The first paper from my PhD has finally been published! Using an exciting combination of advanced simulations and microscopy, the paper reveals the multiple ways in which a protein found in most bacteria bends DNA and demonstrates that the protein can hold together two separate DNA helices. This has some important consequences for our understanding of DNA organisation in bacteria and the stability of infectious bacterial colonies, and the tightly coupled combination of experiment and simulation presents a promising foundation for future studies into other important biological systems. Unfortunately, a scientific paper is by its very nature a relatively dry, technical document, but the fruits of science belong to us all and I think it’s important that we share our research outside the academic bubble. With that in mind, please do sit tight while I walk you through our work in terms I hope a scientifically curious layperson can understand.
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I love science. I love the academic environment and I love the work I do. I even think I’m quite good at it. But I’m leaving – I’m taking my PhD and heading to pastures new in the big, scary outside world, and I’d like to share my reasons.
I recently encountered the surprisingly difficult task of processing a PDB file
While reading fixed-width files is relatively trivial in certain old-fashioned
languages with support for complex
like my beloved Fortran,
Python makes it
Given the myriad record types
that frequently appear in such files,
doing this processing on an ad-hoc basis seems like a terrible idea.
the fields in these records lend themselves nicely to implementation as objects,
so I went ahead and did just that.
I will be attending the Institute of Physics “Physics of Microorganisms II” conference in London on Monday, with my poster entitled “Atomistic simulations unveil the influence of DNA topology on IHF–DNA interaction”.