Google scholar seems to do a fairly good job of listing my publications. My papers also eventually show up on the ResearcherID service, which provides various official measurements of my importance.

This page is intended to give a less complete but more graphical informal sampling of my work, in no particular order. It is image-heavy, so I have to say sorry if you are on an expensive connection.

Codon Table Colored by Triplet Propensity: High triplet propensity means large evolutionary age Origin of life: Looking at DNA mechanics, we have noticed some very interesting sequence dependence of the propensity to form period-3 structures (triplet propensity). It seems that increased evolutionary age of the sequence (as determined by other people, such as Kenji Ikehara and JTF Wong ) correlates very closely to triplet propensity. Ikehara places the four amino acids GADV (marked ☥ in the table) as the first to be incorportated into biochemistry, by looking at the synthetic chemistry to make them and at their effectiveness together at forming proto-proteins. Wong thinks of the bigger set GADVESPLIT (marked *) as the primal family of amino acids, again reasoning mostly from an understanding of synthetic chemistry: it costs too much energy to make the remaining ten canonical amino acids FQWYMKRNCH out of the GADVESPLIT set for this to happen without somewhat-sophisticated biochemical machinery already being present.

The table on the left is colored by triplet propensity, light-colored squares (like the GADV set) have high triplet propensity. The GADVESPLIT set are mostly higher than average, the GADV set really stands out. The correlation is too strong to be coincidence, so we can be confident that the earliest liforms had genes which popped into triplets with less energy input than is needed in modern organisms.

Why did ancient life-forms need to partition their nucleic acids into groups of three bases/basepairs? In modern life forms this partitioning is carried out by sophisticated enzymes as part of homologous recombination (exchange of genetic information for DNA repair or for sex). Perhaps in ancient lifeforms the biochemistry to perform these important activities was not so sophisticated, so the genome itself had to be structured so as to make these processes easier.

ILQINS spectra and structure Amyloid Aggregation: Computer simulation can be used to `fill in the gaps' when experimental data is not completely explicit. The example figure shows some work to characterise the aggregation of ILQINS peptide (a digestion fragment of Hen's egg white lysozyme or "HEWL"). The spectra were measured using X-ray scattering by Nick Reynolds using the Australian Synchrotron. The structure is a guess made with the aid of MD simulations, which approximately reproduces the measured spectra. Hopefully as computer power becomes more freely available I will be able to begin using more systematic methods of structure determination, but for the moment this aspect of my work contains more art than science. Our latest paper on this topic is at Nature Comms.
Right and Left-Handed DNA helices DNA Mechanics: DNA in high salt can switch helicity from right to left (B to Z). I am quite happy that Tanja and I were able to make the first accurate calculation of the concentration of salt needed to do this. I have some slides for a talk I gave, which might serve as an easy-reading introduction to the free energy method I used.
colorful image of a fibril structure Amyloid polymorphism: On the right is a journal cover from some of my PhD work. The image should hyperlink to the appropriate paper.
colorful image of a fibril structure Rare Events: This figure illustrates the probability of a rare `jamming' event in a simple model of directed transport. Using S-PRES it was possible to measure events occuring at ridiculously low probabilities with negligible sampling error. Software now available for rare event calculation at

polymorphic packings of the gnnqqny peptide

More polymorphism: This figure illustrates polymorphic packings of the GNNQQNY peptide. Even for such a small molecule there are many thermodynamically credible polymorphs.

symmetry effects in amyloid aggregation

This figure illustrates the importance of symmetry in peptide aggregation.