Small Repo of some of my highlighted projects over the last few years.
As part of my 2021 Internship, I had to summarise my completed research via a 3-page poster for display on the Funder's website. My task was to complete a semi-developed 2D LAMMPS (C++) model to simulate vortex dynamics of FtsZ proteins; a protein that exists amongst many bacteria types and is present during the initial stages of cell division.
My complete 4th Yr MPhys Project Report is available for viewing here. I achieved up to a 30% reduction in oxDNA simulation times within LAMMPS by optimising the package's handling of quaternions, a fundamental orientation-dependent co-ordinate system used within the model. My updated source code has now been added into the latest stable releases of LAMMPS, and the updated package was used to explore CAG repeat-sequence hairpin dynamics, representative of dsDNA segments found in a number of degenerative human genome defects.
My 5th yr project was a complementary continuation of my work in 4th yr, and both my interim presentation and final report are available under the "PH570*.pdf" files. I have further investigated coarse-grained modelling of DNA triplet-repeat slip-out migration, and more specifically explored well-tempered and transition-tempered metadynamics to enhance state sampling. I considered additional modelling techniques on the CAG10 sequence, proposed how best these techniques can be utilised, and discussed some of the current insights and limitations found when extending the Trinucleotide-Repeat (TNR) range to CAG20 and beyond.
CAG, or complementary CTG, is the most common of these TNRs found within DNA; responsible for disorders such as Huntington’s Disease, Spinocerebellar Ataxias, and Myotonic Dystrophy. It is hoped that research into these TNRs could one day lead to therapies for these currently untreatable genetic disorders.