Research interests

We are interested in the physics of DNA and RNA, especially about simple models that may describe the main physical properties of these important molecules. Sure enough, you can study these molecules with advanced computer simulations, so what is the point in caring about simple models? Realistic computer simulations of short DNA molecules take weeks of months of computer time to process. That is for one molecule. However, you can combine the nucleotides of DNA in any order you like so that even short sequences may result in millions of combinations. That is precisely the sort of problem occurs in computational biology (also called bioinformatics). You need to understand the physical properties of not just one, but thousands of sequences. That is where simple models come into play: they can do the job quickly and provide the answers that biologist need.

The problem with simple models however is this: if they are too simple, they may be useless. Make them more sophisticated and you end up with the same problem as you had with simulations: it takes too long. One of the models which we are specialized, the Peyrard-Bishop model, fits the bill very well but is still far too complicated for non-physicist to handle.

One thing we discovered with the Peyrard-Bishop model is that we can do chemistry with the model. We used the model to reverse-engineer RNA melting temperatures and were able to work out the AU hydrogen bond.

What can we do for you?

If you are a physicist it is likely that you arrived here for your interest in Peyrard-Bishop models. You may be interested in our software package TfReg which implements the equilibrium calculation of the PB model for various different Hamiltonians. It is free software, you can modify it to your own needs or you may simply wish to compare it to your own results.

We can help chemists who measure oligonucleotide melting temperatures to analyse their data with our model. There is a fair possibility that we can help understanding some their properties which are not accessible with traditional free energy nearest neighbour models.

We have active collaborations with colleagues from biological sciences where we help them understanding the thermodynamic properties of DNA and RNA related to their biological problem. This means that we have some experience with software packages such as RNAfold. But please be aware that we do not do routine bioinformatics such as Blast searches.