PhD project: Topologically Active Polymers (Experimental and/or Computational)

Project description

Two fully-funded PhD positions (one for UK and one for international students) are available thanks to an ERC Starting Grant awarded to Davide Michieletto. One position is for an experimental project while the other for a computational one. See below for details. 

General aim of the projects:

Inspired by how DNA is organised inside our cells, in this project the student will investigate new types of soft materials and complex fluids that are made by polymers which change topology in time. While most of the polymer-based materials that we use every day such as creams, gels and plastics are made by polymers which do not change their architecture or topology (or do so randomly), the DNA inside our cells is constantly precisely mechanically and topologically manipulated by sophisticated proteins. The aim of the group is to design and study systems of entangled polymers which can undergo topological operations that are inspired by those performed by proteins in the cells. The grand goal of this investigation is to create new "topologically active" soft materials which may be patented or find applications in bio- and nano-technology such as drug delivery or cellular scaffolds.

 Experimental Project:

In this experimental project, the student will prepare entangled systems of DNA either purchased from companies or extracted from bacteria in a variety of topological conditions, i.e. linear, circular, supercoiled, knotted or linked. S/he will then study the rheological properties of such a complex fluid once certain classes of proteins (such as Topoisomerase, restriction enzymes, ligases, or others) are added into the system. S/he will be mostly performing microrheology, a technique based on tracking the diffusion of beads embedded in the fluid using microscopy. A variation of this project involves the design and investigation of the rheological properties of entangled solutions of DNA origami

Computational Project:

In this computational project, the student will develop and perform simulations aimed at understanding the behaviour of polymers with “chimeric” topology and/or supercoiled DNA. An example of such polymers can be found in this paper. The student will learn and perform Molecular Dynamics simulations of coarse-grained polymer models for DNA. S/he will develop new algorithms, run large-scale simulations on supercomputers and analyse large datasets. The grand goal of this project is to understand the relationship between polymer topology and the rheology of the complex fluid. This will unlock the possiblity to design fluids with desired rheology by choosing the architecture of the polymer. The student will work closely with other PhDs or PDRAs involved in realising these systems experimentally in particular via DNA origami. 

Project supervisor

The project supervisor welcomes informal enquiries about this project.

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