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Understanding Biology from the Atomistic Scale

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The Structure of Living Matter

It is known from extensive experience in the physical sciences, that the behaviour of systems at the atomistic scale can be accurately predicted using parameter free quantum mechanical calculations based on density functional theory. These calculations are often referred to as ‘first principles’ or ‘_ab initio_’. Such calculations have made a significant contribution to our understanding of many physical and chemical processes. One would hope that providing the same degree of understanding of processes in biology would have a profound impact. However, the system sizes and timescales needed to study biological problems make the application of first principles techniques extraordinarily challenging. In this talk, I shall describe two computational techniques we are currently developing that, we hope, will make first principles calculations on biological systems accessible to all researchers. The first of these techniques is ONETEP , a density functional theory code whose computational cost scales linearly with the number of atoms in the system. ONETEP allows first principles calculations to be routinely performed on systems containing many thousands of atoms. The second of these techniques is a hybrid or ‘QM/MM’ modelling scheme which we are developing in collaboration with Dr. De Vita of King’s College, London. In this scheme, the quantum mechanical calculations are only applied where and when they are needed and, in contrast to other schemes, the choice of where to apply the quantum mechanical calculations can be delegated to the computer.

This talk is part of the Physics of Living Matter PLM6 series.

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