Mar. 19, 2008 The UK’s national computing grid, along with their counterparts in the US (TeraGrid) and Europe have helped UCL (University College London) scientists shed light on how life on earth may have originated.
Deep ocean hydrothermal vents have long been suggested as possible sources of biological molecules such as RNA and DNA but it was unclear how they could survive the high temperatures and pressures that occur round these vents.
Professor Peter Coveney and colleagues at the UCL Centre for Computational Science have used computer simulation to provide insight into the structure and stability of DNA while inserted into layered minerals. Computer simulation techniques have rarely been used to understand the possible chemical pathways to the formation of early biomolecules until now.
Professor Coveney explains, “Computational grids are only now being made easy to use for scientists, enabling simulations of sufficient size to model these large biomolecule and mineral systems”.
Previous experimental studies have shown that molecules such as DNA can be inserted into minerals called layered double hydroxides (LDHs) but no one has thus far been able to show at the level of atoms and molecules how the DNA interacts with the mineral, or how the DNA might look inside the mineral layers. These minerals would have been common in the earliest age of Earth 2500 million years ago.
The simulations reproduced the high temperatures and pressures that occur around hydrothermal vents. It was shown that the structure of DNA inserted into layered minerals becomes stabilized at these conditions and therefore protected from catalytic and thermal degradation.
“Grids of supercomputers are essential for this kind of study”, says Professor Coveney, “The time taken to run these simulations is reduced from the years that a desktop computer would take, to hours by using the many thousands of processors made available across continents”.
Professor Coveney’s group has been researching into the routes to the origin of life for a number of years, studying the way that genetic information may have arisen and been replicated, as well as how small molecules may have formed, working together with colleagues at Nottingham and Durham Universities.
Journal reference: ‘Computer Simulation Study of the Structural Stability and Materials Properties of DNA-Intercalated Layered Double Hydroxides’ by Mary-Ann Thyveetil, Peter Coveney, H. Chris Greenwell and James Suter, is published online in the Journal of the American Chemical Society on Tuesday 18 March 2008.
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