Stefan Auer: Positions

Computer modeling of normal and aberrant self-assembly in biological systems

Understanding the fundamental laws underlying the assembly of peptides and proteins into highly organised structures is one of the scientific grand challenges for the future because of its implications for human health and nanoscience. Biomolecular self-assembly is a key element that determines the way in which biological systems function and are regulated, and its failure is associated with devastating diseases such as Alzheimer~s and Parkinson~s disease. On the other hand controlling the self-assembly of biomolecules into well ordered molecular building blocks represents the essence of modern nanotechnology and applications of peptide building blocks in bio-sensors, tissue engineering, and antibacterial agents have already been demonstrated.

The research project aims to use computational tools developed in soft matter physics to investigate the generic aspects of the nucleation and regulation of normal and aberrant self-assembly in biological systems. Examples of our recent work include the calculation of a peptide phase diagram [1], the self-assembly of peptides on a nanoparticle surface [2], the application of atomistic nucleation theory to describe the fibrillation kinetics of peptides and proteins into amyloid fibrils [3,4]. The complexity of the systems requires a simplifying approach, and statistical mechanics and coarse grained modeling are essential. The project is highly demanding and a good background in statistical physics and computer modeling are desirable.

The PhD project will be supervised by Dr. Stefan Auer (Chemistry) and Prof. Peter Olmsted (Physics). At Leeds we also benefit from excellent collaborations with the theoretical groups of Dr. D. Shalashilin, Dr. S. Harris, Dr. E. Paci, Dr. S. Krivov and the experimental groups of Dr. A. Aggeli, Prof. A. Nelson, Dr. R. Cheng and Prof. S. Radford.
Candidates should be eager to explore research at the interface of physics, chemistry and biology. Applicants should have or expect to earn a first- or upper-second-class honours degree, or the equivalent, in a relevant discipline.

The studentship is eligible for UK students and starts on 1st October 2012. There is no official closing date for applications.

Please contact Dr. Stefan Auer (s.auer@leeds.ac.uk) for further details about this opportunity.


1. Phase diagram of α-helical and β-sheet forming peptides, S. Auer, and D. Kashchiev, Phys. Rev. Lett., 104 168105 (2010)

2. A condensation-ordering mechanism in nanoparticle-catalyzed peptide aggregation, S. Auer, A. Trovato, and M. Vendruscolo, PLoS Comput Biol, 5 e1000458 (2009)

3. Atomistic theory of amyloid fibril nucleation, R. Cabriolu, D. Kashchiev, and S. Auer, J. Chem. Phys., 133 225101 (2010)

4. Amyloid fibrillation kinetics: Insight from atomistic nucleation theory, R. Cabriolu and S. Auer, J. Mol. Biol., 411 275 (2011)