Example Projects

This page will contain brief descriptions of projects undertaken by current and previous students at the LSI DTC. A suitable selection is currently being compiled.

 

Ferdinando Randisi, 2013 Intake – A multiscale computer model of DNA

Computer simulation of DNA via molecular dynamics and Monte Carlo techniques are crucial both to tackle many unanswered questions in molecular biology and to research DNA nanotechnology (including DNA computing). Different models of DNA have different degrees of detail and computational cost, and can be used to simulate DNA in different contexts: coarser models are fast and can simulate large structures, while more detailed models are slower but are sometimes required to provide a faithful representation of a crucial detail of a particular system. How can we build a model that is both fast and detailed enough? In my DPhil I’m bringing together two models of DNA to build a multiscale model: that is, a model that provides a coarse description in the parts of the system where this is sufficient, and a detailed description where this is needed. The model will be applicable to a large range of DNA structures which either are too large or evolve too slowly to be completely modelled with a detailed model of DNA, but which do need to be modelled in detail in some of their parts. Such structures include DNA-histone complexes, DNA plectonemes, long DNA strands under heavy mechanical stress, and many others.