A bit about me
I write software for understanding the structures of proteins to assist Chemistry researchers with finding new medicines, and controlling robotic prosthetic limbs.
I was born in South Africa and lived there until I came to the UK with my family in 1999.
My hometown is Swindon, Wiltshire, but I now live in Leamington Spa.
The academic stuff
1. "Elucidating protein secondary structure with circular dichroism and a self organising map neural network. " V. Hall, A. Nash, E. Hines, A. Rodger, J. Computational Chemistry 2013.
2. "Protein Secondary Structure Prediction from Circular Dichroism Spectra Using a Self-organising Map with Concentration Correction", V. Hall, A. Rodger, accepted by Chirality.
3. "SSNN, a method for neural network protein secondary structure fitting using circular dichroism data", V. Hall, A. Rodger, second submission...
4."Self organising map pattern recognition for real-time prosthetic control: HASSANN", V. Hall, M Ortiz-Catalan, in preparation.
My latest project is to write pattern recognition software for controlling robotic prosthetic arms. These have preset motions. Electrical signals from in vivo nerves were gathered from people with complete arms and missing arms while thinking about moving their arms, wrists and hands in these preset ways. This information is used to train artificial intelligence software to interpret the signals to make the limbs move appropriately. This is in collaboration with Max Ortiz-Catalan, et al. of Chalmers University of Technology. http://www.chalmers.se/en/news/Pages/Thought-controlled-prosthesis-is-changing-the-lives-of-amputees.aspx
One of my projects is to make Intelligent Systems to mine spectroscopic data from Chemistry (Circular Dichroism - a technique ideally suited to obtaining structural information about proteins and other chiral molecules). Intelligent systems are programs that mimic biology (like the brain) to solve a problem. I work mainly in self ofganising maps - a type of neural network - but I have written a genetic algorithm just for fun. I spend my time in MOAC, Senate House. My Chemistry supervisor is Alison Rodger. My Engineering supervisor is Evor Hines. I wrote a program, 'SSNN', to cluster CD spectra and make predictions of secondary structures of globular proteins to aid drug design. The next step is to apply other data to SSNN in Chemistry and more, and make more predictions. Currently I'm mostly working in the Matlab environment.
SSNN: Secondary structure prediction software
The software for estimating protein secondary structures is available at http://www2.warwick.ac.uk/fac/sci/chemistry/research/arodger/arodgergroup/research_intro/instrumentation/ssnn/
The trained self organising map (SOM) called SSNN maps showing clustered CD spectra of proteins. These maps are used to make models of protein CD spectra and estimate their structures.
Output of the CD spectrum model made by SSNN. SSNN makes a model of the input spectrum to estimate how good it's prediction of secondary structure will be for this protein.
The masters year with MOAC:
- My first miniproject was in Biological Sciences, looking at the action of gramicidin – a peptide antibiotic – on bacteria, specifically E. Coli. My supervisor was Will Gaze, with advice from Liz Wellington, and some more from Alison Rodger and Matt Hicks.
- My second mini project was in Chemistry, looking at the specific mechanisms used by gramicidin and various antibiotics of the class aurein to kill bacteria. We studied the effect of these antibiotics on models of cell membranes, liposomes made from DMPC, and on membranes made from lipids of E. coli. I used linear dichroism, LD, to study if the antibiotics inserted into the membranes, and dynamic light scattering, DLS, to measure the size distribution of the liposomes. I worked with Matt Hicks and Alison Rodger on this project.
- My third and final mini project was in simulation, also in Chemistry: Simulations of surface active proteins – hydrophobins from the fungus Trichoderma reesei. We were using the martini force field, coarse grained model of the protein. The aim was to understand how the protein behaves at a water/air interface. I was working with David Cheung in the Alessandro Troisi Group.
University of Leeds
I studied physics at the University of Leeds 2005-2009 to get a bachelors plus masters in straight physics.
My final year project at Leeds
- My final year project was: Using Resolating Superconducting Cavities towards making a Quantum Computing Processor. Here I worked with the Experimental Quantum Information group, QIX, under Prof. Ben Varcoe.
- The year before that in the summer of 2008, I worked on a 2 month project with Dr Luis Hueso (now Prof Hueso at CIC Nanogune, Spain) on using organic molecules for the insulating layers in tunnel junctions (organic tunnel junctions). This involved sputtering to fabricate the electronics and x-ray diffraction, AFM to characterise/image the surfaces.
I went to New College, Swindon during 2002 – 2004, where I did A-levels in Physics, Maths and Chemistry.
There's hiking, skiing/snowboarding, reading about science and scientists.
I did once go gliding, which was fun, really should get back into that – flying a plane is fun!
I was in the hiking club at Leeds in my final year - Yorkshire is a great place to be in a hiking club. Every walk ended at a pub.
Nothing else significant – I really should learn some foreign languages, being monolingual is embarrassing for a South African (I'm South African and British).
Skiing in France in March 2013