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Peter's MOAC MSc

I'm one of the original MOAC intake of summer 2004, the first batch of students to earn a MOAC Masters degree in Mathematical Biology and Biophysical Chemistry.

Then, as now, the MOAC MSc was divided into two parts:

I used the typesetting language LaTeX (the free MiKTeX distribution for Windows to be exact) for most of my reports (having reminded myself why I don't like Microsoft Word). Those from a Maths or Physics background may well have heard of it, as one of its great strengths is dealing with complicated equations. Its somewhat more rare in Biology, which means that there are less journal templates available - For the CH927 Module Lab Report I used the OUP Bioinformatics journal template (try bioinfo.zip [ZIP])

I'm reluctant to put much assessed work from the taught modules up online, as I don't want future students freeloading ;)

The taught modules were essentially the same for all students, while the mini-research projects were all unique. Some students did linked projects (e.g. Hiroko) which followed on from each other. Mine were all free standing.

[PHOTO]

More graduation photos...



 

Mini Project I - Yeast Two Hybrid Assay for Protein Interactions

[PHOTO] Supervisor: David Whitworth
Department: Biology - Molecular Microbiology
Assessment: A1 Poster [PowerPoint] (image [PNG Image]), and Presentation [PowerPoint]

The talk and poster were presented at the 2004 MOAC Annual Conference. The poster shows an enormous "flow chart" explaining how the Yeast Two Hybrid Assay works, which includes manipulating plasmids in both E. Coli and yeast. This project really taught me how slow lab work is - even when things work, and how frustrating it can be when your ligations (or even PCR) just won't work.

I was using the assay to probe interactions in the two component systems (TCS) of the social bacteria Myxococcus xanthus, something I am studying further in my PhD project...

[POSTER]


 

Mini Project II - Lipid Simulations with MMTK

[PHOTO] Supervisor: Mike Allen
Department: Centre for Scientific Computing
Assessment: Thesis Style Report [PDF]

I spent this project extending The Molecular Modelling Toolkit (MMTK) for Lipid Simulations. MMTK is a Python library for Molecular Simulation. See also my Python page.

MMTK has mainly been used for simulating "real" molecules made of "real" atoms, while we wanted to consider simplified lipids made out of a chain of beads, each of which would represent many atoms - and use our own specific forcefields for their interactions. In particular, the lipid solvent we considered was a "phantom solvent" which did not interact with itself.

This required defining additional atom types and forcefields in MMTK, which I had done by the end of the project - however the resulting simulations did not act as expected. I believe (due to the system behaviour) that this was mainly a problem with setting up the initial system state, and given more time this could be rectified.

[Lipid simulation with MMTK]


 

Mini Project III - Simulating SECM Imaging with FEMLAB

[PHOTO] Supervisor: Anna Barker / Whitworth
Department: Chemistry - Electrochemistry
Assessment: Scientific Paper Style Report [PDF] and Presentation [PowerPoint]

Those of you paying attention will realise from the titles that I ended doing two "simulation" projects. Well my third project was supposed to be "Experimental Physical Chemistry", and while I did spend some of my time and budget making platinum and iridium SECM electrodes with Ilenia Ciani - this was not as straight forward as it might have been, and the secondary aspect of the project rather took over.

As explained in the Presentation [PowerPoint], I used the finite element method package FEMLAB to run a series of diffusion simulations to find steady state currents for SECM ring electrodes. By repeating these simulations for different geometries, it is possible to simulate scanning the probe slowly across a target, producing simulated scan images. Because each simulation takes some time to run, I spent a lot of effort in automating this though MATLAB.

You can find me (and lots of other MOAC students) on the Electrochemistry Alumni - Masters Students page.

[FEMLAB Screenshot]