... understanding life in molecular detail

Dr Sarah Harris

Computational Biophysics, Molecular Dynamics, DNA Supercoiling, Statistical Mechanics of Biomolecules

The research groups uses high performance computing to model biomolecules and aim to cover all of the time and length-scales of relevance to molecular biology. This requires computational methods ranging from quantum mechanical, through atomistic to mesoscale modelling.

Current major projects include:
  • DNA supercoiling and topology
  • Developing new method for mesoscale modelling of biomolecules
  • Calculating configurational entropy change in biomolecular recognition

Our research group uses state of the art computational methods to model the physical behaviour of biological macromolecules with the ultimate aim of addressing biological questions. As computational models at the atomistic level allow statistical physics and thermodynamics to be combined with models that are chemically accurate, they have huge potential to provide insight into molecular biology that cannot be obtained by experiment alone.

Our current specific research interests include:

  1. Atomistic molecular dynamics (MD) simulations of DNA circles to understand the role of DNA topology and supercoiling in genetic control.
  2. The thermodynamics of molecular recognition, specifically the development of new methods to calculate changes in biomolecular flexibility.
  3. Using atomistic models of amyloid-like peptide aggregates to investigate the thermodynamics of self-assembly with a focus on amyloid polymorphism; namely how the same peptide sequence can aggregate into fibrils with differing morphologies.
  4. Using molecular simulation to determine the mechanical properties of DNA, RNA and proteins, and how these molecules respond to external factors such as electric fields, increases in temperature or an applied force.
  5. The use of computer simulation to understand information transfer in biomolecules and how these molecules can act as molecular switches.
  6. The development of new computational algorithms based on Finite Element Analysis to expand the range of length and time-scales that can be explored with simulation.

These projects span a significant proportion of the length and timescales relevant to molecular biology and require variety of computational techniques and collaborations with scientists from other disciplines at the national and international level.


Detailed research programme                  Close ▲

Lecturer in Biological Physics Leeds 2004-present
PhD (Nottingham)

Postdoc University College London 2001-2004

Physics 9.310
School of Physics
0113 343 3816


Selected Publications

  1. Harris S. A., Laughton C. A. & Liverpool T. B. “Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations” (2008) Nucleic. Acids. Res. 36, 21-29.

  2. Mitchell J. & Harris S. A. “The thermodynamics of DNA writhe from atomistic molecular dynamics simulations” Phys. Rev Letts. (2013) 110, 148105

  3. Oliver R., Read D.J., Harlen O. G. & Harris S. “A stochastic finite element model for the dynamics of globular macromolecules” J. Comp. Phys. (2013) 239, 147-165.

  4. Harris S. A., Sands Z. & Laughton C. A. “Molecular Dynamics Simulations of DNA Stretching Reveal the Importance of Entropy in Determining the Biomechanical Properties of DNA”, Biophys J. (2005) 88, 1684-1691.