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In silico simulation with GAMESS-UK
On HPCx, Dr Marcus Durrant of the John Innes Centre is carrying out in silico simulation of molecular evolution, by means of quantum calculations. In molecular evolution, genes are transcribed into functional molecules (proteins), which then carry out specific chemical processes. The survival of a gene is therefore determined primarily by the ability of its associated protein to carry out its target chemical reaction. In this project, we are using very small genes (nanogenes) to code for specific molecules, namely transition metal complexes. Individual nanogenes are transcribed to give sets of input files for quantum calculations using the GAMESS-UK quantum chemistry package. Survival of individual nanogenes within the population depends upon the ability of each complex to perform a specified chemical reaction, assessed by the results of the quantum calculations. Surviving nanogenes are allowed to breed and mutate in order to provide the next generation, and the process is repeated until all the survivors are fully competent for the target reaction.
To date, we have completed a pilot study, which has successfully demonstrated the basic concept. This pilot study consisted of a total of 18 generations, comprising 289 individual nanogenes. Of these, 17 nanogenes that satisfied the selection criteria were found. Interestingly, these were all closely related to an experimentally characterised complex, which has been shown to carry out the target reaction. Hence, the pilot study has demonstrated a number of key points:
We are currently extending our studies to search for a catalyst capable of reducing dinitrogen to hydrazine.
Caption for figure: Three successive generations of nanogenes, showing the spread of desirable characteristics through a population. In each case, the top six nanogenes are chosen as survivors to form the next generation through breeding and mutation algorithms.
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