Cutting-edge Computing Helps Discover Origin Of Life On Earth
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. (Credit: OAR/National Undersea Research Program (NURP); NOAA)
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.
译文:
尖端技术探索物种起源
英国国家计算网格，与其在美国(TeraGrid)和欧洲的相同机构共同努力下，帮助UCL(University College London)的科学家们了解地球上的物种起源。
深海中的热液喷口一直以来被认为是诸如RNA和DNA的生物分子的可能来源，但它们是如何才能在这些喷口周围所产生的高温高压的条件下存活的，至今仍原因不明。
Peter Coveney教授和他在计算科学UCL中心的同事们，利用计算机模拟技术，洞察在注入分层矿物质后DNA的结构及其稳定性。至今，计算机模拟技术鲜少被用于研究早期生物大分子形成的可能的化学方法。
Conveney教授解释道：“计算网格的简易操作现在仅对于科学家适用，使他们能模拟足够小的模型，来模仿这些大生命分子和矿物质体系。”
以前的实验研究表明，诸如DNA之类的分子可以被注入叫做水滑石(LDHs)的矿物质，但是至今为止，没有人能够展现DNA是如何在原子层和分子层内与矿物质发生作用的，或者DNA在矿物层内看起来是怎样的。在25亿年前的最早期的地球上，这些矿物质是十分常见的。
模拟使热液喷口周围所产生的高温高压现象重现。实验表明注入分层矿物质的DNA，在这种情况下结构稳定，因此没有发生催化降解或热降解。
“巨型电子计算机的网格对于这类研究而言很重要。”Coveney教授说，“一台台式机在进行模拟时所花的时间从好几年减少到几个小时，这一进步是依靠跨越好几个洲的上千台处理器才完成的。”
Coveney教授的团队研究物种起源已经好几年了。他与诺丁汉大学和杜伦大学的同事们一起工作，研究遗传信息产生和复制的方式，以及小分子是如何形成的。
参考文献：“关于LDHs夹层DNA的结构稳定性和材料性能的计算机模拟研究”，作者：Mary-Ann Thyveetil, Peter Coveney, H. Chris Greenwell, James Suter，在线发表于2008年3月18日星期二的《美国化学学会》杂志上。