opportunity to present their projects to Prof Essex and seek advice.
Prof Essex presented seminars to the unit entitled: "Dual resolution modelling of lipid systems" and "What’s wrong with free energy calculations?". He presented a departmental lecture "Protein-Ligand Binding by Free Energy Simulations: Issues, Successes and Failures".
Dr Robert Best from the NIH was the SCILS visitor for 2016. SCILS took place during 19 - 23rd September 2016.
The postgraduate students has the opportunity to meet with Dr Best and present their projects and ask for advice.
Dr Best presented seminars to the Scientific Computing Research Unit entitled: "Finding good reaction coordinates to sample/analyze macromolecular conformational transitions" and "Systematic approaches to improving force fields from ab initio and empirical data"
Dr Best presented a departmental lecture at UCT and at Stellenbosch University entitled "Investigating the properties of unfolded and intrinsically disordered proteins via experiment and molecular simulation".
SCILS 2016 was a successful event and we ended it by enjoying some local cuisine at Tokara wine and olive farm.
Professors Dirk Zahn, Bernd Meyer and Tim Clark from the Interdisciplinary Centre for Molecular Materials and Computer Chemistry Centre, Friedrich-Alexander University, Erlangen-Nurnberg, Germany, were the SCILS visitors for 2015. SCILS took place during the week of 28 September – 2 October 2015.
The postgraduate students at SCRU had the opportunity to meet with these world renowned researchers to discuss their research projects. Meetings were arranged with Academic Staff in the Department of Chemistry and with the Dean of Science.
A mini-symposium was held on Thursday, 1 October 2015, the following lectures were given at the symposium: Professor Bernd Meyer – ‘Proton dynamics at the solid/liquid interface and in confined liquids‘, Professor Dirk Zahn – ‘Using molecular dynamics simulations to understand how crystals grow and materials behave‘ and Professor Tim Clark ‘What can metadynamics tell us about G-protein-coupled receptors?‘.
SCILS 2015 was a successful event that provided the way forward to set up possible collaborations with the FAU in the future.
Professor Timothy Clark
Professor Timothy Clark, Technical Director at Computer Chemie Centrum, Friedrich-Alexander Universitat Erlangen-Nurnberg, Germany was the SCILS visitor for 2014.
The SCILS week took place from 25-29 August, during this week Professor Clark gave a Departmental Lecture, titled: “Anisotropic interatomic interactions (sigma-holes, anisotropic electrostatics and dispersion)“. The lecture was followed by a social function in the Informatics and Visualisation Laboratory.
One of the core functions of the SCILS event is the interaction with students. Professor Clark gave a lecture to the third year Chemistry class, this was titled: “Modeling and Simulation – The Third Pillar of Science“. Two seminar were given to the postgraduate students in the SCRU lab.
The week ended with a lecture at the Department of Chemistry and Polymer Science, Stellenbosch University. This lecture was titled: “Simulating “Soft” Electronics (MD calucaltions and DQMC simulations of electron and hole transport“.
The SCILS 2014 week was enlightening and rewarding to both the researchers and the students who had the opportunity to discuss their research projects with Professor Clark.
Professor Wilfred van Gunsteren
Professor Wilfred van Gunsteren, ETH Swiss Federal Institute of Technology, Zürich, Switzerland was the SCILS visitor for 2013.
The SCILS week took place from 30 September – 4 October, during this week Professor van Gunsteren gave a Departmental Lecture, titled: “Is the quest for quality or performance measures or indices destroying academic values and obstructing scientific progress?” and an undergraduate lecture to 3rd year Chemistry class, titled: “Biomolecular simulation: 1976, 2013, 2050”.
Professor van Gunsteren gave three seminars to the SCRU postgraduate students. He also met individually with the postgraduate students and postdoctoral fellows in the research unit.
This was a very successful and enriching visit.
Professor Gernot Frenking
In 2012 SCILS combined with the Frontiers in Scientific Computing Symposium (FSC), held at the Graduate School of Business Breakwater Lodge, V&A Waterfront, on 1-2 October 2012 and Professor Kevin J. Naidoo’s Inaugural Lecture held on 3 October 2014, at the Kramer Law Building, Middle Campus, UCT.
Professor Gernot Frenking visited SCRU from 30 September – 5 October 2012. In addition to giving an invited lecture at the FSC, he gave two seminars to the postgraduate students at SCRU, titled: “Computational Techniques” and “ADF Decomposition“. These students also had the opportunity to meet and discuss their research projects with Professor Frenking.
Professor Frenking gave a further lecture to the 2nd year Chemistry Class, titled “Our present understanding of the nature of the chemical bond“.
Professor Jiali Gao
Professor Jiali Gao from the Department of Chemistry at the University of Minnesota visited SCRU from 12-18 September as the SCILS Visitor in 2011.
Professor Gao gave a public lecture to the Department of Chemistry titled, “Dynamic Contributions to Enzyme Catalysis as Illustrated by Orotidine Monophosphate Decarbonylase”. A second lecture, to 2nd year undergraduate Chemistry Students was given on the topic of “An understanding of intermolecular interactions through energy decomposition analysis”. This lecture was well received by the class.
During this week Professor Gao gave two seminars to SCRU postgraduate students and invited researchers, the titles of these seminars were; “Combined QM/MM approaches to chemical and enzymatic reactions” and “X-Pol potential: The incorporation of explicit polarization and charge transfer into the next-generation quantum force field“.
The postgraduate students at SCRU were also given the opportunity to meet with Professor Gao individually to discuss their research projects.
Professor Sason Shaik
Professor Sason Shaik from the Lise Meitner-Minerva Center for Computational Quantum Chemistry, Institute of Chemistry, The Hebrew University of Jerusalem, was the first SCILS visitor.
The SCILS week took place from 20-24 August 2010. One of the highlights of this visit was the entertaining lecture given to the 2nd and 3rd year undergraduate Chemistry classes titled: Chemistry – A Centre Pillar of Human Culture.
Professor Shaik gave a Departmental Lecture titled; “Cytochrome P450 and its Reactivity Patterns: What a Versitile Catalyst. This lecture was followed by a social event where guests could mingle with Professor Shaik.
During the SCILS week, the Postgraduate students at SCRU had the opportunity to discuss their research with Professor Shaik.
