Principles of molecular information processors.

During the biologically crucial processes of DNA replication, transcription of DNA into RNA and translation of RNA into proteins, a new “polymer” is produced with a sequence of specific monomers (nucleotides or amino acids) determined by a template. Crucially, this copied polymer must detach from the template and retain the copied sequence. This requirement of “persistence” in copying has major thermodynamic consequences, and makes the design of copying systems far more subtle than if the copy merely had to self-assemble on the template.

Previous work on the creation of persistent polymer copies has been restricted to the simplest case in which each monomer type in the template has a unique analog in the copy (the polymers have equivalent “alphabets”). However, as in the production of proteins from mRNA, it is possible that multiple distinct monomer types in the template could code for the same monomer type in the copy. Similarly, previous work has ignored the fact that monomer-specific interactions between monomers within the copy, as well as between copy and template, can play a role in determining the sequence produced. The fundamental consequences and opportunities that then arise are unknown.

The successful candidate will investigate both monomer-specific intra-polymer interactions and “compression” of the monomer alphabet during the production of polymers from a template, through a combination of theory and simulation. The project will first focus on the efficacy of copying and will then consider the possibility of new computational functionality over and above sequence copying.

A successful candidate should have an undergraduate or master degree in natural sciences, mathematics, engineering or computer science, with evidence of strong theoretical and numerical skills. The project will involve the development and analysis of stochastic models for biomolecular processes, both analytically and through simulation, and interpreting the results in terms of thermodynamics, computation and information theory (expertise in these particular disciplines is not expected, but an interest is important). The student will be expected to share ideas and collaborate with other members of the group (http://www.imperial.ac.uk/principles-of-biomolecular-systems/people/), including both experimentalists and theorists. To apply, please send a single PDF document including a one-page cover letter discussing research interest and experiences, a two-page CV, a copy of transcripts, and contact information of two references to Thomas Ouldridge ([Email Address Removed]). We strongly encourage applications from female and minority candidates.