Apple Technology Drives Carbohydrate Research

Profiles in Success: University of Cape Town

More effective vaccines and safer food storage are just two potential benefits of new carbohydrate research being undertaken at the University of Cape Town. Supported by the Apple Research & Technology Support (ARTS) programme, the project simulates and visualises the molecular dynamics of large carbohydrate systems — to better understand the body’s immune reactions, and the mysterious ways some plants are protected from cold and dehydration.

“Large assemblies of carbohydrates are not nearly as well understood as proteins”, says Dr Michelle Kuttel, Senior Lecturer in the university’s Computer Science Department, who is leading the two-year project and has become Apple’s first ARTS Laureate in Africa.

“We need a lot of computing power to model them because carbohydrates are very flexible molecules. However, understanding them is so important because carbohydrates are involved in fundamental biological processes such as the body’s ability to detect viruses, and the infection mechanisms of many diseases. Running the project on Apple Xgrid technology with Apple’s visualisation capabilities is just a perfect solution”.

The University of Cape Town (UCT) is South Africa’s oldest university, and is one of Africa’s leading teaching and research institutions. Dr Kuttel is a computational chemistry specialist, based in the Computer Science Department so that she can access the IT resources and skills she needs to support her carbohydrate research.

“Computer simulations are increasingly used to provide insights into molecular conformations and interactions unobtainable by experiment”, she explains. “There have been a number of simulations of single carbohydrate molecules in vacuum or solution, but to date little work on larger assemblies of carbohydrates. This is because these simulations require expensive computing power and long simulation times”.

“Yet there is little doubt that simulations of carbohydrate systems containing varying amounts of water — what we call gels and glasses — could greatly improve our understanding of important biological processes”.

Dr Kuttel is a self-confessed Mac convert. “I came from a UNIX research background, but I was never happy using a PC for presenting my PhD work on carbohydrates, or creating visualisations”, she says. “Discovering Apple was like a religious conversion. My MacBook Pro has wowed me completely. It’s got brilliant visualisation capabilities, and I can use Linux with all Apple’s user friendly tools”.

Attending an Apple presentation in Cape Town, she became aware of the ARTS programme and its opportunity for young researchers to become ARTS Laureates and receive up to US$30,000 worth of Apple solutions to help their research. She submitted a successful proposal for research into large assemblies of carbohydrates, and a specification for an Apple Workgroup Cluster with the power to perform the computationally-intensive calculations of the project.

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