Latest news for the Scientific Computing Research Unit
BXQ-350 is a first-of-its-kind cancer treatment that weaponizes the special mechanics of cancer to destroy it. Discovered by Xiaoyang Qi - Professor of Medicine, Co-Division Chief for Basic Science Research - BXQ-350 is a protein which can fuse to the walls of cancerous cells, causing those cells to die off.
The South African Health Minister Aaron Motsoaledi acknowledged that the national healthcare system is battling a rise in cancer cases. Some patients die before receiving treatment (Read full article).
We are developing cancer diagnostics with a focus on early detection, read more about our research.
See our Unsupervised Learning method "Denoising Autoencoder Self-Organising Map" (DASOM) although developed for the Early Cancer Diagnostics Project it is universally applicable to a wide range of applications. DASOM integrates autoencoders into a hierarchically organised hybrid model where the front-end component is a grid of topologically ordered neurons. The model maintains clustering properties but by extending and enhancing its visualisation capacity it enables an inclusion and analysis of the intermediate representative space. Download the paper for free at https://authors.elsevier.com/a/1X5v~3BBjKVz76
Prof Levitt one of the 2013 Nobel Prize laureates visited the Scientific Computing Research Unit in November 2017. Prof Levitt’s diverse interests have included RNA & DNA modelling, protein folding simulation, classification of protein folds & protein geometry, antibody modelling, x-ray refinement, antibody humanisation, side-chain geometry, torsional normal mode, molecular dynamics in solution, secondary structure prediction, aromatic hydrogen bonds, structure databases, and mass spectrometry.
We are thankful that Prof Levitt took time out of his busy schedule to engage with the students and trust he enjoyed discussing their research projects.
Public Lecture by Prof Michael Levitt, Stanford University
Birth & Future of Multiscale Modeling
Date: Friday 17th November, 2017
Venue: PD Hahn Lecture Theatre 3
Public Lecture available at http://media.uct.ac.za/engage/theodul/ui/core.html?id=4796c0df-188d-4220-bc7e-e221e5cf711a
Born in South Africa in 1947, Prof Levitt was awarded the 2013 Nobel Prize for Chemistry (shared with Martin Karplus and Arieh Warshel). Prof Levitt’s diverse interests have included RNA & DNA modelling, protein folding simulation, classification of protein folds & protein geometry, antibody modelling, x-ray refinement, antibody humanisation, side-chain geometry, torsional normal mode, molecular dynamics in solution, secondary structure prediction, aromatic hydrogen bonds, structure databases, and mass spectrometry. He has a passion in helping today’s young scientists gain the recognition and independence that his generation enjoyed.
In his talk, Prof Levitt will review how the development of multiscale models for complex chemical systems began in 1967. These same multiscale models have become increasingly popular in applications that range from simulation of atomic protein motion, to protein folding and explanation of enzyme catalysis.
October is Breast Cancer Awareness Month, which is an annual campaign to increase awareness of the disease
This is relevant to our research unit as we aim to classify cancer at the genetic and molecular (Glycan) level. Using our mechanistic understanding of glycosylation and glycolysis of tumours we design leads for molecular classes of Cancer. SCRU laboratories collaborate closely with medicinal laboratories as well as human biology laboratories to translate basic research findings into new clinical strategies for diagnosis and therapy.
Professor Jonathan W. Essex (Director of Research, Computational Systems Chemistry, Chemistry Department, University of Southampton) has been invited as part of the SCILS.
He will present a DEPARTMENTAL LECTURE on Protein-Ligand Binding by Free Energy Simulations: Issues, Successes and Failures.
Further information about Prof Essex and his research is available at https://www.southampton.ac.uk/chemistry/jessex/
Dr Karl Wilkinson : 19-02-1981 to 25-08-2017
There are moments in the lives of even the most rationale amongst us when we are reminded of our frailty and of the strength we draw from being amongst like minded souls. Today is such a day for the colleagues and students in the Scientific Computing Research Unit and the Department of Chemistry. We have lost Karl Wilkinson a friend, a colleague, a mentor, a young mind that gave us so much.
Members of the Scientific Computing Research Unit (SCRU) celebrated with Tharindu Senapathi as he became the first graduate of the Master degree in Computational Science at UCT and in South Africa.
Multidimensional Reaction Dynamics Reveal How the Enzyme TcTS Suppresses Competing Side Reactions and Their Side Products. The suppression of competing reactions that lead to side products is one of the key mechanistic actions defining enzyme catalysis. The transfer of sialic acid (SA) in a water solution is susceptible to two competing side reactions, but a single product is the outcome in the glycosylation and deglycosylation.
As a SACI Post-Graduate Awardee, Mr Rogers was nominated as a young innovative chemist and is the University of Cape Town recipient.
The recipients of the award should be considered as being “young innovative chemists”. The characteristics of such a person are: Innovation, Independence, Enterprise. This award is made to students engaged in research towards an MSc or PhD degree at a University, or a MTech or DTech degree at a University of Technology. The number of medals awarded shall not exceed five per annum, and the awards are limited to one per institution.
The combined effect of differential expression leading to cancer segregation and highly ranked importance of GT genes in cancer identification emphasizes that the biochemical pathways underlying key phenotypes across cancers differ significantly.